I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 5 16:03:25 +14 2020 I: pbuilder-time-stamp: 1604541805 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [transdecoder_5.0.1-2.dsc] I: copying [./transdecoder_5.0.1.orig.tar.gz] I: copying [./transdecoder_5.0.1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Oct 31 03:43:14 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./transdecoder_5.0.1-2.dsc dpkg-source: info: extracting transdecoder in transdecoder-5.0.1 dpkg-source: info: unpacking transdecoder_5.0.1.orig.tar.gz dpkg-source: info: unpacking transdecoder_5.0.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-whatis dpkg-source: info: applying reproducible-sample_data.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2479/tmp/hooks/D01_modify_environment starting debug: Running on codethink10-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2479/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2479/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2479 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.n3kDg3sKMB/pbuilderrc_zlw9 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.n3kDg3sKMB/b2 --logfile b2/build.log transdecoder_5.0.1-2.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.4.0-190-generic #220-Ubuntu SMP Fri Aug 28 23:03:33 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 35576 Mar 1 2019 cat -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash -rwxr-xr-x 1 root root 97136 Mar 1 2019 date -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd -rwxr-xr-x 1 root root 93752 Mar 1 2019 df -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir -rwxr-xr-x 1 root root 75984 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 27256 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 6 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln -rwxr-xr-x 1 root root 52544 Jul 27 2018 login -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 10 2019 more -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138736 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Nov 5 16:03 sh -> bash lrwxrwxrwx 1 root root 4 Oct 21 22:26 sh.distrib -> dash -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty -rwsr-xr-x 1 root root 59424 Jan 10 2019 su -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch -rwxr-xr-x 1 root root 27256 Mar 1 2019 true -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/2479/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), liburi-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on liburi-perl; however: Package liburi-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} liburi-perl{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After unpacking 69.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 liburi-perl all 1.76-1 [89.9 kB] Fetched 18.7 MB in 1s (19.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../27-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../33-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up liburi-perl (1.76-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... 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Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/transdecoder-5.0.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package transdecoder dpkg-buildpackage: info: source version 5.0.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/transdecoder-5.0.1' cd ./sample_data && for script in ./*/cleanme.pl; do $($script); done make[1]: Leaving directory '/build/transdecoder-5.0.1' debian/rules override_dh_clean make[1]: Entering directory '/build/transdecoder-5.0.1' # generated man pages dh_clean debian/TransDecoder.LongOrfs.1 debian/TransDecoder.Predict.1 make[1]: Leaving directory '/build/transdecoder-5.0.1' debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_test make[1]: Entering directory '/build/transdecoder-5.0.1' dh_auto_test make -j8 test make[2]: Entering directory '/build/transdecoder-5.0.1' cd ./sample_data/ && make test make[3]: Entering directory '/build/transdecoder-5.0.1/sample_data' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Running example in $... make[4]: Entering directory '/build/transdecoder-5.0.1/sample_data/cufflinks_example' ./runMe.sh #!/bin/bash -ve export PERL_HASH_SEED=0 if [ ! -e test.genome.fasta ]; then gunzip -c test.genome.fasta.gz > test.genome.fasta fi if [ ! -e transcripts.gtf ]; then gunzip -c transcripts.gtf.gz > transcripts.gtf fi if [ ! -e blastp.outfmt6 ]; then gunzip -c blastp.outfmt6.gz > blastp.outfmt6 fi if [ ! -e pfam.domtblout ]; then gunzip -c pfam.domtblout.gz > pfam.domtblout fi ## generate alignment gff3 formatted output ../../util/cufflinks_gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 ## generate transcripts fasta file PERL_HASH_SEED=0 ../../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta -parsing cufflinks output: transcripts.gtf -parsing genome fasta: test.genome.fasta -done parsing genome. // processing 7000000090838467 ## Extract the long ORFs ../../TransDecoder.LongOrfs -t transcripts.fasta -first extracting base frequencies, we'll need them later. CMD: /build/transdecoder-5.0.1/util/compute_base_probs.pl transcripts.fasta 0 > transcripts.fasta.transdecoder_dir/base_freqs.dat CMD: touch transcripts.fasta.transdecoder_dir/base_freqs.dat.ok - extracting ORFs from transcripts. -total transcripts to examine: 64 CMD: touch transcripts.fasta.transdecoder_dir/__longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. ## Predict likely ORFs if [ 1 ]; then # always doing this now. # this is how I would have run blast and pfam but I'm using precomputed results for ease of demonstration. #BLASTDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/uniprot_sprot.pep #PFAMDB=/seq/RNASEQ/DBs/TRINOTATE_RESOURCES/TRINOTATE_V3/Pfam-A.hmm # ## run blast #blastp -query transcripts.fasta.transdecoder_dir/longest_orfs.pep -db $BLASTDB -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > blastp.outfmt6 # ## run pfam #hmmscan --domtblout pfam.domtblout $PFAMDB transcripts.fasta.transdecoder_dir/longest_orfs.pep > pfam.log ## use pfam and blast results: ../../TransDecoder.Predict -t transcripts.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6 -v else # just coding metrics ../../TransDecoder.Predict -t transcripts.fasta fi * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * Running CMD: /build/transdecoder-5.0.1/util/exclude_similar_proteins.pl transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: Gene.94::CUFF.60.1::g.94::m.94, not unique enough -skipping training candidate: Gene.62::CUFF.26.1::g.62::m.62, not unique enough -skipping training candidate: Gene.39::CUFF.38.1::g.39::m.39, not unique enough -skipping training candidate: Gene.43::CUFF.48.1::g.43::m.43, not unique enough -skipping training candidate: Gene.95::CUFF.60.1::g.95::m.95, not unique enough -skipping training candidate: Gene.51::CUFF.30.1::g.51::m.51, not unique enough -skipping training candidate: Gene.30::CUFF.40.1::g.30::m.30, not unique enough -skipping training candidate: Gene.31::CUFF.40.1::g.31::m.31, not unique enough -skipping training candidate: Gene.50::CUFF.30.2::g.50::m.50, not unique enough -skipping training candidate: Gene.28::CUFF.52.1::g.28::m.28, not unique enough -skipping training candidate: Gene.57::CUFF.20.1::g.57::m.57, not unique enough -skipping training candidate: Gene.90::CUFF.47.1::g.90::m.90, not unique enough -skipping training candidate: Gene.45::CUFF.48.1::g.45::m.45, not unique enough -skipping training candidate: Gene.47::CUFF.13.3::g.47::m.47, not unique enough -skipping training candidate: Gene.86::CUFF.29.1::g.86::m.86, not unique enough -skipping training candidate: Gene.3::CUFF.34.1::g.3::m.3, not unique enough -skipping training candidate: Gene.41::CUFF.38.1::g.41::m.41, not unique enough -skipping training candidate: Gene.48::CUFF.13.1::g.48::m.48, not unique enough -skipping training candidate: Gene.63::CUFF.26.1::g.63::m.63, not unique enough -skipping training candidate: Gene.24::CUFF.41.1::g.24::m.24, not unique enough -skipping training candidate: Gene.49::CUFF.13.1::g.49::m.49, not unique enough -skipping training candidate: Gene.64::CUFF.26.1::g.64::m.64, not unique enough -skipping training candidate: Gene.32::CUFF.40.1::g.32::m.32, not unique enough -redundancy-minimized set includes 72 / 95 = 75.79% * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 37 * Running CMD: /build/transdecoder-5.0.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest transcripts.fasta.transdecoder_dir/base_freqs.dat > transcripts.fasta.transdecoder_dir/hexamer.scores * Running CMD: /build/transdecoder-5.0.1/util/score_CDS_likelihood_all_6_frames.pl transcripts.fasta.transdecoder_dir/longest_orfs.cds transcripts.fasta.transdecoder_dir/hexamer.scores > transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores * Running CMD: /build/transdecoder-5.0.1/util/select_best_ORFs_per_transcript.pl --gff3_file transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 -indexing [Gene.53::CUFF.1.1::g.53] -indexing [Gene.36::CUFF.11.1::g.36] -indexing [Gene.78::CUFF.12.1::g.78] -indexing [Gene.79::CUFF.12.1::g.79] -indexing [Gene.49::CUFF.13.1::g.49] -indexing [Gene.48::CUFF.13.1::g.48] -indexing [Gene.46::CUFF.13.2::g.46] -indexing [Gene.47::CUFF.13.3::g.47] -indexing [Gene.34::CUFF.14.1::g.34] -indexing [Gene.66::CUFF.15.1::g.66] -indexing [Gene.20::CUFF.16.1::g.20] -indexing [Gene.52::CUFF.17.1::g.52] -indexing [Gene.7::CUFF.18.1::g.7] -indexing [Gene.35::CUFF.19.1::g.35] -indexing [Gene.16::CUFF.2.1::g.16] -indexing [Gene.56::CUFF.20.1::g.56] -indexing [Gene.57::CUFF.20.1::g.57] -indexing [Gene.87::CUFF.24.1::g.87] -indexing [Gene.21::CUFF.25.1::g.21] -indexing [Gene.63::CUFF.26.1::g.63] -indexing [Gene.62::CUFF.26.1::g.62] -indexing [Gene.64::CUFF.26.1::g.64] -indexing [Gene.15::CUFF.27.1::g.15] -indexing [Gene.14::CUFF.27.1::g.14] -indexing [Gene.13::CUFF.27.1::g.13] -indexing [Gene.74::CUFF.28.1::g.74] -indexing [Gene.86::CUFF.29.1::g.86] -indexing [Gene.75::CUFF.3.1::g.75] -indexing [Gene.51::CUFF.30.1::g.51] -indexing [Gene.50::CUFF.30.2::g.50] -indexing [Gene.8::CUFF.31.1::g.8] -indexing [Gene.59::CUFF.32.1::g.59] -indexing [Gene.58::CUFF.32.1::g.58] -indexing [Gene.61::CUFF.32.1::g.61] -indexing [Gene.60::CUFF.32.1::g.60] -indexing [Gene.3::CUFF.34.1::g.3] -indexing [Gene.2::CUFF.34.1::g.2] -indexing [Gene.80::CUFF.35.1::g.80] -indexing [Gene.42::CUFF.36.1::g.42] -indexing [Gene.77::CUFF.37.1::g.77] -indexing [Gene.76::CUFF.37.1::g.76] -indexing [Gene.39::CUFF.38.1::g.39] -indexing [Gene.37::CUFF.38.1::g.37] -indexing [Gene.38::CUFF.38.1::g.38] -indexing [Gene.41::CUFF.38.1::g.41] -indexing [Gene.40::CUFF.38.1::g.40] -indexing [Gene.4::CUFF.39.1::g.4] -indexing [Gene.5::CUFF.39.1::g.5] -indexing [Gene.91::CUFF.4.1::g.91] -indexing [Gene.31::CUFF.40.1::g.31] -indexing [Gene.30::CUFF.40.1::g.30] -indexing [Gene.32::CUFF.40.1::g.32] -indexing [Gene.29::CUFF.40.1::g.29] -indexing [Gene.24::CUFF.41.1::g.24] -indexing [Gene.25::CUFF.41.1::g.25] -indexing [Gene.22::CUFF.41.1::g.22] -indexing [Gene.23::CUFF.41.1::g.23] -indexing [Gene.69::CUFF.42.1::g.69] -indexing [Gene.67::CUFF.42.1::g.67] -indexing [Gene.68::CUFF.42.1::g.68] -indexing [Gene.9::CUFF.43.1::g.9] -indexing [Gene.19::CUFF.44.1::g.19] -indexing [Gene.89::CUFF.45.1::g.89] -indexing [Gene.88::CUFF.45.1::g.88] -indexing [Gene.33::CUFF.46.1::g.33] -indexing [Gene.90::CUFF.47.1::g.90] -indexing [Gene.43::CUFF.48.1::g.43] -indexing [Gene.44::CUFF.48.1::g.44] -indexing [Gene.45::CUFF.48.1::g.45] -indexing [Gene.17::CUFF.49.1::g.17] -indexing [Gene.18::CUFF.49.1::g.18] -indexing [Gene.12::CUFF.5.1::g.12] -indexing [Gene.71::CUFF.50.1::g.71] -indexing [Gene.70::CUFF.50.1::g.70] -indexing [Gene.72::CUFF.50.1::g.72] -indexing [Gene.73::CUFF.50.1::g.73] -indexing [Gene.83::CUFF.51.1::g.83] -indexing [Gene.84::CUFF.51.1::g.84] -indexing [Gene.27::CUFF.52.1::g.27] -indexing [Gene.28::CUFF.52.1::g.28] -indexing [Gene.26::CUFF.52.1::g.26] -indexing [Gene.85::CUFF.53.1::g.85] -indexing [Gene.82::CUFF.54.1::g.82] -indexing [Gene.10::CUFF.55.1::g.10] -indexing [Gene.11::CUFF.57.1::g.11] -indexing [Gene.55::CUFF.58.1::g.55] -indexing [Gene.54::CUFF.58.1::g.54] -indexing [Gene.81::CUFF.59.1::g.81] -indexing [Gene.1::CUFF.6.1::g.1] -indexing [Gene.95::CUFF.60.1::g.95] -indexing [Gene.94::CUFF.60.1::g.94] -indexing [Gene.93::CUFF.60.2::g.93] -indexing [Gene.92::CUFF.60.2::g.92] -indexing [Gene.6::CUFF.7.1::g.6] -indexing [Gene.65::CUFF.9.1::g.65] * Running CMD: /build/transdecoder-5.0.1/util/train_start_PWM.pl --transcripts transcripts.fasta --selected_orfs transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix transcripts.fasta.transdecoder_dir/start_refinement * Running CMD: /build/transdecoder-5.0.1/util/PWM/build_atgPWM_+-.pl --transcripts transcripts.fasta --selected_orfs transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/deplete_feature_noise.pl --features_plus transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 62 num_incorporate: 18 -feature swap of score: -0.0897855943740242 instead of -1.69196225399733 -feature swap of score: 1.95623810054525 instead of -0.899765876764533 -feature swap of score: 2.15720530108386 instead of -0.614166413980579 -feature swap of score: 2.41765107522193 instead of 1.32547524833398 -feature swap of score: 3.39515832886515 instead of 1.85550973002738 -feature swap of score: 3.60253711362061 instead of 3.25340563653541 -feature swap of score: 5.6586417191496 instead of 3.45056029200281 -num feature swaps: 7 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/start_codon_refinement.pl --transcripts transcripts.fasta --gff3_file transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 > transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 -ignoring line PFAM output found and processing... -indexing [Gene.53::CUFF.1.1::g.53] -indexing [Gene.36::CUFF.11.1::g.36] -indexing [Gene.78::CUFF.12.1::g.78] -indexing [Gene.49::CUFF.13.1::g.49] -indexing [Gene.46::CUFF.13.2::g.46] -indexing [Gene.47::CUFF.13.3::g.47] -indexing [Gene.34::CUFF.14.1::g.34] -indexing [Gene.66::CUFF.15.1::g.66] -indexing [Gene.20::CUFF.16.1::g.20] -indexing [Gene.52::CUFF.17.1::g.52] -indexing [Gene.7::CUFF.18.1::g.7] -indexing [Gene.35::CUFF.19.1::g.35] -indexing [Gene.16::CUFF.2.1::g.16] -indexing [Gene.56::CUFF.20.1::g.56] -indexing [Gene.87::CUFF.24.1::g.87] -indexing [Gene.21::CUFF.25.1::g.21] -indexing [Gene.62::CUFF.26.1::g.62] -indexing [Gene.13::CUFF.27.1::g.13] -indexing [Gene.74::CUFF.28.1::g.74] -indexing [Gene.86::CUFF.29.1::g.86] -indexing [Gene.75::CUFF.3.1::g.75] -indexing [Gene.51::CUFF.30.1::g.51] -indexing [Gene.50::CUFF.30.2::g.50] -indexing [Gene.8::CUFF.31.1::g.8] -indexing [Gene.58::CUFF.32.1::g.58] -indexing [Gene.2::CUFF.34.1::g.2] -indexing [Gene.80::CUFF.35.1::g.80] -indexing [Gene.42::CUFF.36.1::g.42] -indexing [Gene.76::CUFF.37.1::g.76] -indexing [Gene.38::CUFF.38.1::g.38] -indexing [Gene.4::CUFF.39.1::g.4] -indexing [Gene.91::CUFF.4.1::g.91] -indexing [Gene.29::CUFF.40.1::g.29] -indexing [Gene.22::CUFF.41.1::g.22] -indexing [Gene.67::CUFF.42.1::g.67] -indexing [Gene.9::CUFF.43.1::g.9] -indexing [Gene.19::CUFF.44.1::g.19] -indexing [Gene.88::CUFF.45.1::g.88] -indexing [Gene.33::CUFF.46.1::g.33] -indexing [Gene.90::CUFF.47.1::g.90] -indexing [Gene.43::CUFF.48.1::g.43] -indexing [Gene.17::CUFF.49.1::g.17] -indexing [Gene.12::CUFF.5.1::g.12] -indexing [Gene.70::CUFF.50.1::g.70] -indexing [Gene.84::CUFF.51.1::g.84] -indexing [Gene.26::CUFF.52.1::g.26] -indexing [Gene.85::CUFF.53.1::g.85] -indexing [Gene.82::CUFF.54.1::g.82] -indexing [Gene.10::CUFF.55.1::g.10] -indexing [Gene.11::CUFF.57.1::g.11] -indexing [Gene.54::CUFF.58.1::g.54] -indexing [Gene.81::CUFF.59.1::g.81] -indexing [Gene.1::CUFF.6.1::g.1] -indexing [Gene.94::CUFF.60.1::g.94] -indexing [Gene.92::CUFF.60.2::g.92] -indexing [Gene.6::CUFF.7.1::g.6] -indexing [Gene.65::CUFF.9.1::g.65] -number of revised start positions: 1 CMD: cp transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 transcripts.fasta.transdecoder.gff3 CMD: /build/transdecoder-5.0.1/util/gff3_file_to_bed.pl transcripts.fasta.transdecoder.gff3 > transcripts.fasta.transdecoder.bed -indexing [Gene.53::CUFF.1.1::g.53] -indexing [Gene.36::CUFF.11.1::g.36] -indexing [Gene.78::CUFF.12.1::g.78] -indexing [Gene.49::CUFF.13.1::g.49] -indexing [Gene.46::CUFF.13.2::g.46] -indexing [Gene.47::CUFF.13.3::g.47] -indexing [Gene.34::CUFF.14.1::g.34] -indexing [Gene.66::CUFF.15.1::g.66] -indexing [Gene.20::CUFF.16.1::g.20] -indexing [Gene.52::CUFF.17.1::g.52] -indexing [Gene.7::CUFF.18.1::g.7] -indexing [Gene.35::CUFF.19.1::g.35] -indexing [Gene.16::CUFF.2.1::g.16] -indexing [Gene.56::CUFF.20.1::g.56] -indexing [Gene.87::CUFF.24.1::g.87] -indexing [Gene.21::CUFF.25.1::g.21] -indexing [Gene.62::CUFF.26.1::g.62] -indexing [Gene.13::CUFF.27.1::g.13] -indexing [Gene.74::CUFF.28.1::g.74] -indexing [Gene.86::CUFF.29.1::g.86] -indexing [Gene.75::CUFF.3.1::g.75] -indexing [Gene.51::CUFF.30.1::g.51] -indexing [Gene.50::CUFF.30.2::g.50] -indexing [Gene.8::CUFF.31.1::g.8] -indexing [Gene.58::CUFF.32.1::g.58] -indexing [Gene.2::CUFF.34.1::g.2] -indexing [Gene.80::CUFF.35.1::g.80] -indexing [Gene.42::CUFF.36.1::g.42] -indexing [Gene.76::CUFF.37.1::g.76] -indexing [Gene.38::CUFF.38.1::g.38] -indexing [Gene.4::CUFF.39.1::g.4] -indexing [Gene.91::CUFF.4.1::g.91] -indexing [Gene.29::CUFF.40.1::g.29] -indexing [Gene.22::CUFF.41.1::g.22] -indexing [Gene.67::CUFF.42.1::g.67] -indexing [Gene.9::CUFF.43.1::g.9] -indexing [Gene.19::CUFF.44.1::g.19] -indexing [Gene.88::CUFF.45.1::g.88] -indexing [Gene.33::CUFF.46.1::g.33] -indexing [Gene.90::CUFF.47.1::g.90] -indexing [Gene.43::CUFF.48.1::g.43] -indexing [Gene.17::CUFF.49.1::g.17] -indexing [Gene.12::CUFF.5.1::g.12] -indexing [Gene.70::CUFF.50.1::g.70] -indexing [Gene.84::CUFF.51.1::g.84] -indexing [Gene.26::CUFF.52.1::g.26] -indexing [Gene.85::CUFF.53.1::g.85] -indexing [Gene.82::CUFF.54.1::g.82] -indexing [Gene.10::CUFF.55.1::g.10] -indexing [Gene.11::CUFF.57.1::g.11] -indexing [Gene.54::CUFF.58.1::g.54] -indexing [Gene.81::CUFF.59.1::g.81] -indexing [Gene.1::CUFF.6.1::g.1] -indexing [Gene.94::CUFF.60.1::g.94] -indexing [Gene.92::CUFF.60.2::g.92] -indexing [Gene.6::CUFF.7.1::g.6] -indexing [Gene.65::CUFF.9.1::g.65] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta > transcripts.fasta.transdecoder.pep -indexing [Gene.53::CUFF.1.1::g.53] -indexing [Gene.36::CUFF.11.1::g.36] -indexing [Gene.78::CUFF.12.1::g.78] -indexing [Gene.49::CUFF.13.1::g.49] -indexing [Gene.46::CUFF.13.2::g.46] -indexing [Gene.47::CUFF.13.3::g.47] -indexing [Gene.34::CUFF.14.1::g.34] -indexing [Gene.66::CUFF.15.1::g.66] -indexing [Gene.20::CUFF.16.1::g.20] -indexing [Gene.52::CUFF.17.1::g.52] -indexing [Gene.7::CUFF.18.1::g.7] -indexing [Gene.35::CUFF.19.1::g.35] -indexing [Gene.16::CUFF.2.1::g.16] -indexing [Gene.56::CUFF.20.1::g.56] -indexing [Gene.87::CUFF.24.1::g.87] -indexing [Gene.21::CUFF.25.1::g.21] -indexing [Gene.62::CUFF.26.1::g.62] -indexing [Gene.13::CUFF.27.1::g.13] -indexing [Gene.74::CUFF.28.1::g.74] -indexing [Gene.86::CUFF.29.1::g.86] -indexing [Gene.75::CUFF.3.1::g.75] -indexing [Gene.51::CUFF.30.1::g.51] -indexing [Gene.50::CUFF.30.2::g.50] -indexing [Gene.8::CUFF.31.1::g.8] -indexing [Gene.58::CUFF.32.1::g.58] -indexing [Gene.2::CUFF.34.1::g.2] -indexing [Gene.80::CUFF.35.1::g.80] -indexing [Gene.42::CUFF.36.1::g.42] -indexing [Gene.76::CUFF.37.1::g.76] -indexing [Gene.38::CUFF.38.1::g.38] -indexing [Gene.4::CUFF.39.1::g.4] -indexing [Gene.91::CUFF.4.1::g.91] -indexing [Gene.29::CUFF.40.1::g.29] -indexing [Gene.22::CUFF.41.1::g.22] -indexing [Gene.67::CUFF.42.1::g.67] -indexing [Gene.9::CUFF.43.1::g.9] -indexing [Gene.19::CUFF.44.1::g.19] -indexing [Gene.88::CUFF.45.1::g.88] -indexing [Gene.33::CUFF.46.1::g.33] -indexing [Gene.90::CUFF.47.1::g.90] -indexing [Gene.43::CUFF.48.1::g.43] -indexing [Gene.17::CUFF.49.1::g.17] -indexing [Gene.12::CUFF.5.1::g.12] -indexing [Gene.70::CUFF.50.1::g.70] -indexing [Gene.84::CUFF.51.1::g.84] -indexing [Gene.26::CUFF.52.1::g.26] -indexing [Gene.85::CUFF.53.1::g.85] -indexing [Gene.82::CUFF.54.1::g.82] -indexing [Gene.10::CUFF.55.1::g.10] -indexing [Gene.11::CUFF.57.1::g.11] -indexing [Gene.54::CUFF.58.1::g.54] -indexing [Gene.81::CUFF.59.1::g.81] -indexing [Gene.1::CUFF.6.1::g.1] -indexing [Gene.94::CUFF.60.1::g.94] -indexing [Gene.92::CUFF.60.2::g.92] -indexing [Gene.6::CUFF.7.1::g.6] -indexing [Gene.65::CUFF.9.1::g.65] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 transcripts.fasta.transdecoder.gff3 --fasta transcripts.fasta --seqType CDS > transcripts.fasta.transdecoder.cds -indexing [Gene.53::CUFF.1.1::g.53] -indexing [Gene.36::CUFF.11.1::g.36] -indexing [Gene.78::CUFF.12.1::g.78] -indexing [Gene.49::CUFF.13.1::g.49] -indexing [Gene.46::CUFF.13.2::g.46] -indexing [Gene.47::CUFF.13.3::g.47] -indexing [Gene.34::CUFF.14.1::g.34] -indexing [Gene.66::CUFF.15.1::g.66] -indexing [Gene.20::CUFF.16.1::g.20] -indexing [Gene.52::CUFF.17.1::g.52] -indexing [Gene.7::CUFF.18.1::g.7] -indexing [Gene.35::CUFF.19.1::g.35] -indexing [Gene.16::CUFF.2.1::g.16] -indexing [Gene.56::CUFF.20.1::g.56] -indexing [Gene.87::CUFF.24.1::g.87] -indexing [Gene.21::CUFF.25.1::g.21] -indexing [Gene.62::CUFF.26.1::g.62] -indexing [Gene.13::CUFF.27.1::g.13] -indexing [Gene.74::CUFF.28.1::g.74] -indexing [Gene.86::CUFF.29.1::g.86] -indexing [Gene.75::CUFF.3.1::g.75] -indexing [Gene.51::CUFF.30.1::g.51] -indexing [Gene.50::CUFF.30.2::g.50] -indexing [Gene.8::CUFF.31.1::g.8] -indexing [Gene.58::CUFF.32.1::g.58] -indexing [Gene.2::CUFF.34.1::g.2] -indexing [Gene.80::CUFF.35.1::g.80] -indexing [Gene.42::CUFF.36.1::g.42] -indexing [Gene.76::CUFF.37.1::g.76] -indexing [Gene.38::CUFF.38.1::g.38] -indexing [Gene.4::CUFF.39.1::g.4] -indexing [Gene.91::CUFF.4.1::g.91] -indexing [Gene.29::CUFF.40.1::g.29] -indexing [Gene.22::CUFF.41.1::g.22] -indexing [Gene.67::CUFF.42.1::g.67] -indexing [Gene.9::CUFF.43.1::g.9] -indexing [Gene.19::CUFF.44.1::g.19] -indexing [Gene.88::CUFF.45.1::g.88] -indexing [Gene.33::CUFF.46.1::g.33] -indexing [Gene.90::CUFF.47.1::g.90] -indexing [Gene.43::CUFF.48.1::g.43] -indexing [Gene.17::CUFF.49.1::g.17] -indexing [Gene.12::CUFF.5.1::g.12] -indexing [Gene.70::CUFF.50.1::g.70] -indexing [Gene.84::CUFF.51.1::g.84] -indexing [Gene.26::CUFF.52.1::g.26] -indexing [Gene.85::CUFF.53.1::g.85] -indexing [Gene.82::CUFF.54.1::g.82] -indexing [Gene.10::CUFF.55.1::g.10] -indexing [Gene.11::CUFF.57.1::g.11] -indexing [Gene.54::CUFF.58.1::g.54] -indexing [Gene.81::CUFF.59.1::g.81] -indexing [Gene.1::CUFF.6.1::g.1] -indexing [Gene.94::CUFF.60.1::g.94] -indexing [Gene.92::CUFF.60.2::g.92] -indexing [Gene.6::CUFF.7.1::g.6] -indexing [Gene.65::CUFF.9.1::g.65] transdecoder is finished. See output files transcripts.fasta.transdecoder.* ## convert to genome coordinates ../../util/cdna_alignment_orf_to_genome_orf.pl transcripts.fasta.transdecoder.gff3 transcripts.gff3 transcripts.fasta > transcripts.fasta.transdecoder.genome.gff3 -indexing [Gene.53::CUFF.1.1::g.53] -indexing [Gene.36::CUFF.11.1::g.36] -indexing [Gene.78::CUFF.12.1::g.78] -indexing [Gene.49::CUFF.13.1::g.49] -indexing [Gene.46::CUFF.13.2::g.46] -indexing [Gene.47::CUFF.13.3::g.47] -indexing [Gene.34::CUFF.14.1::g.34] -indexing [Gene.66::CUFF.15.1::g.66] -indexing [Gene.20::CUFF.16.1::g.20] -indexing [Gene.52::CUFF.17.1::g.52] -indexing [Gene.7::CUFF.18.1::g.7] -indexing [Gene.35::CUFF.19.1::g.35] -indexing [Gene.16::CUFF.2.1::g.16] -indexing [Gene.56::CUFF.20.1::g.56] -indexing [Gene.87::CUFF.24.1::g.87] -indexing [Gene.21::CUFF.25.1::g.21] -indexing [Gene.62::CUFF.26.1::g.62] -indexing [Gene.13::CUFF.27.1::g.13] -indexing [Gene.74::CUFF.28.1::g.74] -indexing [Gene.86::CUFF.29.1::g.86] -indexing [Gene.75::CUFF.3.1::g.75] -indexing [Gene.51::CUFF.30.1::g.51] -indexing [Gene.50::CUFF.30.2::g.50] -indexing [Gene.8::CUFF.31.1::g.8] -indexing [Gene.58::CUFF.32.1::g.58] -indexing [Gene.2::CUFF.34.1::g.2] -indexing [Gene.80::CUFF.35.1::g.80] -indexing [Gene.42::CUFF.36.1::g.42] -indexing [Gene.76::CUFF.37.1::g.76] -indexing [Gene.38::CUFF.38.1::g.38] -indexing [Gene.4::CUFF.39.1::g.4] -indexing [Gene.91::CUFF.4.1::g.91] -indexing [Gene.29::CUFF.40.1::g.29] -indexing [Gene.22::CUFF.41.1::g.22] -indexing [Gene.67::CUFF.42.1::g.67] -indexing [Gene.9::CUFF.43.1::g.9] -indexing [Gene.19::CUFF.44.1::g.19] -indexing [Gene.88::CUFF.45.1::g.88] -indexing [Gene.33::CUFF.46.1::g.33] -indexing [Gene.90::CUFF.47.1::g.90] -indexing [Gene.43::CUFF.48.1::g.43] -indexing [Gene.17::CUFF.49.1::g.17] -indexing [Gene.12::CUFF.5.1::g.12] -indexing [Gene.70::CUFF.50.1::g.70] -indexing [Gene.84::CUFF.51.1::g.84] -indexing [Gene.26::CUFF.52.1::g.26] -indexing [Gene.85::CUFF.53.1::g.85] -indexing [Gene.82::CUFF.54.1::g.82] -indexing [Gene.10::CUFF.55.1::g.10] -indexing [Gene.11::CUFF.57.1::g.11] -indexing [Gene.54::CUFF.58.1::g.54] -indexing [Gene.81::CUFF.59.1::g.81] -indexing [Gene.1::CUFF.6.1::g.1] -indexing [Gene.94::CUFF.60.1::g.94] -indexing [Gene.92::CUFF.60.2::g.92] -indexing [Gene.6::CUFF.7.1::g.6] -indexing [Gene.65::CUFF.9.1::g.65] Warning [1], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry Gene.50::CUFF.30.2::g.50::m.50. Done. 56 / 57 transcript orfs could be propagated to the genome ## make bed files for viewing with GenomeView # covert cufflinks gtf to bed ../../util/cufflinks_gtf_to_bed.pl transcripts.gtf > transcripts.bed # convert the genome-based gene-gff3 file to bed ../../util/gff3_file_to_bed.pl transcripts.fasta.transdecoder.genome.gff3 > transcripts.fasta.transdecoder.genome.bed -indexing [CUFF.6] -indexing [CUFF.34] -indexing [CUFF.39] -indexing [CUFF.7] -indexing [CUFF.18] -indexing [CUFF.31] -indexing [CUFF.43] -indexing [CUFF.55] -indexing [CUFF.57] -indexing [CUFF.5] -indexing [CUFF.27] -indexing [CUFF.2] -indexing [CUFF.16] -indexing [CUFF.44] -indexing [CUFF.49] -indexing [CUFF.25] -indexing [CUFF.41] -indexing [CUFF.52] -indexing [CUFF.40] -indexing [CUFF.14] -indexing [CUFF.19] -indexing [CUFF.46] -indexing [CUFF.11] -indexing [CUFF.38] -indexing [CUFF.36] -indexing [CUFF.13] -indexing [CUFF.48] -indexing [CUFF.30] -indexing [CUFF.17] -indexing [CUFF.1] -indexing [CUFF.58] -indexing [CUFF.20] -indexing [CUFF.26] -indexing [CUFF.32] -indexing [CUFF.9] -indexing [CUFF.15] -indexing [CUFF.42] -indexing [CUFF.50] -indexing [CUFF.28] -indexing [CUFF.3] -indexing [CUFF.37] -indexing [CUFF.12] -indexing [CUFF.35] -indexing [CUFF.59] -indexing [CUFF.54] -indexing [CUFF.51] -indexing [CUFF.53] -indexing [CUFF.24] -indexing [CUFF.29] -indexing [CUFF.45] -indexing [CUFF.47] -indexing [CUFF.4] -indexing [CUFF.60] # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* exit 0 make[4]: Leaving directory '/build/transdecoder-5.0.1/sample_data/cufflinks_example' Running example in $... make[4]: Entering directory '/build/transdecoder-5.0.1/sample_data/pasa_example' ./runMe.sh #!/bin/bash -ve if [ ! -e genome.fasta ]; then gunzip -c genome.fasta.gz > genome.fasta fi if [ ! -e pasa_assemblies.fasta ]; then gunzip -c pasa_assemblies.fasta.gz > pasa_assemblies.fasta fi if [ ! -e pasa_assemblies.gff3 ]; then gunzip -c pasa_assemblies.gff3.gz > pasa_assemblies.gff3 fi if [ ! -e pasa_assemblies_described.txt ]; then gunzip -c pasa_assemblies_described.txt.gz > pasa_assemblies_described.txt fi # get the gene-to-transcript relationships cut -f2,3 pasa_assemblies_described.txt > pasa.gene_trans_map.txt ../../TransDecoder.LongOrfs -t pasa_assemblies.fasta --gene_trans_map pasa.gene_trans_map.txt -first extracting base frequencies, we'll need them later. CMD: /build/transdecoder-5.0.1/util/compute_base_probs.pl pasa_assemblies.fasta 0 > pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat CMD: touch pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat.ok - extracting ORFs from transcripts. -total transcripts to examine: 858 [100/858] = 11.66% done [200/858] = 23.31% done [300/858] = 34.97% done [400/858] = 46.62% done [500/858] = 58.28% done [600/858] = 69.93% done [700/858] = 81.59% done [800/858] = 93.24% done CMD: touch pasa_assemblies.fasta.transdecoder_dir/__longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: pasa_assemblies.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. ../../TransDecoder.Predict -t pasa_assemblies.fasta * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * Running CMD: /build/transdecoder-5.0.1/util/exclude_similar_proteins.pl pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: 631::asmbl_804::g.1028::m.1028, not unique enough -skipping training candidate: 307::asmbl_395::g.471::m.471, not unique enough -skipping training candidate: 631::asmbl_805::g.1035::m.1035, not unique enough -skipping training candidate: 350::asmbl_446::g.556::m.556, not unique enough -skipping training candidate: 584::asmbl_745::g.916::m.916, not unique enough -skipping training candidate: 540::asmbl_692::g.846::m.846, not unique enough -skipping training candidate: 444::asmbl_570::g.688::m.688, not unique enough -skipping training candidate: 434::asmbl_558::g.704::m.704, not unique enough -skipping training candidate: 542::asmbl_694::g.868::m.868, not unique enough -skipping training candidate: 342::asmbl_434::g.577::m.577, not unique enough -skipping training candidate: 537::asmbl_688::g.852::m.852, not unique enough -skipping training candidate: 569::asmbl_725::g.900::m.900, not unique enough -skipping training candidate: 393::asmbl_507::g.644::m.644, not unique enough -skipping training candidate: 639::asmbl_814::g.1033::m.1033, not unique enough -skipping training candidate: 492::asmbl_632::g.726::m.726, not unique enough -skipping training candidate: 508::asmbl_654::g.815::m.815, not unique enough -skipping training candidate: 606::asmbl_777::g.984::m.984, not unique enough -skipping training candidate: 224::asmbl_290::g.365::m.365, not unique enough -skipping training candidate: 584::asmbl_745::g.917::m.917, not unique enough -skipping training candidate: 584::asmbl_746::g.927::m.927, not unique enough -skipping training candidate: 224::asmbl_290::g.366::m.366, not unique enough -skipping training candidate: 584::asmbl_746::g.928::m.928, not unique enough -skipping training candidate: 84::asmbl_115::g.169::m.169, not unique enough -skipping training candidate: 436::asmbl_560::g.679::m.679, not unique enough -skipping training candidate: 436::asmbl_561::g.690::m.690, not unique enough -skipping training candidate: 613::asmbl_784::g.965::m.965, not unique enough -skipping training candidate: 607::asmbl_778::g.993::m.993, not unique enough -skipping training candidate: 394::asmbl_508::g.657::m.657, not unique enough -skipping training candidate: 13::asmbl_21::g.21::m.21, not unique enough -skipping training candidate: 13::asmbl_22::g.35::m.35, not unique enough -skipping training candidate: 352::asmbl_450::g.550::m.550, not unique enough 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candidate: 263::asmbl_343::g.455::m.455, not unique enough -skipping training candidate: 379::asmbl_491::g.599::m.599, not unique enough -skipping training candidate: 379::asmbl_492::g.604::m.604, not unique enough -skipping training candidate: 379::asmbl_489::g.618::m.618, not unique enough -skipping training candidate: 379::asmbl_490::g.625::m.625, not unique enough -skipping training candidate: 620::asmbl_793::g.964::m.964, not unique enough -skipping training candidate: 151::asmbl_198::g.195::m.195, not unique enough -skipping training candidate: 151::asmbl_199::g.213::m.213, not unique enough -skipping training candidate: 151::asmbl_200::g.226::m.226, not unique enough -skipping training candidate: 393::asmbl_507::g.646::m.646, not unique enough -skipping training candidate: 460::asmbl_592::g.742::m.742, not unique enough -skipping training candidate: 471::asmbl_606::g.746::m.746, not unique enough -skipping training candidate: 460::asmbl_593::g.757::m.757, not unique enough -skipping training candidate: 460::asmbl_594::g.769::m.769, not unique enough -skipping training candidate: 658::asmbl_839::g.1044::m.1044, not unique enough -skipping training candidate: 4::asmbl_6::g.5::m.5, not unique enough -skipping training candidate: 109::asmbl_146::g.184::m.184, not unique enough -skipping training candidate: 350::asmbl_446::g.557::m.557, not unique enough -skipping training candidate: 361::asmbl_466::g.578::m.578, not unique enough -skipping training candidate: 411::asmbl_531::g.659::m.659, not unique enough -skipping training candidate: 455::asmbl_585::g.720::m.720, not unique enough -skipping training candidate: 455::asmbl_586::g.724::m.724, not unique enough -skipping training candidate: 471::asmbl_606::g.747::m.747, not unique enough -skipping training candidate: 494::asmbl_635::g.809::m.809, not unique enough -skipping training candidate: 570::asmbl_726::g.910::m.910, not unique enough -skipping training candidate: 6::asmbl_8::g.31::m.31, not unique enough -skipping training candidate: 6::asmbl_9::g.45::m.45, not unique enough -skipping training candidate: 37::asmbl_57::g.65::m.65, not unique enough -skipping training candidate: 282::asmbl_365::g.449::m.449, not unique enough -skipping training candidate: 358::asmbl_459::g.549::m.549, not unique enough -skipping training candidate: 358::asmbl_460::g.562::m.562, not unique enough -skipping training candidate: 359::asmbl_461::g.571::m.571, not unique enough -skipping training candidate: 358::asmbl_462::g.585::m.585, not unique enough -skipping training candidate: 376::asmbl_484::g.614::m.614, not unique enough -skipping training candidate: 601::asmbl_770::g.963::m.963, not unique enough -skipping training candidate: 601::asmbl_771::g.973::m.973, not unique enough -skipping training candidate: 644::asmbl_820::g.1001::m.1001, not unique enough -skipping training candidate: 198::asmbl_259::g.324::m.324, not unique enough -skipping training candidate: 268::asmbl_349::g.429::m.429, not unique enough -skipping training candidate: 540::asmbl_692::g.847::m.847, not unique enough -skipping training candidate: 560::asmbl_713::g.875::m.875, not unique enough -skipping training candidate: 597::asmbl_765::g.939::m.939, not unique enough -skipping training candidate: 615::asmbl_787::g.992::m.992, not unique enough -skipping training candidate: 59::asmbl_85::g.104::m.104, not unique enough -skipping training candidate: 401::asmbl_518::g.629::m.629, not unique enough -skipping training candidate: 401::asmbl_517::g.656::m.656, not unique enough -skipping training candidate: 556::asmbl_709::g.880::m.880, not unique enough -skipping training candidate: 607::asmbl_778::g.995::m.995, not unique enough -skipping training candidate: 653::asmbl_830::g.1010::m.1010, not unique enough -skipping training candidate: 666::asmbl_847::g.1051::m.1051, not unique enough -skipping training candidate: 410::asmbl_530::g.649::m.649, not unique enough -skipping training candidate: 567::asmbl_722::g.915::m.915, not unique enough -skipping training candidate: 642::asmbl_817::g.1018::m.1018, not unique enough -skipping training candidate: 626::asmbl_799::g.1024::m.1024, not unique enough -skipping training candidate: 638::asmbl_813::g.1027::m.1027, not unique enough -skipping training candidate: 224::asmbl_290::g.370::m.370, not unique enough -skipping training candidate: 584::asmbl_746::g.932::m.932, not unique enough -skipping training candidate: 416::asmbl_536::g.665::m.665, not unique enough -skipping training candidate: 414::asmbl_534::g.694::m.694, not unique enough -skipping training candidate: 540::asmbl_692::g.848::m.848, not unique enough -skipping training candidate: 84::asmbl_115::g.170::m.170, not unique enough -skipping training candidate: 216::asmbl_278::g.336::m.336, not unique enough -skipping training candidate: 247::asmbl_320::g.421::m.421, not unique enough -skipping training candidate: 353::asmbl_452::g.574::m.574, not unique enough -skipping training candidate: 443::asmbl_569::g.678::m.678, not unique enough -skipping training candidate: 436::asmbl_560::g.680::m.680, not unique enough -skipping training candidate: 436::asmbl_561::g.691::m.691, not unique enough -skipping training candidate: 541::asmbl_693::g.860::m.860, not unique enough -skipping training candidate: 541::asmbl_695::g.877::m.877, not unique enough -skipping training candidate: 575::asmbl_734::g.899::m.899, not unique enough -skipping training candidate: 566::asmbl_721::g.905::m.905, not unique enough -skipping training candidate: 597::asmbl_765::g.940::m.940, not unique enough -skipping training candidate: 597::asmbl_766::g.944::m.944, not unique enough -skipping training candidate: 633::asmbl_807::g.1009::m.1009, not unique enough -skipping training candidate: 627::asmbl_800::g.1032::m.1032, not unique enough -skipping training candidate: 122::asmbl_164::g.234::m.234, not unique enough -skipping training candidate: 411::asmbl_531::g.660::m.660, not unique enough -skipping training candidate: 434::asmbl_558::g.705::m.705, not unique enough -skipping training candidate: 488::asmbl_626::g.771::m.771, not unique enough -skipping training candidate: 654::asmbl_831::g.1020::m.1020, not unique enough -redundancy-minimized set includes 396 / 1067 = 37.11% * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 42 * Running CMD: /build/transdecoder-5.0.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest pasa_assemblies.fasta.transdecoder_dir/base_freqs.dat > pasa_assemblies.fasta.transdecoder_dir/hexamer.scores * Running CMD: /build/transdecoder-5.0.1/util/score_CDS_likelihood_all_6_frames.pl pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds pasa_assemblies.fasta.transdecoder_dir/hexamer.scores > pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores * Running CMD: /build/transdecoder-5.0.1/util/select_best_ORFs_per_transcript.pl --gff3_file pasa_assemblies.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 645 > pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 -indexing [1::asmbl_1::g.1] -indexing [7::asmbl_10::g.55] -indexing [7::asmbl_10::g.56] -indexing [71::asmbl_100::g.117] -indexing [72::asmbl_101::g.121] -indexing [73::asmbl_102::g.130] -indexing [75::asmbl_104::g.153] -indexing [75::asmbl_105::g.162] -indexing [76::asmbl_106::g.172] -indexing [76::asmbl_106::g.171] -indexing [77::asmbl_107::g.136] -indexing [77::asmbl_107::g.135] -indexing [78::asmbl_108::g.147] -indexing [79::asmbl_109::g.157] -indexing [6::asmbl_11::g.10] -indexing [6::asmbl_11::g.11] -indexing [79::asmbl_110::g.165] -indexing [81::asmbl_112::g.141] -indexing [83::asmbl_114::g.161] -indexing [84::asmbl_115::g.170] -indexing [84::asmbl_115::g.169] -indexing [84::asmbl_116::g.134] -indexing [84::asmbl_116::g.133] -indexing [85::asmbl_117::g.146] -indexing [85::asmbl_117::g.145] -indexing [86::asmbl_118::g.155] -indexing [86::asmbl_118::g.156] -indexing [87::asmbl_119::g.164] -indexing [8::asmbl_12::g.23] -indexing [8::asmbl_12::g.24] -indexing [88::asmbl_120::g.128] -indexing [89::asmbl_121::g.139] -indexing [89::asmbl_121::g.140] -indexing [89::asmbl_122::g.152] -indexing [89::asmbl_122::g.151] -indexing [90::asmbl_123::g.160] -indexing [91::asmbl_124::g.168] -indexing [91::asmbl_125::g.132] -indexing [92::asmbl_126::g.144] -indexing [93::asmbl_127::g.154] -indexing [94::asmbl_128::g.163] -indexing [95::asmbl_129::g.127] -indexing [8::asmbl_13::g.37] -indexing [8::asmbl_13::g.38] -indexing [97::asmbl_131::g.150] -indexing [98::asmbl_132::g.159] -indexing [97::asmbl_133::g.167] -indexing [97::asmbl_134::g.131] -indexing [99::asmbl_135::g.143] -indexing [102::asmbl_138::g.173] -indexing [103::asmbl_139::g.138] -indexing [103::asmbl_139::g.137] -indexing [9::asmbl_14::g.48] -indexing [104::asmbl_140::g.148] -indexing [104::asmbl_140::g.149] -indexing [105::asmbl_141::g.158] -indexing [106::asmbl_142::g.166] -indexing [107::asmbl_143::g.129] -indexing [108::asmbl_144::g.142] -indexing [109::asmbl_145::g.178] -indexing [109::asmbl_145::g.179] -indexing [109::asmbl_146::g.184] -indexing [109::asmbl_146::g.183] -indexing [109::asmbl_146::g.182] -indexing [110::asmbl_147::g.188] -indexing [110::asmbl_147::g.187] -indexing [111::asmbl_148::g.174] -indexing [112::asmbl_149::g.176] -indexing [9::asmbl_15::g.4] -indexing [112::asmbl_150::g.180] -indexing [112::asmbl_151::g.185] -indexing [113::asmbl_153::g.175] -indexing [114::asmbl_154::g.177] -indexing [115::asmbl_155::g.181] -indexing [116::asmbl_156::g.186] -indexing [117::asmbl_157::g.198] -indexing [117::asmbl_158::g.217] -indexing [118::asmbl_159::g.229] -indexing [10::asmbl_16::g.16] -indexing [119::asmbl_160::g.237] -indexing [120::asmbl_161::g.190] -indexing [121::asmbl_162::g.204] -indexing [121::asmbl_162::g.205] -indexing [121::asmbl_163::g.221] -indexing [122::asmbl_164::g.233] -indexing [122::asmbl_164::g.234] -indexing [122::asmbl_165::g.242] -indexing [122::asmbl_165::g.241] -indexing [123::asmbl_166::g.196] -indexing [123::asmbl_167::g.214] -indexing [124::asmbl_168::g.227] -indexing [125::asmbl_169::g.236] -indexing [11::asmbl_17::g.29] -indexing [126::asmbl_170::g.245] -indexing [127::asmbl_171::g.202] -indexing [127::asmbl_172::g.219] -indexing [127::asmbl_173::g.231] -indexing [128::asmbl_174::g.239] -indexing [130::asmbl_176::g.209] -indexing [130::asmbl_176::g.210] -indexing [131::asmbl_177::g.223] -indexing [132::asmbl_178::g.235] -indexing [133::asmbl_179::g.243] -indexing [12::asmbl_18::g.43] -indexing [134::asmbl_180::g.199] -indexing [136::asmbl_182::g.230] -indexing [137::asmbl_183::g.238] -indexing [138::asmbl_184::g.192] -indexing [138::asmbl_184::g.191] -indexing [139::asmbl_185::g.207] -indexing [139::asmbl_185::g.208] -indexing [139::asmbl_185::g.206] -indexing [140::asmbl_186::g.222] -indexing [143::asmbl_189::g.197] -indexing [12::asmbl_19::g.52] -indexing [12::asmbl_19::g.53] -indexing [12::asmbl_19::g.54] -indexing [144::asmbl_190::g.216] -indexing [144::asmbl_190::g.215] -indexing [145::asmbl_191::g.228] -indexing [147::asmbl_193::g.189] -indexing [148::asmbl_194::g.203] -indexing [149::asmbl_195::g.220] -indexing [150::asmbl_196::g.232] -indexing [150::asmbl_197::g.240] -indexing [151::asmbl_198::g.193] -indexing [151::asmbl_198::g.194] -indexing [151::asmbl_198::g.195] -indexing [151::asmbl_199::g.212] -indexing [151::asmbl_199::g.211] -indexing [151::asmbl_199::g.213] -indexing [2::asmbl_2::g.12] -indexing [13::asmbl_20::g.8] -indexing [13::asmbl_20::g.9] -indexing [151::asmbl_200::g.224] -indexing [151::asmbl_200::g.226] -indexing [151::asmbl_200::g.225] -indexing [152::asmbl_202::g.244] -indexing [153::asmbl_203::g.201] -indexing [153::asmbl_203::g.200] -indexing [154::asmbl_204::g.218] -indexing [155::asmbl_205::g.274] -indexing [156::asmbl_206::g.281] -indexing [156::asmbl_207::g.249] -indexing [157::asmbl_208::g.259] -indexing [13::asmbl_21::g.22] -indexing [13::asmbl_21::g.21] -indexing [159::asmbl_210::g.278] -indexing [162::asmbl_213::g.266] -indexing [163::asmbl_214::g.273] -indexing [163::asmbl_214::g.272] -indexing [164::asmbl_216::g.247] -indexing [164::asmbl_216::g.248] -indexing [165::asmbl_217::g.258] -indexing [165::asmbl_218::g.270] -indexing [166::asmbl_219::g.277] -indexing [13::asmbl_22::g.35] -indexing [13::asmbl_22::g.36] -indexing [167::asmbl_220::g.286] -indexing [167::asmbl_220::g.285] -indexing [167::asmbl_221::g.254] -indexing [168::asmbl_222::g.265] -indexing [170::asmbl_224::g.280] -indexing [170::asmbl_225::g.246] -indexing [171::asmbl_226::g.256] -indexing [171::asmbl_226::g.257] -indexing [172::asmbl_227::g.269] -indexing [172::asmbl_227::g.268] -indexing [172::asmbl_228::g.275] -indexing [172::asmbl_228::g.276] -indexing [173::asmbl_229::g.283] -indexing [173::asmbl_229::g.284] -indexing [14::asmbl_23::g.47] -indexing [174::asmbl_230::g.252] -indexing [174::asmbl_230::g.253] -indexing [174::asmbl_231::g.263] -indexing [174::asmbl_231::g.264] -indexing [174::asmbl_232::g.271] -indexing [175::asmbl_233::g.279] -indexing [176::asmbl_234::g.287] -indexing [176::asmbl_235::g.255] -indexing [177::asmbl_236::g.267] -indexing [179::asmbl_238::g.282] -indexing [180::asmbl_239::g.251] -indexing [180::asmbl_239::g.250] -indexing [15::asmbl_24::g.3] -indexing [15::asmbl_24::g.2] -indexing [181::asmbl_240::g.262] -indexing [181::asmbl_240::g.261] -indexing [181::asmbl_240::g.260] -indexing [182::asmbl_241::g.298] -indexing [183::asmbl_242::g.304] -indexing [184::asmbl_243::g.308] -indexing [184::asmbl_243::g.306] -indexing [184::asmbl_243::g.307] -indexing [185::asmbl_244::g.289] -indexing [186::asmbl_245::g.295] -indexing [186::asmbl_245::g.296] -indexing [186::asmbl_245::g.294] -indexing [186::asmbl_245::g.293] -indexing [187::asmbl_246::g.302] -indexing [187::asmbl_246::g.300] -indexing [187::asmbl_246::g.301] -indexing [187::asmbl_246::g.299] -indexing [189::asmbl_249::g.291] -indexing [189::asmbl_249::g.290] -indexing [16::asmbl_25::g.15] -indexing [190::asmbl_250::g.297] -indexing [191::asmbl_251::g.303] -indexing [192::asmbl_252::g.305] -indexing [193::asmbl_253::g.288] -indexing [194::asmbl_254::g.292] -indexing [196::asmbl_256::g.343] -indexing [197::asmbl_257::g.310] -indexing [197::asmbl_257::g.309] -indexing [198::asmbl_258::g.315] -indexing [198::asmbl_258::g.316] -indexing [198::asmbl_259::g.323] -indexing [198::asmbl_259::g.324] -indexing [17::asmbl_26::g.28] -indexing [198::asmbl_260::g.338] -indexing [199::asmbl_261::g.349] -indexing [199::asmbl_261::g.348] -indexing [200::asmbl_262::g.313] -indexing [201::asmbl_263::g.320] -indexing [202::asmbl_264::g.328] -indexing [202::asmbl_264::g.329] -indexing [203::asmbl_265::g.342] -indexing [204::asmbl_266::g.352] -indexing [207::asmbl_269::g.337] -indexing [18::asmbl_27::g.41] -indexing [18::asmbl_27::g.42] -indexing [208::asmbl_270::g.347] -indexing [209::asmbl_271::g.312] -indexing [211::asmbl_273::g.326] -indexing [211::asmbl_273::g.327] -indexing [212::asmbl_274::g.341] -indexing [213::asmbl_275::g.351] -indexing [214::asmbl_276::g.314] -indexing [215::asmbl_277::g.322] -indexing [216::asmbl_278::g.333] -indexing [216::asmbl_278::g.334] -indexing [216::asmbl_278::g.332] -indexing [216::asmbl_278::g.336] -indexing [216::asmbl_278::g.335] -indexing [217::asmbl_279::g.346] -indexing [19::asmbl_28::g.51] -indexing [216::asmbl_280::g.311] -indexing [218::asmbl_281::g.319] -indexing [218::asmbl_281::g.317] -indexing [218::asmbl_281::g.318] -indexing [219::asmbl_282::g.325] -indexing [220::asmbl_283::g.339] -indexing [220::asmbl_283::g.340] -indexing [220::asmbl_284::g.350] -indexing [223::asmbl_286::g.321] -indexing [222::asmbl_287::g.330] -indexing [222::asmbl_287::g.331] -indexing [222::asmbl_288::g.345] -indexing [222::asmbl_288::g.344] -indexing [224::asmbl_289::g.356] -indexing [224::asmbl_289::g.355] -indexing [224::asmbl_289::g.357] -indexing [224::asmbl_289::g.354] -indexing [224::asmbl_289::g.353] -indexing [20::asmbl_29::g.7] -indexing [224::asmbl_290::g.368] -indexing [224::asmbl_290::g.370] -indexing [224::asmbl_290::g.367] -indexing [224::asmbl_290::g.366] -indexing [224::asmbl_290::g.365] -indexing [224::asmbl_290::g.369] -indexing [225::asmbl_291::g.379] -indexing [225::asmbl_292::g.390] -indexing [226::asmbl_293::g.397] -indexing [226::asmbl_293::g.398] -indexing [227::asmbl_294::g.361] -indexing [227::asmbl_295::g.374] -indexing [228::asmbl_296::g.382] -indexing [230::asmbl_298::g.401] -indexing [231::asmbl_299::g.364] -indexing [3::asmbl_3::g.25] -indexing [20::asmbl_30::g.20] -indexing [232::asmbl_300::g.378] -indexing [233::asmbl_301::g.388] -indexing [233::asmbl_301::g.389] -indexing [234::asmbl_302::g.396] -indexing [234::asmbl_303::g.359] -indexing [234::asmbl_303::g.360] -indexing [234::asmbl_304::g.373] -indexing [234::asmbl_305::g.381] -indexing [236::asmbl_307::g.400] -indexing [237::asmbl_308::g.363] -indexing [238::asmbl_309::g.377] -indexing [238::asmbl_309::g.376] -indexing [238::asmbl_309::g.375] -indexing [20::asmbl_31::g.34] -indexing [239::asmbl_310::g.384] -indexing [239::asmbl_310::g.383] -indexing [239::asmbl_310::g.385] -indexing [239::asmbl_310::g.386] -indexing [239::asmbl_310::g.387] -indexing [239::asmbl_311::g.395] -indexing [239::asmbl_311::g.394] -indexing [239::asmbl_311::g.393] -indexing [240::asmbl_312::g.358] -indexing [241::asmbl_313::g.371] -indexing [241::asmbl_313::g.372] -indexing [242::asmbl_314::g.380] -indexing [243::asmbl_315::g.391] -indexing [243::asmbl_315::g.392] -indexing [244::asmbl_316::g.399] -indexing [245::asmbl_317::g.362] -indexing [247::asmbl_319::g.414] -indexing [247::asmbl_319::g.413] -indexing [247::asmbl_319::g.415] -indexing [247::asmbl_319::g.416] -indexing [247::asmbl_319::g.417] -indexing [20::asmbl_32::g.46] -indexing [247::asmbl_320::g.421] -indexing [248::asmbl_321::g.402] -indexing [250::asmbl_323::g.408] -indexing [251::asmbl_324::g.419] -indexing [254::asmbl_327::g.407] -indexing [254::asmbl_328::g.412] -indexing [254::asmbl_328::g.411] -indexing [254::asmbl_329::g.420] -indexing [254::asmbl_330::g.423] -indexing [254::asmbl_331::g.406] -indexing [254::asmbl_331::g.405] -indexing [255::asmbl_333::g.418] -indexing [256::asmbl_334::g.422] -indexing [256::asmbl_335::g.403] -indexing [256::asmbl_335::g.404] -indexing [258::asmbl_337::g.410] -indexing [258::asmbl_337::g.409] -indexing [260::asmbl_339::g.462] -indexing [21::asmbl_34::g.13] -indexing [21::asmbl_34::g.14] -indexing [261::asmbl_340::g.430] -indexing [262::asmbl_341::g.437] -indexing [262::asmbl_341::g.436] -indexing [263::asmbl_342::g.447] -indexing [263::asmbl_343::g.455] -indexing [264::asmbl_344::g.425] -indexing [265::asmbl_345::g.433] -indexing [266::asmbl_346::g.443] -indexing [267::asmbl_347::g.452] -indexing [267::asmbl_347::g.453] -indexing [268::asmbl_348::g.460] -indexing [268::asmbl_348::g.461] -indexing [268::asmbl_349::g.428] -indexing [268::asmbl_349::g.429] -indexing [21::asmbl_35::g.27] -indexing [21::asmbl_35::g.26] -indexing [269::asmbl_350::g.435] -indexing [270::asmbl_351::g.446] -indexing [270::asmbl_351::g.445] -indexing [272::asmbl_353::g.424] -indexing [274::asmbl_355::g.440] -indexing [274::asmbl_355::g.441] -indexing [274::asmbl_355::g.442] -indexing [275::asmbl_356::g.450] -indexing [275::asmbl_356::g.451] -indexing [276::asmbl_357::g.458] -indexing [276::asmbl_357::g.457] -indexing [276::asmbl_357::g.459] -indexing [277::asmbl_358::g.427] -indexing [278::asmbl_359::g.434] -indexing [22::asmbl_36::g.40] -indexing [279::asmbl_360::g.444] -indexing 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[525::asmbl_675::g.832] -indexing [526::asmbl_676::g.833] -indexing [527::asmbl_677::g.836] -indexing [527::asmbl_677::g.837] -indexing [528::asmbl_678::g.827] -indexing [528::asmbl_678::g.825] -indexing [528::asmbl_678::g.826] -indexing [528::asmbl_678::g.828] -indexing [47::asmbl_68::g.78] -indexing [47::asmbl_68::g.79] -indexing [531::asmbl_681::g.834] -indexing [532::asmbl_682::g.838] -indexing [532::asmbl_682::g.840] -indexing [532::asmbl_682::g.839] -indexing [533::asmbl_683::g.829] -indexing [534::asmbl_684::g.831] -indexing [535::asmbl_685::g.870] -indexing [535::asmbl_685::g.869] -indexing [536::asmbl_686::g.878] -indexing [535::asmbl_687::g.844] -indexing [535::asmbl_687::g.843] -indexing [537::asmbl_688::g.852] -indexing [537::asmbl_688::g.853] -indexing [537::asmbl_689::g.864] -indexing [47::asmbl_69::g.85] -indexing [47::asmbl_69::g.86] -indexing [539::asmbl_691::g.883] -indexing [540::asmbl_692::g.847] -indexing [540::asmbl_692::g.846] -indexing [540::asmbl_692::g.848] -indexing [541::asmbl_693::g.859] -indexing [541::asmbl_693::g.857] -indexing [541::asmbl_693::g.858] -indexing [541::asmbl_693::g.860] -indexing [541::asmbl_693::g.856] -indexing [542::asmbl_694::g.868] -indexing [541::asmbl_695::g.877] -indexing [543::asmbl_696::g.842] -indexing [544::asmbl_697::g.851] -indexing [545::asmbl_698::g.863] -indexing [546::asmbl_699::g.873] -indexing [5::asmbl_7::g.18] -indexing [5::asmbl_7::g.17] -indexing [547::asmbl_700::g.881] -indexing [547::asmbl_700::g.882] -indexing [549::asmbl_702::g.855] -indexing [550::asmbl_703::g.867] -indexing [551::asmbl_704::g.876] -indexing [553::asmbl_706::g.850] -indexing [555::asmbl_708::g.872] -indexing [556::asmbl_709::g.880] -indexing [556::asmbl_709::g.879] -indexing [49::asmbl_71::g.99] -indexing [49::asmbl_71::g.101] -indexing [49::asmbl_71::g.100] -indexing [557::asmbl_710::g.845] -indexing [558::asmbl_711::g.854] -indexing [559::asmbl_712::g.865] -indexing [559::asmbl_712::g.866] -indexing [560::asmbl_713::g.875] -indexing [560::asmbl_713::g.874] -indexing [560::asmbl_714::g.884] -indexing [560::asmbl_715::g.849] -indexing [561::asmbl_716::g.862] -indexing [561::asmbl_716::g.861] -indexing [562::asmbl_717::g.871] -indexing [563::asmbl_718::g.923] -indexing [564::asmbl_719::g.887] -indexing [564::asmbl_719::g.886] -indexing [50::asmbl_72::g.110] -indexing [50::asmbl_72::g.111] -indexing [565::asmbl_720::g.896] -indexing [566::asmbl_721::g.905] -indexing [567::asmbl_722::g.915] -indexing [567::asmbl_722::g.914] -indexing [568::asmbl_723::g.926] -indexing [569::asmbl_724::g.894] -indexing [569::asmbl_724::g.893] -indexing [569::asmbl_724::g.892] -indexing [569::asmbl_724::g.895] -indexing [569::asmbl_724::g.891] -indexing [569::asmbl_725::g.900] -indexing [569::asmbl_725::g.901] -indexing [569::asmbl_725::g.902] -indexing [570::asmbl_726::g.908] -indexing [570::asmbl_726::g.909] -indexing [570::asmbl_726::g.910] -indexing [571::asmbl_727::g.922] -indexing [572::asmbl_728::g.885] -indexing [50::asmbl_73::g.118] -indexing [574::asmbl_730::g.904] -indexing [574::asmbl_731::g.912] -indexing [574::asmbl_731::g.913] -indexing [574::asmbl_732::g.925] -indexing [574::asmbl_733::g.890] -indexing [575::asmbl_734::g.899] -indexing [575::asmbl_734::g.898] -indexing [576::asmbl_735::g.907] -indexing [577::asmbl_736::g.921] -indexing [578::asmbl_737::g.933] -indexing [580::asmbl_739::g.903] -indexing [50::asmbl_74::g.125] -indexing [50::asmbl_74::g.124] -indexing [50::asmbl_74::g.126] -indexing [581::asmbl_740::g.911] -indexing [581::asmbl_741::g.924] -indexing [582::asmbl_742::g.889] -indexing [582::asmbl_742::g.888] -indexing [583::asmbl_743::g.897] -indexing [583::asmbl_744::g.906] -indexing [584::asmbl_745::g.919] -indexing [584::asmbl_745::g.917] -indexing [584::asmbl_745::g.920] -indexing [584::asmbl_745::g.916] -indexing [584::asmbl_745::g.918] -indexing [584::asmbl_746::g.927] -indexing [584::asmbl_746::g.932] -indexing [584::asmbl_746::g.930] -indexing [584::asmbl_746::g.928] -indexing [584::asmbl_746::g.929] -indexing [584::asmbl_746::g.931] -indexing [586::asmbl_748::g.947] -indexing [586::asmbl_748::g.948] -indexing [588::asmbl_750::g.953] -indexing [588::asmbl_751::g.935] -indexing [588::asmbl_751::g.934] -indexing [589::asmbl_752::g.943] -indexing [590::asmbl_753::g.949] -indexing [590::asmbl_754::g.952] -indexing [590::asmbl_754::g.951] -indexing [590::asmbl_755::g.955] -indexing [590::asmbl_756::g.941] -indexing [590::asmbl_757::g.945] -indexing [590::asmbl_757::g.946] -indexing [52::asmbl_76::g.105] -indexing [593::asmbl_761::g.942] -indexing [595::asmbl_763::g.950] -indexing [596::asmbl_764::g.954] -indexing [597::asmbl_765::g.939] -indexing [597::asmbl_765::g.937] -indexing [597::asmbl_765::g.940] -indexing [597::asmbl_765::g.938] -indexing [597::asmbl_765::g.936] -indexing [597::asmbl_766::g.944] -indexing [599::asmbl_768::g.985] -indexing [600::asmbl_769::g.996] -indexing [52::asmbl_77::g.116] -indexing [601::asmbl_770::g.963] -indexing [601::asmbl_770::g.962] -indexing [601::asmbl_771::g.973] -indexing [601::asmbl_771::g.972] -indexing [602::asmbl_772::g.979] -indexing [602::asmbl_772::g.980] -indexing [602::asmbl_773::g.988] -indexing [602::asmbl_773::g.989] -indexing [603::asmbl_774::g.957] -indexing [604::asmbl_775::g.967] -indexing [605::asmbl_776::g.977] -indexing [606::asmbl_777::g.984] -indexing [607::asmbl_778::g.993] -indexing [607::asmbl_778::g.994] -indexing [607::asmbl_778::g.995] -indexing [608::asmbl_779::g.960] -indexing [608::asmbl_779::g.961] -indexing [53::asmbl_78::g.120] -indexing [609::asmbl_780::g.969] -indexing [609::asmbl_780::g.970] -indexing [609::asmbl_780::g.971] -indexing [611::asmbl_782::g.987] -indexing [613::asmbl_784::g.966] -indexing [613::asmbl_784::g.965] -indexing [614::asmbl_785::g.976] -indexing [615::asmbl_786::g.983] -indexing [615::asmbl_786::g.982] -indexing [615::asmbl_787::g.991] -indexing [615::asmbl_787::g.992] -indexing [616::asmbl_788::g.958] -indexing [616::asmbl_788::g.959] -indexing [617::asmbl_789::g.968] -indexing [54::asmbl_79::g.92] -indexing [618::asmbl_790::g.978] -indexing [619::asmbl_791::g.986] -indexing [620::asmbl_792::g.956] -indexing [620::asmbl_793::g.964] -indexing [621::asmbl_794::g.974] -indexing [621::asmbl_794::g.975] -indexing [622::asmbl_795::g.981] -indexing [623::asmbl_796::g.990] -indexing [624::asmbl_797::g.1002] -indexing [625::asmbl_798::g.1013] -indexing [626::asmbl_799::g.1023] -indexing [626::asmbl_799::g.1024] -indexing [6::asmbl_8::g.30] -indexing [6::asmbl_8::g.31] -indexing [55::asmbl_80::g.98] -indexing [627::asmbl_800::g.1032] -indexing [629::asmbl_802::g.1004] -indexing [630::asmbl_803::g.1015] -indexing [631::asmbl_804::g.1028] -indexing [631::asmbl_805::g.1035] -indexing [633::asmbl_807::g.1008] -indexing [633::asmbl_807::g.1009] -indexing [634::asmbl_808::g.1019] -indexing [635::asmbl_809::g.1030] -indexing [56::asmbl_81::g.109] -indexing [635::asmbl_810::g.1038] -indexing [636::asmbl_811::g.1003] -indexing [637::asmbl_812::g.1014] -indexing [638::asmbl_813::g.1026] -indexing [638::asmbl_813::g.1027] -indexing [638::asmbl_813::g.1025] -indexing [639::asmbl_814::g.1033] -indexing [639::asmbl_814::g.1034] -indexing [640::asmbl_815::g.997] -indexing [640::asmbl_815::g.999] -indexing [640::asmbl_815::g.998] -indexing [641::asmbl_816::g.1007] -indexing [641::asmbl_816::g.1006] -indexing [642::asmbl_817::g.1017] -indexing [642::asmbl_817::g.1018] -indexing [643::asmbl_818::g.1029] -indexing [643::asmbl_819::g.1037] -indexing [644::asmbl_820::g.1001] -indexing [645::asmbl_821::g.1012] -indexing [645::asmbl_821::g.1011] -indexing [646::asmbl_822::g.1022] -indexing [646::asmbl_822::g.1021] -indexing [647::asmbl_823::g.1031] -indexing [648::asmbl_824::g.1039] -indexing [649::asmbl_825::g.1005] -indexing [650::asmbl_826::g.1016] -indexing [652::asmbl_828::g.1036] -indexing [653::asmbl_829::g.1000] -indexing [58::asmbl_83::g.122] -indexing [58::asmbl_83::g.123] -indexing [653::asmbl_830::g.1010] -indexing [654::asmbl_831::g.1020] -indexing [656::asmbl_833::g.1048] -indexing [656::asmbl_834::g.1042] -indexing [656::asmbl_835::g.1045] -indexing [658::asmbl_837::g.1046] -indexing [658::asmbl_837::g.1047] -indexing [658::asmbl_838::g.1040] -indexing [658::asmbl_838::g.1041] -indexing [658::asmbl_839::g.1044] -indexing [658::asmbl_839::g.1043] -indexing [59::asmbl_84::g.94] -indexing [59::asmbl_84::g.95] -indexing [663::asmbl_844::g.1056] -indexing [664::asmbl_845::g.1061] -indexing [665::asmbl_846::g.1064] -indexing [666::asmbl_847::g.1049] -indexing [666::asmbl_847::g.1050] -indexing [666::asmbl_847::g.1051] -indexing [667::asmbl_848::g.1054] -indexing [668::asmbl_849::g.1058] -indexing [59::asmbl_85::g.104] -indexing [59::asmbl_85::g.103] -indexing [670::asmbl_851::g.1065] -indexing [671::asmbl_852::g.1052] -indexing [672::asmbl_853::g.1055] -indexing [673::asmbl_854::g.1059] -indexing [673::asmbl_854::g.1060] -indexing [674::asmbl_855::g.1063] -indexing [674::asmbl_855::g.1062] -indexing [675::asmbl_856::g.1066] -indexing [675::asmbl_856::g.1067] -indexing [676::asmbl_857::g.1053] -indexing [677::asmbl_858::g.1057] -indexing [60::asmbl_86::g.115] -indexing [61::asmbl_87::g.119] -indexing [62::asmbl_88::g.91] -indexing [63::asmbl_89::g.96] -indexing [63::asmbl_89::g.97] -indexing [6::asmbl_9::g.45] -indexing [6::asmbl_9::g.44] -indexing [63::asmbl_90::g.107] -indexing [63::asmbl_90::g.108] -indexing [65::asmbl_93::g.93] -indexing [66::asmbl_94::g.102] -indexing [67::asmbl_95::g.112] -indexing [67::asmbl_95::g.113] -indexing [67::asmbl_95::g.114] -indexing [69::asmbl_97::g.90] -indexing [70::asmbl_99::g.106] * Running CMD: /build/transdecoder-5.0.1/util/train_start_PWM.pl --transcripts pasa_assemblies.fasta --selected_orfs pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix pasa_assemblies.fasta.transdecoder_dir/start_refinement * Running CMD: /build/transdecoder-5.0.1/util/PWM/build_atgPWM_+-.pl --transcripts pasa_assemblies.fasta --selected_orfs pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix pasa_assemblies.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --features_minus pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores > pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl pasa_assemblies.fasta.transdecoder_dir/start_refinement.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/deplete_feature_noise.pl --features_plus pasa_assemblies.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced num features: 238 num_incorporate: 71 -feature swap of score: 0.52233068358735 instead of -2.4838353992418 -feature swap of score: 3.4925122435335 instead of -2.69571560364119 -feature swap of score: -0.479799656028566 instead of -2.28706103601398 -feature swap of score: -0.0881342990948846 instead of -2.01923571762916 -feature swap of score: 3.70320425069563 instead of -2.540266312821 -feature swap of score: -1.18001089627022 instead of -2.19874275195072 -feature swap of score: 0.890711131288117 instead of -1.48110814799594 -feature swap of score: -1.05010135127967 instead of -1.29405271062499 -feature swap of score: -0.0660971314530546 instead of -1.10945144224631 -feature swap of score: 4.44453897240347 instead of -0.978468124148539 -feature swap of score: -0.464399759591707 instead of -0.841794961146521 -feature swap of score: 0.255068847557726 instead of -0.83142113951215 -feature swap of score: 1.95582633064074 instead of -0.76896518568472 -feature swap of score: -0.0332453222172366 instead of -0.682979129272786 -feature swap of score: 1.8228745697833 instead of -0.653744437026382 -feature swap of score: 1.00115669145456 instead of -0.336891026477184 -feature swap of score: 0.672803798904712 instead of -0.578246064931 -feature swap of score: 1.8162642359003 instead of -0.452564095078051 -feature swap of score: 0.280846761877589 instead of -0.647264557316993 -feature swap of score: 0.366355095526699 instead of -0.615212412314209 -feature swap of score: 2.52986097726451 instead of -0.758989032460075 -feature swap of score: -0.0952627696553691 instead of -0.817191160815284 -feature swap of score: 0.996754631653053 instead of -0.80551837636419 -feature swap of score: 0.354999699462731 instead of -0.274911636492182 -feature swap of score: 1.28605443964402 instead of 0.0980797372313064 -feature swap of score: 0.32578718956916 instead of -0.042861330285221 -feature swap of score: 2.48770150611293 instead of -0.0868957590364158 -feature swap of score: 2.64754362015744 instead of 0.2916904256282 -feature swap of score: 1.01988302433125 instead of 0.036666467034015 -feature swap of score: 0.702376236311601 instead of -0.128287580103504 -feature swap of score: 2.99676647453095 instead of 0.320673377955444 -feature swap of score: 4.3305495710187 instead of 0.295875888654129 -feature swap of score: 1.17421891679809 instead of 0.254710288367653 -feature swap of score: 0.401521517315352 instead of 0.370606147577384 -feature swap of score: 3.89634731515857 instead of 0.389772413567672 -feature swap of score: 2.74749373854816 instead of 0.451140083480975 -feature swap of score: 4.14790539102617 instead of 0.173512045799991 -feature swap of score: 2.68928352460324 instead of 0.0987413441847772 -feature swap of score: 0.570947526770153 instead of -0.152678189275884 -feature swap of score: 2.87693452246047 instead of 0.175971771120871 -feature swap of score: 0.345761582949679 instead of 0.189210540579853 -feature swap of score: 1.75381703871986 instead of -0.176138170873724 -feature swap of score: 6.3225755214291 instead of 0.182318752228176 -feature swap of score: -0.00356336589610784 instead of -0.074332288426649 -feature swap of score: 1.25652300984573 instead of 0.440440454930295 -feature swap of score: 4.35627103288236 instead of 0.601792868596411 -feature swap of score: 3.34305077634812 instead of 0.646355594435306 -feature swap of score: 0.89148415481126 instead of 0.847522010634187 -feature swap of score: 3.6953445371134 instead of 0.751030612474935 -feature swap of score: 5.78699079524925 instead of 0.699840066363169 -feature swap of score: 2.15409587173251 instead of 0.715035855107118 -feature swap of score: 1.47994164306661 instead of 0.417255934795064 -feature swap of score: 4.91570803685393 instead of 0.612782191206777 -feature swap of score: 0.527551455366298 instead of 0.495108302468003 -feature swap of score: 3.40423853426828 instead of 0.883665117310717 -feature swap of score: 0.802539851871931 instead of 0.787642557429234 -num feature swaps: 56 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus pasa_assemblies.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript pasa_assemblies.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/start_codon_refinement.pl --transcripts pasa_assemblies.fasta --gff3_file pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 > pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 -indexing [1::asmbl_1::g.1] -indexing [7::asmbl_10::g.55] -indexing [71::asmbl_100::g.117] -indexing [72::asmbl_101::g.121] -indexing [73::asmbl_102::g.130] -indexing [75::asmbl_104::g.153] -indexing [75::asmbl_105::g.162] -indexing [76::asmbl_106::g.171] -indexing [77::asmbl_107::g.135] -indexing [78::asmbl_108::g.147] -indexing [79::asmbl_109::g.157] -indexing [6::asmbl_11::g.10] -indexing [79::asmbl_110::g.165] -indexing [81::asmbl_112::g.141] -indexing [83::asmbl_114::g.161] -indexing [84::asmbl_115::g.169] -indexing [84::asmbl_116::g.133] -indexing [85::asmbl_117::g.145] -indexing [86::asmbl_118::g.155] -indexing [87::asmbl_119::g.164] -indexing [8::asmbl_12::g.23] -indexing [88::asmbl_120::g.128] -indexing [89::asmbl_121::g.139] -indexing [89::asmbl_122::g.151] -indexing [90::asmbl_123::g.160] -indexing [91::asmbl_124::g.168] -indexing [91::asmbl_125::g.132] -indexing [92::asmbl_126::g.144] -indexing [93::asmbl_127::g.154] -indexing [94::asmbl_128::g.163] -indexing [95::asmbl_129::g.127] -indexing [8::asmbl_13::g.37] -indexing [97::asmbl_131::g.150] -indexing [98::asmbl_132::g.159] -indexing [97::asmbl_133::g.167] -indexing [97::asmbl_134::g.131] -indexing [99::asmbl_135::g.143] -indexing [102::asmbl_138::g.173] -indexing [103::asmbl_139::g.137] -indexing [9::asmbl_14::g.48] -indexing [104::asmbl_140::g.148] -indexing [105::asmbl_141::g.158] -indexing [106::asmbl_142::g.166] -indexing [107::asmbl_143::g.129] -indexing [108::asmbl_144::g.142] -indexing [109::asmbl_145::g.178] -indexing [109::asmbl_146::g.182] -indexing [110::asmbl_147::g.187] -indexing [111::asmbl_148::g.174] -indexing [112::asmbl_149::g.176] -indexing [9::asmbl_15::g.4] -indexing [112::asmbl_150::g.180] -indexing [112::asmbl_151::g.185] -indexing [113::asmbl_153::g.175] -indexing [114::asmbl_154::g.177] -indexing [115::asmbl_155::g.181] -indexing [116::asmbl_156::g.186] -indexing [117::asmbl_157::g.198] -indexing [117::asmbl_158::g.217] -indexing [118::asmbl_159::g.229] -indexing [10::asmbl_16::g.16] -indexing [119::asmbl_160::g.237] -indexing [120::asmbl_161::g.190] -indexing [121::asmbl_162::g.204] -indexing [121::asmbl_163::g.221] -indexing [122::asmbl_164::g.233] -indexing [122::asmbl_165::g.241] -indexing [123::asmbl_166::g.196] -indexing [123::asmbl_167::g.214] -indexing [124::asmbl_168::g.227] -indexing [125::asmbl_169::g.236] -indexing [11::asmbl_17::g.29] -indexing [126::asmbl_170::g.245] -indexing [127::asmbl_171::g.202] -indexing [127::asmbl_172::g.219] -indexing [127::asmbl_173::g.231] -indexing [128::asmbl_174::g.239] -indexing [130::asmbl_176::g.209] -indexing [131::asmbl_177::g.223] -indexing [132::asmbl_178::g.235] -indexing [133::asmbl_179::g.243] -indexing [12::asmbl_18::g.43] -indexing [134::asmbl_180::g.199] -indexing [136::asmbl_182::g.230] -indexing [137::asmbl_183::g.238] -indexing [138::asmbl_184::g.191] -indexing [139::asmbl_185::g.206] -indexing [140::asmbl_186::g.222] -indexing [143::asmbl_189::g.197] -indexing [12::asmbl_19::g.52] -indexing [144::asmbl_190::g.215] -indexing [145::asmbl_191::g.228] -indexing [147::asmbl_193::g.189] -indexing [148::asmbl_194::g.203] -indexing [149::asmbl_195::g.220] -indexing [150::asmbl_196::g.232] -indexing [150::asmbl_197::g.240] -indexing [151::asmbl_198::g.193] -indexing [151::asmbl_199::g.212] -indexing [2::asmbl_2::g.12] -indexing [13::asmbl_20::g.8] -indexing [151::asmbl_200::g.224] -indexing [152::asmbl_202::g.244] -indexing [153::asmbl_203::g.200] -indexing [154::asmbl_204::g.218] -indexing [155::asmbl_205::g.274] -indexing [156::asmbl_206::g.281] -indexing [156::asmbl_207::g.249] -indexing [157::asmbl_208::g.259] -indexing [13::asmbl_21::g.21] -indexing [159::asmbl_210::g.278] -indexing [162::asmbl_213::g.266] -indexing [163::asmbl_214::g.272] -indexing [164::asmbl_216::g.247] -indexing [165::asmbl_217::g.258] -indexing [165::asmbl_218::g.270] -indexing [166::asmbl_219::g.277] -indexing [13::asmbl_22::g.35] -indexing [167::asmbl_220::g.285] -indexing [167::asmbl_221::g.254] -indexing [168::asmbl_222::g.265] -indexing [170::asmbl_224::g.280] -indexing [170::asmbl_225::g.246] -indexing [171::asmbl_226::g.256] -indexing [172::asmbl_227::g.268] -indexing [172::asmbl_228::g.275] -indexing [173::asmbl_229::g.283] -indexing [14::asmbl_23::g.47] -indexing [174::asmbl_230::g.252] -indexing [174::asmbl_231::g.263] -indexing [174::asmbl_232::g.271] -indexing [175::asmbl_233::g.279] -indexing [176::asmbl_234::g.287] -indexing [176::asmbl_235::g.255] -indexing [177::asmbl_236::g.267] -indexing [179::asmbl_238::g.282] -indexing [180::asmbl_239::g.250] -indexing [15::asmbl_24::g.2] -indexing [181::asmbl_240::g.260] -indexing [182::asmbl_241::g.298] -indexing [183::asmbl_242::g.304] -indexing [184::asmbl_243::g.306] -indexing [185::asmbl_244::g.289] -indexing [186::asmbl_245::g.293] -indexing [187::asmbl_246::g.299] -indexing [189::asmbl_249::g.290] -indexing [16::asmbl_25::g.15] -indexing [190::asmbl_250::g.297] -indexing [191::asmbl_251::g.303] -indexing [192::asmbl_252::g.305] -indexing [193::asmbl_253::g.288] -indexing [194::asmbl_254::g.292] -indexing [196::asmbl_256::g.343] -indexing [197::asmbl_257::g.309] -indexing [198::asmbl_258::g.315] -indexing [198::asmbl_259::g.323] -indexing [17::asmbl_26::g.28] -indexing [198::asmbl_260::g.338] -indexing [199::asmbl_261::g.348] -indexing [200::asmbl_262::g.313] -indexing [201::asmbl_263::g.320] -indexing [202::asmbl_264::g.328] -indexing [203::asmbl_265::g.342] -indexing [204::asmbl_266::g.352] -indexing [207::asmbl_269::g.337] -indexing [18::asmbl_27::g.41] -indexing [208::asmbl_270::g.347] -indexing [209::asmbl_271::g.312] -indexing [211::asmbl_273::g.326] -indexing [212::asmbl_274::g.341] -indexing [213::asmbl_275::g.351] -indexing [214::asmbl_276::g.314] -indexing [215::asmbl_277::g.322] -indexing [216::asmbl_278::g.332] -indexing [217::asmbl_279::g.346] -indexing [19::asmbl_28::g.51] -indexing [216::asmbl_280::g.311] -indexing [218::asmbl_281::g.317] -indexing [219::asmbl_282::g.325] -indexing [220::asmbl_283::g.339] -indexing [220::asmbl_284::g.350] -indexing [223::asmbl_286::g.321] -indexing [222::asmbl_287::g.330] -indexing [222::asmbl_288::g.344] -indexing [224::asmbl_289::g.354] -indexing [20::asmbl_29::g.7] -indexing [224::asmbl_290::g.365] -indexing [225::asmbl_291::g.379] -indexing [225::asmbl_292::g.390] -indexing [226::asmbl_293::g.397] -indexing [227::asmbl_294::g.361] -indexing [227::asmbl_295::g.374] -indexing [228::asmbl_296::g.382] -indexing [230::asmbl_298::g.401] -indexing [231::asmbl_299::g.364] -indexing [3::asmbl_3::g.25] -indexing [20::asmbl_30::g.20] -indexing [232::asmbl_300::g.378] -indexing [233::asmbl_301::g.388] -indexing [234::asmbl_302::g.396] -indexing [234::asmbl_303::g.359] -indexing [234::asmbl_304::g.373] -indexing [234::asmbl_305::g.381] -indexing [236::asmbl_307::g.400] -indexing [237::asmbl_308::g.363] -indexing [238::asmbl_309::g.375] -indexing [20::asmbl_31::g.34] -indexing [239::asmbl_310::g.383] -indexing [239::asmbl_311::g.393] -indexing [240::asmbl_312::g.358] -indexing [241::asmbl_313::g.371] -indexing [242::asmbl_314::g.380] -indexing [243::asmbl_315::g.391] -indexing [244::asmbl_316::g.399] -indexing [245::asmbl_317::g.362] -indexing [247::asmbl_319::g.414] -indexing [20::asmbl_32::g.46] -indexing [247::asmbl_320::g.421] -indexing [248::asmbl_321::g.402] -indexing [250::asmbl_323::g.408] -indexing [251::asmbl_324::g.419] -indexing [254::asmbl_327::g.407] -indexing [254::asmbl_328::g.411] -indexing [254::asmbl_329::g.420] -indexing [254::asmbl_330::g.423] -indexing [254::asmbl_331::g.405] -indexing [255::asmbl_333::g.418] -indexing [256::asmbl_334::g.422] -indexing [256::asmbl_335::g.404] -indexing [258::asmbl_337::g.410] -indexing [260::asmbl_339::g.462] -indexing [21::asmbl_34::g.14] -indexing [261::asmbl_340::g.430] -indexing [262::asmbl_341::g.436] -indexing [263::asmbl_342::g.447] -indexing [263::asmbl_343::g.455] -indexing [264::asmbl_344::g.425] -indexing [265::asmbl_345::g.433] -indexing [266::asmbl_346::g.443] -indexing [267::asmbl_347::g.452] -indexing [268::asmbl_348::g.460] -indexing [268::asmbl_349::g.428] -indexing [21::asmbl_35::g.27] -indexing [269::asmbl_350::g.435] -indexing [270::asmbl_351::g.445] -indexing [272::asmbl_353::g.424] -indexing [274::asmbl_355::g.440] -indexing [275::asmbl_356::g.450] -indexing [276::asmbl_357::g.457] -indexing [277::asmbl_358::g.427] -indexing [278::asmbl_359::g.434] -indexing [22::asmbl_36::g.40] -indexing [279::asmbl_360::g.444] -indexing [280::asmbl_361::g.454] -indexing [281::asmbl_362::g.463] -indexing [281::asmbl_363::g.431] -indexing [282::asmbl_364::g.438] -indexing [282::asmbl_365::g.448] -indexing [283::asmbl_366::g.456] -indexing [284::asmbl_367::g.426] -indexing [285::asmbl_368::g.478] -indexing [286::asmbl_369::g.488] -indexing [23::asmbl_37::g.50] -indexing [286::asmbl_370::g.498] -indexing [287::asmbl_371::g.508] -indexing [289::asmbl_373::g.481] -indexing [290::asmbl_374::g.492] -indexing [291::asmbl_375::g.503] -indexing [292::asmbl_376::g.468] -indexing [294::asmbl_377::g.474] -indexing [293::asmbl_378::g.485] -indexing [293::asmbl_379::g.495] -indexing [24::asmbl_38::g.6] -indexing [295::asmbl_380::g.506] -indexing [296::asmbl_381::g.470] -indexing [296::asmbl_382::g.480] -indexing [297::asmbl_383::g.490] -indexing [298::asmbl_384::g.501] -indexing [299::asmbl_385::g.465] -indexing [300::asmbl_386::g.472] -indexing [301::asmbl_387::g.482] -indexing [302::asmbl_388::g.494] -indexing [303::asmbl_389::g.505] -indexing [25::asmbl_39::g.19] -indexing [304::asmbl_390::g.469] -indexing [304::asmbl_391::g.479] -indexing [305::asmbl_392::g.489] -indexing [306::asmbl_393::g.499] -indexing [307::asmbl_394::g.509] -indexing [307::asmbl_395::g.471] -indexing [309::asmbl_397::g.493] -indexing [310::asmbl_398::g.504] -indexing [4::asmbl_4::g.39] -indexing [26::asmbl_40::g.32] -indexing [312::asmbl_400::g.477] -indexing [313::asmbl_401::g.487] -indexing [314::asmbl_402::g.497] -indexing [315::asmbl_403::g.507] -indexing [320::asmbl_408::g.510] -indexing [320::asmbl_409::g.514] -indexing [320::asmbl_410::g.516] -indexing [322::asmbl_412::g.518] 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[346::asmbl_442::g.564] -indexing [347::asmbl_443::g.575] -indexing [348::asmbl_444::g.587] -indexing [349::asmbl_445::g.544] -indexing [350::asmbl_446::g.556] -indexing [351::asmbl_447::g.568] -indexing [352::asmbl_448::g.581] -indexing [352::asmbl_449::g.592] -indexing [352::asmbl_450::g.550] -indexing [353::asmbl_451::g.563] -indexing [353::asmbl_452::g.572] -indexing [354::asmbl_453::g.586] -indexing [355::asmbl_454::g.543] -indexing [356::asmbl_455::g.555] -indexing [356::asmbl_456::g.567] -indexing [357::asmbl_457::g.579] -indexing [357::asmbl_458::g.590] -indexing [358::asmbl_459::g.548] -indexing [32::asmbl_46::g.84] -indexing [358::asmbl_460::g.561] -indexing [359::asmbl_461::g.570] -indexing [358::asmbl_462::g.584] -indexing [360::asmbl_463::g.541] -indexing [361::asmbl_464::g.554] -indexing [361::asmbl_465::g.566] -indexing [361::asmbl_466::g.578] -indexing [362::asmbl_467::g.589] -indexing [363::asmbl_468::g.547] -indexing [364::asmbl_469::g.560] -indexing [33::asmbl_47::g.58] -indexing [365::asmbl_470::g.610] -indexing [365::asmbl_471::g.620] -indexing [365::asmbl_472::g.594] -indexing [370::asmbl_477::g.597] -indexing [371::asmbl_478::g.602] -indexing [372::asmbl_479::g.608] -indexing [34::asmbl_48::g.66] -indexing [373::asmbl_480::g.619] -indexing [374::asmbl_481::g.626] -indexing [375::asmbl_482::g.600] -indexing [376::asmbl_483::g.605] -indexing [376::asmbl_484::g.613] -indexing [377::asmbl_485::g.623] -indexing [378::asmbl_486::g.596] -indexing [378::asmbl_487::g.601] -indexing [378::asmbl_488::g.607] -indexing [379::asmbl_489::g.617] -indexing [34::asmbl_49::g.74] -indexing [379::asmbl_490::g.624] -indexing [379::asmbl_491::g.598] -indexing [379::asmbl_492::g.603] -indexing [380::asmbl_493::g.612] -indexing [381::asmbl_494::g.622] -indexing [384::asmbl_497::g.606] -indexing [385::asmbl_498::g.615] -indexing [4::asmbl_5::g.49] -indexing [34::asmbl_50::g.81] -indexing [388::asmbl_501::g.637] -indexing [389::asmbl_502::g.641] 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[415::asmbl_535::g.703] -indexing [416::asmbl_536::g.664] -indexing [417::asmbl_537::g.675] -indexing [418::asmbl_538::g.687] -indexing [419::asmbl_539::g.698] -indexing [35::asmbl_54::g.77] -indexing [422::asmbl_542::g.682] -indexing [423::asmbl_543::g.693] -indexing [422::asmbl_544::g.702] -indexing [422::asmbl_545::g.710] -indexing [424::asmbl_546::g.674] -indexing [426::asmbl_548::g.697] -indexing [427::asmbl_549::g.706] -indexing [36::asmbl_55::g.83] -indexing [428::asmbl_550::g.669] -indexing [429::asmbl_551::g.681] -indexing [429::asmbl_552::g.692] -indexing [430::asmbl_553::g.701] -indexing [431::asmbl_554::g.708] -indexing [431::asmbl_555::g.672] -indexing [432::asmbl_556::g.686] -indexing [433::asmbl_557::g.696] -indexing [434::asmbl_558::g.704] -indexing [435::asmbl_559::g.667] -indexing [37::asmbl_56::g.57] -indexing [436::asmbl_560::g.679] -indexing [436::asmbl_561::g.690] -indexing [437::asmbl_562::g.700] -indexing [439::asmbl_564::g.671] -indexing [440::asmbl_565::g.685] -indexing [440::asmbl_566::g.695] -indexing [442::asmbl_568::g.666] -indexing [443::asmbl_569::g.677] -indexing [37::asmbl_57::g.64] -indexing [444::asmbl_570::g.688] -indexing [445::asmbl_571::g.699] -indexing [445::asmbl_572::g.707] -indexing [447::asmbl_574::g.683] -indexing [448::asmbl_575::g.717] -indexing [449::asmbl_576::g.721] -indexing [450::asmbl_577::g.725] -indexing [451::asmbl_578::g.712] -indexing [451::asmbl_579::g.714] -indexing [38::asmbl_58::g.73] -indexing [451::asmbl_580::g.718] -indexing [452::asmbl_582::g.711] -indexing [453::asmbl_583::g.713] -indexing [454::asmbl_584::g.715] -indexing [455::asmbl_585::g.719] -indexing [455::asmbl_586::g.722] -indexing [456::asmbl_587::g.736] -indexing [457::asmbl_588::g.750] -indexing [458::asmbl_589::g.765] -indexing [39::asmbl_59::g.80] -indexing [459::asmbl_590::g.777] -indexing [459::asmbl_591::g.728] -indexing [460::asmbl_592::g.740] -indexing [460::asmbl_593::g.756] -indexing [460::asmbl_594::g.767] -indexing [461::asmbl_596::g.732] -indexing [462::asmbl_597::g.748] -indexing [463::asmbl_598::g.762] -indexing [464::asmbl_599::g.774] -indexing [4::asmbl_6::g.5] -indexing [40::asmbl_60::g.87] -indexing [466::asmbl_601::g.737] -indexing [467::asmbl_602::g.753] -indexing [470::asmbl_605::g.731] -indexing [471::asmbl_606::g.745] -indexing [472::asmbl_607::g.760] -indexing [473::asmbl_608::g.773] -indexing [474::asmbl_609::g.782] -indexing [41::asmbl_61::g.59] -indexing [476::asmbl_611::g.752] -indexing [477::asmbl_612::g.766] -indexing [478::asmbl_613::g.778] -indexing [479::asmbl_614::g.729] -indexing [480::asmbl_615::g.744] -indexing [481::asmbl_616::g.759] -indexing [481::asmbl_617::g.772] -indexing [481::asmbl_618::g.781] -indexing [482::asmbl_619::g.735] -indexing [42::asmbl_62::g.68] -indexing [484::asmbl_621::g.764] -indexing [485::asmbl_622::g.776] -indexing [486::asmbl_623::g.727] -indexing [487::asmbl_624::g.743] -indexing [487::asmbl_625::g.758] -indexing [488::asmbl_626::g.770] -indexing [488::asmbl_627::g.779] -indexing [489::asmbl_628::g.733] -indexing [489::asmbl_629::g.749] -indexing [43::asmbl_63::g.76] -indexing [490::asmbl_630::g.763] -indexing [491::asmbl_631::g.775] -indexing [492::asmbl_632::g.726] -indexing [493::asmbl_633::g.739] -indexing [493::asmbl_634::g.754] -indexing [494::asmbl_635::g.807] -indexing [495::asmbl_636::g.818] -indexing [496::asmbl_637::g.787] -indexing [498::asmbl_639::g.802] -indexing [498::asmbl_640::g.814] -indexing [499::asmbl_641::g.824] -indexing [500::asmbl_642::g.792] -indexing [501::asmbl_643::g.797] -indexing [501::asmbl_644::g.805] -indexing [501::asmbl_645::g.817] -indexing [502::asmbl_646::g.785] -indexing [503::asmbl_647::g.794] -indexing [503::asmbl_648::g.800] -indexing [504::asmbl_649::g.812] -indexing [505::asmbl_650::g.823] -indexing [505::asmbl_651::g.791] -indexing [507::asmbl_653::g.804] -indexing [508::asmbl_654::g.815] -indexing [508::asmbl_655::g.784] -indexing [509::asmbl_656::g.793] -indexing [510::asmbl_657::g.799] -indexing [510::asmbl_658::g.811] -indexing [511::asmbl_659::g.821] -indexing [512::asmbl_660::g.789] -indexing [513::asmbl_662::g.803] -indexing [515::asmbl_664::g.783] -indexing [518::asmbl_667::g.810] -indexing [519::asmbl_668::g.820] -indexing [519::asmbl_669::g.788] -indexing [47::asmbl_67::g.71] -indexing [520::asmbl_670::g.796] -indexing [522::asmbl_672::g.835] -indexing [523::asmbl_673::g.841] -indexing [524::asmbl_674::g.830] -indexing [525::asmbl_675::g.832] -indexing [526::asmbl_676::g.833] -indexing [527::asmbl_677::g.836] -indexing [528::asmbl_678::g.825] -indexing [47::asmbl_68::g.78] -indexing [531::asmbl_681::g.834] -indexing [532::asmbl_682::g.838] -indexing [533::asmbl_683::g.829] -indexing [534::asmbl_684::g.831] -indexing [535::asmbl_685::g.869] -indexing [536::asmbl_686::g.878] -indexing [535::asmbl_687::g.843] -indexing [537::asmbl_688::g.852] -indexing [537::asmbl_689::g.864] -indexing [47::asmbl_69::g.85] -indexing [539::asmbl_691::g.883] -indexing [540::asmbl_692::g.846] -indexing [541::asmbl_693::g.856] -indexing [542::asmbl_694::g.868] -indexing [541::asmbl_695::g.877] -indexing [543::asmbl_696::g.842] -indexing [544::asmbl_697::g.851] -indexing [545::asmbl_698::g.863] -indexing [546::asmbl_699::g.873] -indexing [5::asmbl_7::g.17] -indexing [547::asmbl_700::g.881] -indexing [549::asmbl_702::g.855] -indexing [550::asmbl_703::g.867] -indexing [551::asmbl_704::g.876] -indexing [553::asmbl_706::g.850] -indexing [555::asmbl_708::g.872] -indexing [556::asmbl_709::g.879] -indexing [49::asmbl_71::g.99] -indexing [557::asmbl_710::g.845] -indexing [558::asmbl_711::g.854] -indexing [559::asmbl_712::g.865] -indexing [560::asmbl_713::g.874] -indexing [560::asmbl_714::g.884] -indexing [560::asmbl_715::g.849] -indexing [561::asmbl_716::g.861] -indexing [562::asmbl_717::g.871] -indexing [563::asmbl_718::g.923] -indexing [564::asmbl_719::g.886] -indexing [50::asmbl_72::g.110] -indexing [565::asmbl_720::g.896] -indexing [566::asmbl_721::g.905] -indexing [567::asmbl_722::g.914] -indexing [568::asmbl_723::g.926] -indexing [569::asmbl_724::g.891] -indexing [569::asmbl_725::g.900] -indexing [570::asmbl_726::g.908] -indexing [571::asmbl_727::g.922] -indexing [572::asmbl_728::g.885] -indexing [50::asmbl_73::g.118] -indexing [574::asmbl_730::g.904] -indexing [574::asmbl_731::g.912] -indexing [574::asmbl_732::g.925] -indexing [574::asmbl_733::g.890] -indexing [575::asmbl_734::g.898] -indexing [576::asmbl_735::g.907] -indexing [577::asmbl_736::g.921] -indexing [578::asmbl_737::g.933] -indexing [580::asmbl_739::g.903] -indexing [50::asmbl_74::g.124] -indexing [581::asmbl_740::g.911] -indexing [581::asmbl_741::g.924] -indexing [582::asmbl_742::g.888] -indexing [583::asmbl_743::g.897] -indexing [583::asmbl_744::g.906] -indexing [584::asmbl_745::g.917] -indexing [584::asmbl_746::g.927] -indexing [586::asmbl_748::g.948] -indexing [588::asmbl_750::g.953] -indexing [588::asmbl_751::g.935] -indexing [589::asmbl_752::g.943] -indexing [590::asmbl_753::g.949] -indexing [590::asmbl_754::g.951] -indexing [590::asmbl_755::g.955] -indexing [590::asmbl_756::g.941] -indexing [590::asmbl_757::g.945] -indexing [52::asmbl_76::g.105] -indexing [593::asmbl_761::g.942] -indexing [595::asmbl_763::g.950] -indexing [596::asmbl_764::g.954] -indexing [597::asmbl_765::g.937] -indexing [597::asmbl_766::g.944] -indexing [599::asmbl_768::g.985] -indexing [600::asmbl_769::g.996] -indexing [52::asmbl_77::g.116] -indexing [601::asmbl_770::g.962] -indexing [601::asmbl_771::g.972] -indexing [602::asmbl_772::g.979] -indexing [602::asmbl_773::g.988] -indexing [603::asmbl_774::g.957] -indexing [604::asmbl_775::g.967] -indexing [605::asmbl_776::g.977] -indexing [606::asmbl_777::g.984] -indexing [607::asmbl_778::g.993] -indexing [608::asmbl_779::g.960] -indexing [53::asmbl_78::g.120] -indexing [609::asmbl_780::g.969] -indexing [611::asmbl_782::g.987] -indexing [613::asmbl_784::g.965] -indexing [614::asmbl_785::g.976] -indexing [615::asmbl_786::g.982] -indexing [615::asmbl_787::g.991] -indexing [616::asmbl_788::g.958] -indexing [617::asmbl_789::g.968] -indexing [54::asmbl_79::g.92] -indexing [618::asmbl_790::g.978] -indexing [619::asmbl_791::g.986] -indexing [620::asmbl_792::g.956] -indexing [620::asmbl_793::g.964] -indexing [621::asmbl_794::g.974] -indexing [622::asmbl_795::g.981] -indexing [623::asmbl_796::g.990] -indexing [624::asmbl_797::g.1002] -indexing [625::asmbl_798::g.1013] -indexing [626::asmbl_799::g.1024] -indexing [6::asmbl_8::g.30] -indexing [55::asmbl_80::g.98] -indexing [627::asmbl_800::g.1032] -indexing [629::asmbl_802::g.1004] -indexing [630::asmbl_803::g.1015] -indexing [631::asmbl_804::g.1028] -indexing [631::asmbl_805::g.1035] -indexing [633::asmbl_807::g.1008] -indexing [634::asmbl_808::g.1019] -indexing [635::asmbl_809::g.1030] -indexing [56::asmbl_81::g.109] -indexing [635::asmbl_810::g.1038] -indexing [636::asmbl_811::g.1003] -indexing [637::asmbl_812::g.1014] -indexing [638::asmbl_813::g.1025] -indexing [639::asmbl_814::g.1033] -indexing [640::asmbl_815::g.997] -indexing [641::asmbl_816::g.1006] -indexing [642::asmbl_817::g.1017] -indexing [643::asmbl_818::g.1029] -indexing [643::asmbl_819::g.1037] -indexing [644::asmbl_820::g.1001] -indexing [645::asmbl_821::g.1011] -indexing [646::asmbl_822::g.1021] -indexing [647::asmbl_823::g.1031] -indexing [648::asmbl_824::g.1039] -indexing [649::asmbl_825::g.1005] -indexing [650::asmbl_826::g.1016] -indexing [652::asmbl_828::g.1036] -indexing [653::asmbl_829::g.1000] -indexing [58::asmbl_83::g.122] -indexing [653::asmbl_830::g.1010] -indexing [654::asmbl_831::g.1020] -indexing [656::asmbl_833::g.1048] -indexing [656::asmbl_834::g.1042] -indexing [656::asmbl_835::g.1045] -indexing [658::asmbl_837::g.1046] -indexing [658::asmbl_838::g.1041] -indexing [658::asmbl_839::g.1043] -indexing [59::asmbl_84::g.94] -indexing [663::asmbl_844::g.1056] -indexing [664::asmbl_845::g.1061] -indexing [665::asmbl_846::g.1064] -indexing [666::asmbl_847::g.1049] -indexing [667::asmbl_848::g.1054] -indexing [668::asmbl_849::g.1058] -indexing [59::asmbl_85::g.103] -indexing [670::asmbl_851::g.1065] -indexing [671::asmbl_852::g.1052] -indexing [672::asmbl_853::g.1055] -indexing [673::asmbl_854::g.1059] -indexing [674::asmbl_855::g.1062] -indexing [675::asmbl_856::g.1066] -indexing [676::asmbl_857::g.1053] -indexing [677::asmbl_858::g.1057] -indexing [60::asmbl_86::g.115] -indexing [61::asmbl_87::g.119] -indexing [62::asmbl_88::g.91] -indexing [63::asmbl_89::g.96] -indexing [6::asmbl_9::g.44] -indexing [63::asmbl_90::g.107] -indexing [65::asmbl_93::g.93] -indexing [66::asmbl_94::g.102] -indexing [67::asmbl_95::g.112] -indexing [69::asmbl_97::g.90] -indexing [70::asmbl_99::g.106] -number of revised start positions: 81 CMD: cp pasa_assemblies.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 pasa_assemblies.fasta.transdecoder.gff3 CMD: /build/transdecoder-5.0.1/util/gff3_file_to_bed.pl pasa_assemblies.fasta.transdecoder.gff3 > pasa_assemblies.fasta.transdecoder.bed -indexing [1::asmbl_1::g.1] -indexing [7::asmbl_10::g.55] -indexing [71::asmbl_100::g.117] -indexing [72::asmbl_101::g.121] -indexing [73::asmbl_102::g.130] -indexing [75::asmbl_104::g.153] -indexing [75::asmbl_105::g.162] -indexing [76::asmbl_106::g.171] -indexing [77::asmbl_107::g.135] -indexing [78::asmbl_108::g.147] -indexing [79::asmbl_109::g.157] -indexing [6::asmbl_11::g.10] -indexing [79::asmbl_110::g.165] -indexing [81::asmbl_112::g.141] -indexing [83::asmbl_114::g.161] -indexing [84::asmbl_115::g.169] -indexing [84::asmbl_116::g.133] -indexing [85::asmbl_117::g.145] -indexing [86::asmbl_118::g.155] -indexing [87::asmbl_119::g.164] -indexing [8::asmbl_12::g.23] -indexing [88::asmbl_120::g.128] -indexing [89::asmbl_121::g.139] -indexing [89::asmbl_122::g.151] -indexing [90::asmbl_123::g.160] -indexing [91::asmbl_124::g.168] -indexing [91::asmbl_125::g.132] -indexing [92::asmbl_126::g.144] -indexing [93::asmbl_127::g.154] -indexing [94::asmbl_128::g.163] -indexing [95::asmbl_129::g.127] -indexing [8::asmbl_13::g.37] -indexing [97::asmbl_131::g.150] -indexing [98::asmbl_132::g.159] -indexing [97::asmbl_133::g.167] -indexing [97::asmbl_134::g.131] -indexing [99::asmbl_135::g.143] -indexing [102::asmbl_138::g.173] -indexing [103::asmbl_139::g.137] -indexing [9::asmbl_14::g.48] -indexing [104::asmbl_140::g.148] -indexing [105::asmbl_141::g.158] -indexing [106::asmbl_142::g.166] -indexing [107::asmbl_143::g.129] -indexing [108::asmbl_144::g.142] -indexing [109::asmbl_145::g.178] -indexing [109::asmbl_146::g.182] -indexing [110::asmbl_147::g.187] -indexing [111::asmbl_148::g.174] -indexing [112::asmbl_149::g.176] -indexing [9::asmbl_15::g.4] -indexing [112::asmbl_150::g.180] -indexing [112::asmbl_151::g.185] -indexing [113::asmbl_153::g.175] -indexing [114::asmbl_154::g.177] -indexing [115::asmbl_155::g.181] -indexing [116::asmbl_156::g.186] -indexing [117::asmbl_157::g.198] -indexing [117::asmbl_158::g.217] -indexing [118::asmbl_159::g.229] -indexing [10::asmbl_16::g.16] -indexing [119::asmbl_160::g.237] -indexing [120::asmbl_161::g.190] -indexing [121::asmbl_162::g.204] -indexing [121::asmbl_163::g.221] -indexing [122::asmbl_164::g.233] -indexing [122::asmbl_165::g.241] -indexing [123::asmbl_166::g.196] -indexing [123::asmbl_167::g.214] -indexing [124::asmbl_168::g.227] -indexing [125::asmbl_169::g.236] -indexing [11::asmbl_17::g.29] -indexing [126::asmbl_170::g.245] -indexing [127::asmbl_171::g.202] -indexing [127::asmbl_172::g.219] -indexing [127::asmbl_173::g.231] -indexing [128::asmbl_174::g.239] -indexing [130::asmbl_176::g.209] -indexing [131::asmbl_177::g.223] -indexing [132::asmbl_178::g.235] -indexing [133::asmbl_179::g.243] -indexing [12::asmbl_18::g.43] -indexing [134::asmbl_180::g.199] -indexing [136::asmbl_182::g.230] -indexing [137::asmbl_183::g.238] -indexing [138::asmbl_184::g.191] -indexing [139::asmbl_185::g.206] -indexing [140::asmbl_186::g.222] -indexing [143::asmbl_189::g.197] -indexing [12::asmbl_19::g.52] -indexing [144::asmbl_190::g.215] -indexing [145::asmbl_191::g.228] -indexing [147::asmbl_193::g.189] -indexing [148::asmbl_194::g.203] -indexing [149::asmbl_195::g.220] -indexing [150::asmbl_196::g.232] -indexing [150::asmbl_197::g.240] -indexing [151::asmbl_198::g.193] -indexing [151::asmbl_199::g.212] -indexing [2::asmbl_2::g.12] -indexing [13::asmbl_20::g.8] -indexing [151::asmbl_200::g.224] -indexing [152::asmbl_202::g.244] -indexing [153::asmbl_203::g.200] -indexing [154::asmbl_204::g.218] -indexing [155::asmbl_205::g.274] -indexing [156::asmbl_206::g.281] -indexing [156::asmbl_207::g.249] -indexing [157::asmbl_208::g.259] -indexing [13::asmbl_21::g.21] -indexing [159::asmbl_210::g.278] -indexing [162::asmbl_213::g.266] -indexing [163::asmbl_214::g.272] -indexing [164::asmbl_216::g.247] -indexing [165::asmbl_217::g.258] -indexing [165::asmbl_218::g.270] -indexing [166::asmbl_219::g.277] -indexing [13::asmbl_22::g.35] -indexing [167::asmbl_220::g.285] -indexing [167::asmbl_221::g.254] -indexing [168::asmbl_222::g.265] -indexing [170::asmbl_224::g.280] -indexing [170::asmbl_225::g.246] -indexing [171::asmbl_226::g.256] -indexing [172::asmbl_227::g.268] -indexing [172::asmbl_228::g.275] -indexing [173::asmbl_229::g.283] -indexing [14::asmbl_23::g.47] -indexing [174::asmbl_230::g.252] -indexing [174::asmbl_231::g.263] -indexing [174::asmbl_232::g.271] -indexing [175::asmbl_233::g.279] -indexing [176::asmbl_234::g.287] -indexing [176::asmbl_235::g.255] -indexing [177::asmbl_236::g.267] -indexing [179::asmbl_238::g.282] -indexing [180::asmbl_239::g.250] -indexing [15::asmbl_24::g.2] -indexing [181::asmbl_240::g.260] -indexing [182::asmbl_241::g.298] -indexing [183::asmbl_242::g.304] -indexing [184::asmbl_243::g.306] -indexing [185::asmbl_244::g.289] -indexing [186::asmbl_245::g.293] -indexing [187::asmbl_246::g.299] -indexing [189::asmbl_249::g.290] -indexing [16::asmbl_25::g.15] -indexing [190::asmbl_250::g.297] -indexing [191::asmbl_251::g.303] -indexing [192::asmbl_252::g.305] -indexing [193::asmbl_253::g.288] -indexing [194::asmbl_254::g.292] -indexing [196::asmbl_256::g.343] -indexing [197::asmbl_257::g.309] -indexing [198::asmbl_258::g.315] -indexing [198::asmbl_259::g.323] -indexing [17::asmbl_26::g.28] -indexing [198::asmbl_260::g.338] -indexing [199::asmbl_261::g.348] -indexing [200::asmbl_262::g.313] -indexing [201::asmbl_263::g.320] -indexing [202::asmbl_264::g.328] -indexing [203::asmbl_265::g.342] -indexing [204::asmbl_266::g.352] -indexing [207::asmbl_269::g.337] -indexing [18::asmbl_27::g.41] -indexing [208::asmbl_270::g.347] -indexing [209::asmbl_271::g.312] -indexing [211::asmbl_273::g.326] -indexing [212::asmbl_274::g.341] -indexing [213::asmbl_275::g.351] -indexing [214::asmbl_276::g.314] -indexing [215::asmbl_277::g.322] -indexing [216::asmbl_278::g.332] -indexing [217::asmbl_279::g.346] -indexing [19::asmbl_28::g.51] -indexing [216::asmbl_280::g.311] -indexing [218::asmbl_281::g.317] -indexing [219::asmbl_282::g.325] -indexing [220::asmbl_283::g.339] -indexing [220::asmbl_284::g.350] -indexing [223::asmbl_286::g.321] -indexing [222::asmbl_287::g.330] -indexing [222::asmbl_288::g.344] -indexing [224::asmbl_289::g.354] -indexing [20::asmbl_29::g.7] -indexing [224::asmbl_290::g.365] -indexing [225::asmbl_291::g.379] -indexing [225::asmbl_292::g.390] -indexing [226::asmbl_293::g.397] -indexing [227::asmbl_294::g.361] -indexing [227::asmbl_295::g.374] -indexing [228::asmbl_296::g.382] -indexing [230::asmbl_298::g.401] -indexing [231::asmbl_299::g.364] -indexing [3::asmbl_3::g.25] -indexing [20::asmbl_30::g.20] -indexing [232::asmbl_300::g.378] -indexing [233::asmbl_301::g.388] -indexing [234::asmbl_302::g.396] -indexing [234::asmbl_303::g.359] -indexing [234::asmbl_304::g.373] -indexing [234::asmbl_305::g.381] -indexing [236::asmbl_307::g.400] -indexing [237::asmbl_308::g.363] -indexing [238::asmbl_309::g.375] -indexing [20::asmbl_31::g.34] -indexing [239::asmbl_310::g.383] -indexing [239::asmbl_311::g.393] -indexing [240::asmbl_312::g.358] -indexing [241::asmbl_313::g.371] -indexing [242::asmbl_314::g.380] -indexing [243::asmbl_315::g.391] -indexing [244::asmbl_316::g.399] -indexing [245::asmbl_317::g.362] -indexing [247::asmbl_319::g.414] -indexing [20::asmbl_32::g.46] -indexing [247::asmbl_320::g.421] -indexing [248::asmbl_321::g.402] -indexing [250::asmbl_323::g.408] -indexing [251::asmbl_324::g.419] -indexing [254::asmbl_327::g.407] -indexing [254::asmbl_328::g.411] -indexing [254::asmbl_329::g.420] -indexing [254::asmbl_330::g.423] -indexing [254::asmbl_331::g.405] -indexing [255::asmbl_333::g.418] -indexing [256::asmbl_334::g.422] -indexing [256::asmbl_335::g.404] -indexing [258::asmbl_337::g.410] -indexing [260::asmbl_339::g.462] -indexing [21::asmbl_34::g.14] -indexing [261::asmbl_340::g.430] -indexing 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[604::asmbl_775::g.967] -indexing [605::asmbl_776::g.977] -indexing [606::asmbl_777::g.984] -indexing [607::asmbl_778::g.993] -indexing [608::asmbl_779::g.960] -indexing [53::asmbl_78::g.120] -indexing [609::asmbl_780::g.969] -indexing [611::asmbl_782::g.987] -indexing [613::asmbl_784::g.965] -indexing [614::asmbl_785::g.976] -indexing [615::asmbl_786::g.982] -indexing [615::asmbl_787::g.991] -indexing [616::asmbl_788::g.958] -indexing [617::asmbl_789::g.968] -indexing [54::asmbl_79::g.92] -indexing [618::asmbl_790::g.978] -indexing [619::asmbl_791::g.986] -indexing [620::asmbl_792::g.956] -indexing [620::asmbl_793::g.964] -indexing [621::asmbl_794::g.974] -indexing [622::asmbl_795::g.981] -indexing [623::asmbl_796::g.990] -indexing [624::asmbl_797::g.1002] -indexing [625::asmbl_798::g.1013] -indexing [626::asmbl_799::g.1024] -indexing [6::asmbl_8::g.30] -indexing [55::asmbl_80::g.98] -indexing [627::asmbl_800::g.1032] -indexing [629::asmbl_802::g.1004] -indexing [630::asmbl_803::g.1015] -indexing [631::asmbl_804::g.1028] -indexing [631::asmbl_805::g.1035] -indexing [633::asmbl_807::g.1008] -indexing [634::asmbl_808::g.1019] -indexing [635::asmbl_809::g.1030] -indexing [56::asmbl_81::g.109] -indexing [635::asmbl_810::g.1038] -indexing [636::asmbl_811::g.1003] -indexing [637::asmbl_812::g.1014] -indexing [638::asmbl_813::g.1025] -indexing [639::asmbl_814::g.1033] -indexing [640::asmbl_815::g.997] -indexing [641::asmbl_816::g.1006] -indexing [642::asmbl_817::g.1017] -indexing [643::asmbl_818::g.1029] -indexing [643::asmbl_819::g.1037] -indexing [644::asmbl_820::g.1001] -indexing [645::asmbl_821::g.1011] -indexing [646::asmbl_822::g.1021] -indexing [647::asmbl_823::g.1031] -indexing [648::asmbl_824::g.1039] -indexing [649::asmbl_825::g.1005] -indexing [650::asmbl_826::g.1016] -indexing [652::asmbl_828::g.1036] -indexing [653::asmbl_829::g.1000] -indexing [58::asmbl_83::g.122] -indexing [653::asmbl_830::g.1010] -indexing [654::asmbl_831::g.1020] -indexing [656::asmbl_833::g.1048] -indexing [656::asmbl_834::g.1042] -indexing [656::asmbl_835::g.1045] -indexing [658::asmbl_837::g.1046] -indexing [658::asmbl_838::g.1041] -indexing [658::asmbl_839::g.1043] -indexing [59::asmbl_84::g.94] -indexing [663::asmbl_844::g.1056] -indexing [664::asmbl_845::g.1061] -indexing [665::asmbl_846::g.1064] -indexing [666::asmbl_847::g.1049] -indexing [667::asmbl_848::g.1054] -indexing [668::asmbl_849::g.1058] -indexing [59::asmbl_85::g.103] -indexing [670::asmbl_851::g.1065] -indexing [671::asmbl_852::g.1052] -indexing [672::asmbl_853::g.1055] -indexing [673::asmbl_854::g.1059] -indexing [674::asmbl_855::g.1062] -indexing [675::asmbl_856::g.1066] -indexing [676::asmbl_857::g.1053] -indexing [677::asmbl_858::g.1057] -indexing [60::asmbl_86::g.115] -indexing [61::asmbl_87::g.119] -indexing [62::asmbl_88::g.91] -indexing [63::asmbl_89::g.96] -indexing [6::asmbl_9::g.44] -indexing [63::asmbl_90::g.107] -indexing [65::asmbl_93::g.93] -indexing [66::asmbl_94::g.102] -indexing [67::asmbl_95::g.112] -indexing [69::asmbl_97::g.90] -indexing [70::asmbl_99::g.106] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta > pasa_assemblies.fasta.transdecoder.pep -indexing [1::asmbl_1::g.1] -indexing [7::asmbl_10::g.55] -indexing [71::asmbl_100::g.117] -indexing [72::asmbl_101::g.121] -indexing [73::asmbl_102::g.130] -indexing [75::asmbl_104::g.153] -indexing [75::asmbl_105::g.162] -indexing [76::asmbl_106::g.171] -indexing [77::asmbl_107::g.135] -indexing [78::asmbl_108::g.147] -indexing [79::asmbl_109::g.157] -indexing [6::asmbl_11::g.10] -indexing [79::asmbl_110::g.165] -indexing [81::asmbl_112::g.141] -indexing [83::asmbl_114::g.161] -indexing [84::asmbl_115::g.169] -indexing [84::asmbl_116::g.133] -indexing [85::asmbl_117::g.145] -indexing [86::asmbl_118::g.155] -indexing [87::asmbl_119::g.164] -indexing [8::asmbl_12::g.23] -indexing [88::asmbl_120::g.128] -indexing [89::asmbl_121::g.139] -indexing [89::asmbl_122::g.151] -indexing [90::asmbl_123::g.160] -indexing [91::asmbl_124::g.168] -indexing [91::asmbl_125::g.132] -indexing [92::asmbl_126::g.144] -indexing [93::asmbl_127::g.154] -indexing [94::asmbl_128::g.163] -indexing [95::asmbl_129::g.127] -indexing [8::asmbl_13::g.37] -indexing [97::asmbl_131::g.150] -indexing [98::asmbl_132::g.159] -indexing [97::asmbl_133::g.167] -indexing [97::asmbl_134::g.131] -indexing [99::asmbl_135::g.143] -indexing [102::asmbl_138::g.173] -indexing [103::asmbl_139::g.137] -indexing [9::asmbl_14::g.48] -indexing [104::asmbl_140::g.148] -indexing [105::asmbl_141::g.158] -indexing [106::asmbl_142::g.166] -indexing [107::asmbl_143::g.129] -indexing [108::asmbl_144::g.142] -indexing [109::asmbl_145::g.178] -indexing [109::asmbl_146::g.182] -indexing [110::asmbl_147::g.187] -indexing [111::asmbl_148::g.174] -indexing [112::asmbl_149::g.176] -indexing [9::asmbl_15::g.4] -indexing [112::asmbl_150::g.180] -indexing [112::asmbl_151::g.185] -indexing [113::asmbl_153::g.175] -indexing [114::asmbl_154::g.177] -indexing [115::asmbl_155::g.181] -indexing [116::asmbl_156::g.186] -indexing [117::asmbl_157::g.198] -indexing [117::asmbl_158::g.217] -indexing [118::asmbl_159::g.229] -indexing [10::asmbl_16::g.16] -indexing [119::asmbl_160::g.237] -indexing [120::asmbl_161::g.190] -indexing [121::asmbl_162::g.204] -indexing [121::asmbl_163::g.221] -indexing [122::asmbl_164::g.233] -indexing [122::asmbl_165::g.241] -indexing [123::asmbl_166::g.196] -indexing [123::asmbl_167::g.214] -indexing [124::asmbl_168::g.227] -indexing [125::asmbl_169::g.236] -indexing [11::asmbl_17::g.29] -indexing [126::asmbl_170::g.245] -indexing [127::asmbl_171::g.202] -indexing [127::asmbl_172::g.219] -indexing [127::asmbl_173::g.231] -indexing [128::asmbl_174::g.239] -indexing [130::asmbl_176::g.209] -indexing [131::asmbl_177::g.223] -indexing [132::asmbl_178::g.235] -indexing [133::asmbl_179::g.243] -indexing [12::asmbl_18::g.43] -indexing [134::asmbl_180::g.199] -indexing [136::asmbl_182::g.230] -indexing [137::asmbl_183::g.238] -indexing [138::asmbl_184::g.191] -indexing [139::asmbl_185::g.206] -indexing [140::asmbl_186::g.222] -indexing [143::asmbl_189::g.197] -indexing [12::asmbl_19::g.52] -indexing [144::asmbl_190::g.215] -indexing [145::asmbl_191::g.228] -indexing [147::asmbl_193::g.189] -indexing [148::asmbl_194::g.203] -indexing [149::asmbl_195::g.220] -indexing [150::asmbl_196::g.232] -indexing [150::asmbl_197::g.240] -indexing [151::asmbl_198::g.193] -indexing [151::asmbl_199::g.212] -indexing [2::asmbl_2::g.12] -indexing [13::asmbl_20::g.8] -indexing [151::asmbl_200::g.224] -indexing [152::asmbl_202::g.244] -indexing [153::asmbl_203::g.200] -indexing [154::asmbl_204::g.218] -indexing [155::asmbl_205::g.274] -indexing [156::asmbl_206::g.281] -indexing [156::asmbl_207::g.249] -indexing [157::asmbl_208::g.259] -indexing [13::asmbl_21::g.21] -indexing [159::asmbl_210::g.278] -indexing [162::asmbl_213::g.266] -indexing [163::asmbl_214::g.272] -indexing [164::asmbl_216::g.247] -indexing [165::asmbl_217::g.258] -indexing [165::asmbl_218::g.270] -indexing [166::asmbl_219::g.277] -indexing [13::asmbl_22::g.35] -indexing [167::asmbl_220::g.285] -indexing [167::asmbl_221::g.254] -indexing [168::asmbl_222::g.265] -indexing [170::asmbl_224::g.280] -indexing [170::asmbl_225::g.246] -indexing [171::asmbl_226::g.256] -indexing [172::asmbl_227::g.268] -indexing [172::asmbl_228::g.275] -indexing [173::asmbl_229::g.283] -indexing [14::asmbl_23::g.47] -indexing [174::asmbl_230::g.252] -indexing [174::asmbl_231::g.263] -indexing [174::asmbl_232::g.271] -indexing [175::asmbl_233::g.279] -indexing [176::asmbl_234::g.287] -indexing [176::asmbl_235::g.255] -indexing [177::asmbl_236::g.267] -indexing [179::asmbl_238::g.282] -indexing [180::asmbl_239::g.250] -indexing [15::asmbl_24::g.2] -indexing [181::asmbl_240::g.260] -indexing [182::asmbl_241::g.298] -indexing [183::asmbl_242::g.304] -indexing [184::asmbl_243::g.306] -indexing [185::asmbl_244::g.289] -indexing [186::asmbl_245::g.293] -indexing [187::asmbl_246::g.299] -indexing [189::asmbl_249::g.290] -indexing [16::asmbl_25::g.15] -indexing [190::asmbl_250::g.297] -indexing [191::asmbl_251::g.303] -indexing [192::asmbl_252::g.305] -indexing [193::asmbl_253::g.288] -indexing [194::asmbl_254::g.292] -indexing [196::asmbl_256::g.343] -indexing [197::asmbl_257::g.309] -indexing [198::asmbl_258::g.315] -indexing [198::asmbl_259::g.323] -indexing [17::asmbl_26::g.28] -indexing [198::asmbl_260::g.338] -indexing [199::asmbl_261::g.348] -indexing [200::asmbl_262::g.313] -indexing [201::asmbl_263::g.320] -indexing [202::asmbl_264::g.328] -indexing [203::asmbl_265::g.342] -indexing [204::asmbl_266::g.352] -indexing [207::asmbl_269::g.337] -indexing [18::asmbl_27::g.41] -indexing [208::asmbl_270::g.347] -indexing [209::asmbl_271::g.312] -indexing [211::asmbl_273::g.326] -indexing [212::asmbl_274::g.341] -indexing [213::asmbl_275::g.351] -indexing [214::asmbl_276::g.314] -indexing [215::asmbl_277::g.322] -indexing [216::asmbl_278::g.332] -indexing [217::asmbl_279::g.346] -indexing [19::asmbl_28::g.51] -indexing [216::asmbl_280::g.311] -indexing [218::asmbl_281::g.317] -indexing [219::asmbl_282::g.325] -indexing [220::asmbl_283::g.339] -indexing [220::asmbl_284::g.350] -indexing [223::asmbl_286::g.321] -indexing [222::asmbl_287::g.330] -indexing [222::asmbl_288::g.344] -indexing [224::asmbl_289::g.354] -indexing [20::asmbl_29::g.7] -indexing [224::asmbl_290::g.365] -indexing [225::asmbl_291::g.379] -indexing [225::asmbl_292::g.390] -indexing [226::asmbl_293::g.397] -indexing [227::asmbl_294::g.361] -indexing [227::asmbl_295::g.374] -indexing [228::asmbl_296::g.382] -indexing [230::asmbl_298::g.401] -indexing [231::asmbl_299::g.364] -indexing [3::asmbl_3::g.25] -indexing [20::asmbl_30::g.20] -indexing [232::asmbl_300::g.378] -indexing [233::asmbl_301::g.388] -indexing [234::asmbl_302::g.396] -indexing [234::asmbl_303::g.359] -indexing [234::asmbl_304::g.373] -indexing [234::asmbl_305::g.381] -indexing [236::asmbl_307::g.400] -indexing [237::asmbl_308::g.363] -indexing [238::asmbl_309::g.375] -indexing [20::asmbl_31::g.34] -indexing [239::asmbl_310::g.383] -indexing [239::asmbl_311::g.393] -indexing [240::asmbl_312::g.358] -indexing [241::asmbl_313::g.371] -indexing [242::asmbl_314::g.380] -indexing [243::asmbl_315::g.391] -indexing [244::asmbl_316::g.399] -indexing [245::asmbl_317::g.362] -indexing [247::asmbl_319::g.414] -indexing [20::asmbl_32::g.46] -indexing [247::asmbl_320::g.421] -indexing [248::asmbl_321::g.402] -indexing [250::asmbl_323::g.408] -indexing [251::asmbl_324::g.419] -indexing [254::asmbl_327::g.407] -indexing [254::asmbl_328::g.411] -indexing [254::asmbl_329::g.420] -indexing [254::asmbl_330::g.423] -indexing [254::asmbl_331::g.405] -indexing [255::asmbl_333::g.418] -indexing [256::asmbl_334::g.422] -indexing [256::asmbl_335::g.404] -indexing [258::asmbl_337::g.410] -indexing [260::asmbl_339::g.462] -indexing [21::asmbl_34::g.14] -indexing [261::asmbl_340::g.430] -indexing [262::asmbl_341::g.436] -indexing [263::asmbl_342::g.447] -indexing [263::asmbl_343::g.455] -indexing [264::asmbl_344::g.425] -indexing [265::asmbl_345::g.433] -indexing [266::asmbl_346::g.443] -indexing [267::asmbl_347::g.452] -indexing [268::asmbl_348::g.460] -indexing [268::asmbl_349::g.428] -indexing [21::asmbl_35::g.27] -indexing [269::asmbl_350::g.435] -indexing [270::asmbl_351::g.445] -indexing [272::asmbl_353::g.424] -indexing [274::asmbl_355::g.440] -indexing [275::asmbl_356::g.450] -indexing [276::asmbl_357::g.457] -indexing [277::asmbl_358::g.427] -indexing [278::asmbl_359::g.434] -indexing [22::asmbl_36::g.40] -indexing [279::asmbl_360::g.444] -indexing [280::asmbl_361::g.454] -indexing [281::asmbl_362::g.463] -indexing [281::asmbl_363::g.431] -indexing [282::asmbl_364::g.438] -indexing [282::asmbl_365::g.448] -indexing [283::asmbl_366::g.456] -indexing [284::asmbl_367::g.426] -indexing [285::asmbl_368::g.478] -indexing [286::asmbl_369::g.488] -indexing [23::asmbl_37::g.50] -indexing [286::asmbl_370::g.498] -indexing [287::asmbl_371::g.508] -indexing [289::asmbl_373::g.481] -indexing [290::asmbl_374::g.492] -indexing [291::asmbl_375::g.503] -indexing [292::asmbl_376::g.468] -indexing [294::asmbl_377::g.474] -indexing [293::asmbl_378::g.485] -indexing [293::asmbl_379::g.495] -indexing [24::asmbl_38::g.6] -indexing [295::asmbl_380::g.506] -indexing [296::asmbl_381::g.470] -indexing [296::asmbl_382::g.480] -indexing [297::asmbl_383::g.490] -indexing [298::asmbl_384::g.501] -indexing [299::asmbl_385::g.465] -indexing [300::asmbl_386::g.472] -indexing [301::asmbl_387::g.482] -indexing [302::asmbl_388::g.494] -indexing [303::asmbl_389::g.505] -indexing [25::asmbl_39::g.19] -indexing [304::asmbl_390::g.469] -indexing [304::asmbl_391::g.479] -indexing [305::asmbl_392::g.489] -indexing [306::asmbl_393::g.499] -indexing [307::asmbl_394::g.509] -indexing [307::asmbl_395::g.471] -indexing [309::asmbl_397::g.493] -indexing [310::asmbl_398::g.504] -indexing [4::asmbl_4::g.39] -indexing [26::asmbl_40::g.32] -indexing [312::asmbl_400::g.477] -indexing [313::asmbl_401::g.487] -indexing [314::asmbl_402::g.497] -indexing [315::asmbl_403::g.507] -indexing [320::asmbl_408::g.510] -indexing [320::asmbl_409::g.514] -indexing [320::asmbl_410::g.516] -indexing [322::asmbl_412::g.518] -indexing [322::asmbl_413::g.512] -indexing [322::asmbl_414::g.515] -indexing [324::asmbl_416::g.533] -indexing [325::asmbl_417::g.537] -indexing [326::asmbl_418::g.523] -indexing [327::asmbl_419::g.527] -indexing [328::asmbl_420::g.530] -indexing [329::asmbl_421::g.535] -indexing [330::asmbl_422::g.519] -indexing [331::asmbl_423::g.525] -indexing [333::asmbl_425::g.532] -indexing [334::asmbl_426::g.536] -indexing [335::asmbl_427::g.520] -indexing [336::asmbl_428::g.526] -indexing [337::asmbl_429::g.529] -indexing [29::asmbl_43::g.62] -indexing [338::asmbl_430::g.534] -indexing [339::asmbl_431::g.539] -indexing [340::asmbl_432::g.553] -indexing [341::asmbl_433::g.565] -indexing [342::asmbl_434::g.577] -indexing [343::asmbl_435::g.588] -indexing [344::asmbl_436::g.546] -indexing [344::asmbl_437::g.559] -indexing [345::asmbl_438::g.569] -indexing [345::asmbl_439::g.583] -indexing [30::asmbl_44::g.70] -indexing [345::asmbl_440::g.538] -indexing [345::asmbl_441::g.552] -indexing [346::asmbl_442::g.564] -indexing [347::asmbl_443::g.575] -indexing [348::asmbl_444::g.587] -indexing [349::asmbl_445::g.544] -indexing [350::asmbl_446::g.556] -indexing [351::asmbl_447::g.568] -indexing [352::asmbl_448::g.581] -indexing [352::asmbl_449::g.592] -indexing [352::asmbl_450::g.550] -indexing [353::asmbl_451::g.563] -indexing [353::asmbl_452::g.572] -indexing [354::asmbl_453::g.586] -indexing [355::asmbl_454::g.543] -indexing [356::asmbl_455::g.555] -indexing [356::asmbl_456::g.567] -indexing [357::asmbl_457::g.579] -indexing [357::asmbl_458::g.590] -indexing [358::asmbl_459::g.548] -indexing [32::asmbl_46::g.84] -indexing [358::asmbl_460::g.561] -indexing [359::asmbl_461::g.570] -indexing [358::asmbl_462::g.584] -indexing [360::asmbl_463::g.541] -indexing [361::asmbl_464::g.554] -indexing [361::asmbl_465::g.566] -indexing [361::asmbl_466::g.578] -indexing [362::asmbl_467::g.589] -indexing [363::asmbl_468::g.547] -indexing [364::asmbl_469::g.560] -indexing [33::asmbl_47::g.58] -indexing [365::asmbl_470::g.610] -indexing [365::asmbl_471::g.620] -indexing [365::asmbl_472::g.594] -indexing [370::asmbl_477::g.597] -indexing [371::asmbl_478::g.602] -indexing [372::asmbl_479::g.608] -indexing [34::asmbl_48::g.66] -indexing [373::asmbl_480::g.619] -indexing [374::asmbl_481::g.626] -indexing [375::asmbl_482::g.600] -indexing [376::asmbl_483::g.605] -indexing [376::asmbl_484::g.613] -indexing [377::asmbl_485::g.623] -indexing [378::asmbl_486::g.596] -indexing [378::asmbl_487::g.601] -indexing [378::asmbl_488::g.607] -indexing [379::asmbl_489::g.617] -indexing [34::asmbl_49::g.74] -indexing [379::asmbl_490::g.624] -indexing [379::asmbl_491::g.598] -indexing [379::asmbl_492::g.603] -indexing [380::asmbl_493::g.612] -indexing [381::asmbl_494::g.622] -indexing [384::asmbl_497::g.606] -indexing [385::asmbl_498::g.615] -indexing [4::asmbl_5::g.49] -indexing [34::asmbl_50::g.81] -indexing [388::asmbl_501::g.637] -indexing [389::asmbl_502::g.641] -indexing [390::asmbl_503::g.653] -indexing [391::asmbl_504::g.627] -indexing [393::asmbl_507::g.644] -indexing [394::asmbl_508::g.657] -indexing [395::asmbl_509::g.630] -indexing [34::asmbl_51::g.88] -indexing [397::asmbl_512::g.651] -indexing [397::asmbl_513::g.662] -indexing [398::asmbl_514::g.632] -indexing [399::asmbl_515::g.639] -indexing [400::asmbl_516::g.643] -indexing [401::asmbl_517::g.655] -indexing [401::asmbl_518::g.628] -indexing [402::asmbl_519::g.635] -indexing [35::asmbl_52::g.61] -indexing [404::asmbl_521::g.650] -indexing [405::asmbl_522::g.661] -indexing [406::asmbl_523::g.631] -indexing [407::asmbl_524::g.638] -indexing [408::asmbl_525::g.642] -indexing [408::asmbl_526::g.654] -indexing [410::asmbl_528::g.633] -indexing [410::asmbl_529::g.640] -indexing [35::asmbl_53::g.69] -indexing [410::asmbl_530::g.647] -indexing [411::asmbl_531::g.658] -indexing [412::asmbl_532::g.670] -indexing [413::asmbl_533::g.684] -indexing [414::asmbl_534::g.694] -indexing [415::asmbl_535::g.703] -indexing [416::asmbl_536::g.664] -indexing [417::asmbl_537::g.675] -indexing [418::asmbl_538::g.687] -indexing [419::asmbl_539::g.698] -indexing [35::asmbl_54::g.77] -indexing [422::asmbl_542::g.682] -indexing [423::asmbl_543::g.693] -indexing [422::asmbl_544::g.702] -indexing [422::asmbl_545::g.710] -indexing [424::asmbl_546::g.674] -indexing [426::asmbl_548::g.697] -indexing [427::asmbl_549::g.706] -indexing [36::asmbl_55::g.83] -indexing [428::asmbl_550::g.669] -indexing [429::asmbl_551::g.681] -indexing [429::asmbl_552::g.692] -indexing [430::asmbl_553::g.701] -indexing [431::asmbl_554::g.708] -indexing [431::asmbl_555::g.672] -indexing [432::asmbl_556::g.686] -indexing [433::asmbl_557::g.696] -indexing [434::asmbl_558::g.704] -indexing [435::asmbl_559::g.667] -indexing [37::asmbl_56::g.57] -indexing [436::asmbl_560::g.679] -indexing [436::asmbl_561::g.690] -indexing [437::asmbl_562::g.700] -indexing [439::asmbl_564::g.671] -indexing [440::asmbl_565::g.685] -indexing [440::asmbl_566::g.695] -indexing [442::asmbl_568::g.666] -indexing [443::asmbl_569::g.677] -indexing [37::asmbl_57::g.64] -indexing [444::asmbl_570::g.688] -indexing [445::asmbl_571::g.699] -indexing [445::asmbl_572::g.707] -indexing [447::asmbl_574::g.683] -indexing [448::asmbl_575::g.717] -indexing [449::asmbl_576::g.721] -indexing [450::asmbl_577::g.725] -indexing [451::asmbl_578::g.712] -indexing [451::asmbl_579::g.714] -indexing [38::asmbl_58::g.73] -indexing [451::asmbl_580::g.718] -indexing [452::asmbl_582::g.711] -indexing [453::asmbl_583::g.713] -indexing [454::asmbl_584::g.715] -indexing [455::asmbl_585::g.719] -indexing [455::asmbl_586::g.722] -indexing [456::asmbl_587::g.736] -indexing [457::asmbl_588::g.750] -indexing [458::asmbl_589::g.765] -indexing [39::asmbl_59::g.80] -indexing [459::asmbl_590::g.777] -indexing [459::asmbl_591::g.728] -indexing [460::asmbl_592::g.740] -indexing [460::asmbl_593::g.756] -indexing [460::asmbl_594::g.767] -indexing [461::asmbl_596::g.732] -indexing [462::asmbl_597::g.748] -indexing [463::asmbl_598::g.762] -indexing [464::asmbl_599::g.774] -indexing [4::asmbl_6::g.5] -indexing [40::asmbl_60::g.87] -indexing [466::asmbl_601::g.737] -indexing [467::asmbl_602::g.753] -indexing [470::asmbl_605::g.731] -indexing [471::asmbl_606::g.745] -indexing [472::asmbl_607::g.760] -indexing [473::asmbl_608::g.773] -indexing [474::asmbl_609::g.782] -indexing [41::asmbl_61::g.59] -indexing [476::asmbl_611::g.752] -indexing [477::asmbl_612::g.766] -indexing [478::asmbl_613::g.778] -indexing [479::asmbl_614::g.729] -indexing [480::asmbl_615::g.744] -indexing [481::asmbl_616::g.759] -indexing [481::asmbl_617::g.772] -indexing [481::asmbl_618::g.781] -indexing [482::asmbl_619::g.735] -indexing [42::asmbl_62::g.68] -indexing [484::asmbl_621::g.764] -indexing [485::asmbl_622::g.776] -indexing [486::asmbl_623::g.727] -indexing [487::asmbl_624::g.743] -indexing [487::asmbl_625::g.758] -indexing [488::asmbl_626::g.770] -indexing [488::asmbl_627::g.779] -indexing [489::asmbl_628::g.733] -indexing [489::asmbl_629::g.749] -indexing [43::asmbl_63::g.76] -indexing [490::asmbl_630::g.763] -indexing [491::asmbl_631::g.775] -indexing [492::asmbl_632::g.726] -indexing [493::asmbl_633::g.739] -indexing [493::asmbl_634::g.754] -indexing [494::asmbl_635::g.807] -indexing [495::asmbl_636::g.818] -indexing [496::asmbl_637::g.787] -indexing [498::asmbl_639::g.802] -indexing [498::asmbl_640::g.814] -indexing [499::asmbl_641::g.824] -indexing [500::asmbl_642::g.792] -indexing [501::asmbl_643::g.797] -indexing [501::asmbl_644::g.805] -indexing [501::asmbl_645::g.817] -indexing [502::asmbl_646::g.785] -indexing [503::asmbl_647::g.794] -indexing [503::asmbl_648::g.800] -indexing [504::asmbl_649::g.812] -indexing [505::asmbl_650::g.823] -indexing [505::asmbl_651::g.791] -indexing [507::asmbl_653::g.804] -indexing [508::asmbl_654::g.815] -indexing [508::asmbl_655::g.784] -indexing [509::asmbl_656::g.793] -indexing [510::asmbl_657::g.799] -indexing [510::asmbl_658::g.811] -indexing [511::asmbl_659::g.821] -indexing [512::asmbl_660::g.789] -indexing [513::asmbl_662::g.803] -indexing [515::asmbl_664::g.783] -indexing [518::asmbl_667::g.810] -indexing [519::asmbl_668::g.820] -indexing [519::asmbl_669::g.788] -indexing [47::asmbl_67::g.71] -indexing [520::asmbl_670::g.796] -indexing [522::asmbl_672::g.835] -indexing [523::asmbl_673::g.841] -indexing [524::asmbl_674::g.830] -indexing [525::asmbl_675::g.832] -indexing [526::asmbl_676::g.833] -indexing [527::asmbl_677::g.836] -indexing [528::asmbl_678::g.825] -indexing [47::asmbl_68::g.78] -indexing [531::asmbl_681::g.834] -indexing [532::asmbl_682::g.838] -indexing [533::asmbl_683::g.829] -indexing [534::asmbl_684::g.831] -indexing [535::asmbl_685::g.869] -indexing [536::asmbl_686::g.878] -indexing [535::asmbl_687::g.843] -indexing [537::asmbl_688::g.852] -indexing [537::asmbl_689::g.864] -indexing [47::asmbl_69::g.85] -indexing [539::asmbl_691::g.883] -indexing [540::asmbl_692::g.846] -indexing [541::asmbl_693::g.856] -indexing [542::asmbl_694::g.868] -indexing [541::asmbl_695::g.877] -indexing [543::asmbl_696::g.842] -indexing [544::asmbl_697::g.851] -indexing [545::asmbl_698::g.863] -indexing [546::asmbl_699::g.873] -indexing [5::asmbl_7::g.17] -indexing [547::asmbl_700::g.881] -indexing [549::asmbl_702::g.855] -indexing [550::asmbl_703::g.867] -indexing [551::asmbl_704::g.876] -indexing [553::asmbl_706::g.850] -indexing [555::asmbl_708::g.872] -indexing [556::asmbl_709::g.879] -indexing [49::asmbl_71::g.99] -indexing [557::asmbl_710::g.845] -indexing [558::asmbl_711::g.854] -indexing [559::asmbl_712::g.865] -indexing [560::asmbl_713::g.874] -indexing [560::asmbl_714::g.884] -indexing [560::asmbl_715::g.849] -indexing [561::asmbl_716::g.861] -indexing [562::asmbl_717::g.871] -indexing [563::asmbl_718::g.923] -indexing [564::asmbl_719::g.886] -indexing [50::asmbl_72::g.110] -indexing [565::asmbl_720::g.896] -indexing [566::asmbl_721::g.905] -indexing [567::asmbl_722::g.914] -indexing [568::asmbl_723::g.926] -indexing [569::asmbl_724::g.891] -indexing [569::asmbl_725::g.900] -indexing [570::asmbl_726::g.908] -indexing [571::asmbl_727::g.922] -indexing [572::asmbl_728::g.885] -indexing [50::asmbl_73::g.118] -indexing [574::asmbl_730::g.904] -indexing [574::asmbl_731::g.912] -indexing [574::asmbl_732::g.925] -indexing [574::asmbl_733::g.890] -indexing [575::asmbl_734::g.898] -indexing [576::asmbl_735::g.907] -indexing [577::asmbl_736::g.921] -indexing [578::asmbl_737::g.933] -indexing [580::asmbl_739::g.903] -indexing [50::asmbl_74::g.124] -indexing [581::asmbl_740::g.911] -indexing [581::asmbl_741::g.924] -indexing [582::asmbl_742::g.888] -indexing [583::asmbl_743::g.897] -indexing [583::asmbl_744::g.906] -indexing [584::asmbl_745::g.917] -indexing [584::asmbl_746::g.927] -indexing [586::asmbl_748::g.948] -indexing [588::asmbl_750::g.953] -indexing [588::asmbl_751::g.935] -indexing [589::asmbl_752::g.943] -indexing [590::asmbl_753::g.949] -indexing [590::asmbl_754::g.951] -indexing [590::asmbl_755::g.955] -indexing [590::asmbl_756::g.941] -indexing [590::asmbl_757::g.945] -indexing [52::asmbl_76::g.105] -indexing [593::asmbl_761::g.942] -indexing [595::asmbl_763::g.950] -indexing [596::asmbl_764::g.954] -indexing [597::asmbl_765::g.937] -indexing [597::asmbl_766::g.944] -indexing [599::asmbl_768::g.985] -indexing [600::asmbl_769::g.996] -indexing [52::asmbl_77::g.116] -indexing [601::asmbl_770::g.962] -indexing [601::asmbl_771::g.972] -indexing [602::asmbl_772::g.979] -indexing [602::asmbl_773::g.988] -indexing [603::asmbl_774::g.957] -indexing [604::asmbl_775::g.967] -indexing [605::asmbl_776::g.977] -indexing [606::asmbl_777::g.984] -indexing [607::asmbl_778::g.993] -indexing [608::asmbl_779::g.960] -indexing [53::asmbl_78::g.120] -indexing [609::asmbl_780::g.969] -indexing [611::asmbl_782::g.987] -indexing [613::asmbl_784::g.965] -indexing [614::asmbl_785::g.976] -indexing [615::asmbl_786::g.982] -indexing [615::asmbl_787::g.991] -indexing [616::asmbl_788::g.958] -indexing [617::asmbl_789::g.968] -indexing [54::asmbl_79::g.92] -indexing [618::asmbl_790::g.978] -indexing [619::asmbl_791::g.986] -indexing [620::asmbl_792::g.956] -indexing [620::asmbl_793::g.964] -indexing [621::asmbl_794::g.974] -indexing [622::asmbl_795::g.981] -indexing [623::asmbl_796::g.990] -indexing [624::asmbl_797::g.1002] -indexing [625::asmbl_798::g.1013] -indexing [626::asmbl_799::g.1024] -indexing [6::asmbl_8::g.30] -indexing [55::asmbl_80::g.98] -indexing [627::asmbl_800::g.1032] -indexing [629::asmbl_802::g.1004] -indexing [630::asmbl_803::g.1015] -indexing [631::asmbl_804::g.1028] -indexing [631::asmbl_805::g.1035] -indexing [633::asmbl_807::g.1008] -indexing [634::asmbl_808::g.1019] -indexing [635::asmbl_809::g.1030] -indexing [56::asmbl_81::g.109] -indexing [635::asmbl_810::g.1038] -indexing [636::asmbl_811::g.1003] -indexing [637::asmbl_812::g.1014] -indexing [638::asmbl_813::g.1025] -indexing [639::asmbl_814::g.1033] -indexing [640::asmbl_815::g.997] -indexing [641::asmbl_816::g.1006] -indexing [642::asmbl_817::g.1017] -indexing [643::asmbl_818::g.1029] -indexing [643::asmbl_819::g.1037] -indexing [644::asmbl_820::g.1001] -indexing [645::asmbl_821::g.1011] -indexing [646::asmbl_822::g.1021] -indexing [647::asmbl_823::g.1031] -indexing [648::asmbl_824::g.1039] -indexing [649::asmbl_825::g.1005] -indexing [650::asmbl_826::g.1016] -indexing [652::asmbl_828::g.1036] -indexing [653::asmbl_829::g.1000] -indexing [58::asmbl_83::g.122] -indexing [653::asmbl_830::g.1010] -indexing [654::asmbl_831::g.1020] -indexing [656::asmbl_833::g.1048] -indexing [656::asmbl_834::g.1042] -indexing [656::asmbl_835::g.1045] -indexing [658::asmbl_837::g.1046] -indexing [658::asmbl_838::g.1041] -indexing [658::asmbl_839::g.1043] -indexing [59::asmbl_84::g.94] -indexing [663::asmbl_844::g.1056] -indexing [664::asmbl_845::g.1061] -indexing [665::asmbl_846::g.1064] -indexing [666::asmbl_847::g.1049] -indexing [667::asmbl_848::g.1054] -indexing [668::asmbl_849::g.1058] -indexing [59::asmbl_85::g.103] -indexing [670::asmbl_851::g.1065] -indexing [671::asmbl_852::g.1052] -indexing [672::asmbl_853::g.1055] -indexing [673::asmbl_854::g.1059] -indexing [674::asmbl_855::g.1062] -indexing [675::asmbl_856::g.1066] -indexing [676::asmbl_857::g.1053] -indexing [677::asmbl_858::g.1057] -indexing [60::asmbl_86::g.115] -indexing [61::asmbl_87::g.119] -indexing [62::asmbl_88::g.91] -indexing [63::asmbl_89::g.96] -indexing [6::asmbl_9::g.44] -indexing [63::asmbl_90::g.107] -indexing [65::asmbl_93::g.93] -indexing [66::asmbl_94::g.102] -indexing [67::asmbl_95::g.112] -indexing [69::asmbl_97::g.90] -indexing [70::asmbl_99::g.106] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 pasa_assemblies.fasta.transdecoder.gff3 --fasta pasa_assemblies.fasta --seqType CDS > pasa_assemblies.fasta.transdecoder.cds -indexing [1::asmbl_1::g.1] -indexing [7::asmbl_10::g.55] -indexing [71::asmbl_100::g.117] -indexing [72::asmbl_101::g.121] -indexing [73::asmbl_102::g.130] -indexing [75::asmbl_104::g.153] -indexing [75::asmbl_105::g.162] -indexing [76::asmbl_106::g.171] -indexing [77::asmbl_107::g.135] -indexing [78::asmbl_108::g.147] -indexing [79::asmbl_109::g.157] -indexing [6::asmbl_11::g.10] -indexing [79::asmbl_110::g.165] -indexing [81::asmbl_112::g.141] -indexing [83::asmbl_114::g.161] -indexing [84::asmbl_115::g.169] -indexing [84::asmbl_116::g.133] -indexing [85::asmbl_117::g.145] -indexing [86::asmbl_118::g.155] -indexing [87::asmbl_119::g.164] -indexing [8::asmbl_12::g.23] -indexing [88::asmbl_120::g.128] -indexing [89::asmbl_121::g.139] -indexing [89::asmbl_122::g.151] -indexing [90::asmbl_123::g.160] -indexing [91::asmbl_124::g.168] -indexing [91::asmbl_125::g.132] -indexing [92::asmbl_126::g.144] -indexing [93::asmbl_127::g.154] -indexing [94::asmbl_128::g.163] -indexing [95::asmbl_129::g.127] -indexing [8::asmbl_13::g.37] -indexing [97::asmbl_131::g.150] -indexing [98::asmbl_132::g.159] -indexing [97::asmbl_133::g.167] -indexing [97::asmbl_134::g.131] -indexing [99::asmbl_135::g.143] -indexing [102::asmbl_138::g.173] -indexing [103::asmbl_139::g.137] -indexing [9::asmbl_14::g.48] -indexing [104::asmbl_140::g.148] -indexing [105::asmbl_141::g.158] -indexing [106::asmbl_142::g.166] -indexing [107::asmbl_143::g.129] -indexing [108::asmbl_144::g.142] -indexing [109::asmbl_145::g.178] -indexing [109::asmbl_146::g.182] -indexing [110::asmbl_147::g.187] -indexing [111::asmbl_148::g.174] -indexing [112::asmbl_149::g.176] -indexing [9::asmbl_15::g.4] -indexing [112::asmbl_150::g.180] -indexing [112::asmbl_151::g.185] -indexing [113::asmbl_153::g.175] -indexing [114::asmbl_154::g.177] -indexing [115::asmbl_155::g.181] -indexing [116::asmbl_156::g.186] -indexing [117::asmbl_157::g.198] -indexing [117::asmbl_158::g.217] -indexing [118::asmbl_159::g.229] -indexing [10::asmbl_16::g.16] -indexing [119::asmbl_160::g.237] -indexing [120::asmbl_161::g.190] -indexing [121::asmbl_162::g.204] -indexing [121::asmbl_163::g.221] -indexing [122::asmbl_164::g.233] -indexing [122::asmbl_165::g.241] -indexing [123::asmbl_166::g.196] -indexing [123::asmbl_167::g.214] -indexing [124::asmbl_168::g.227] -indexing [125::asmbl_169::g.236] -indexing [11::asmbl_17::g.29] -indexing [126::asmbl_170::g.245] -indexing [127::asmbl_171::g.202] -indexing [127::asmbl_172::g.219] -indexing [127::asmbl_173::g.231] -indexing [128::asmbl_174::g.239] -indexing [130::asmbl_176::g.209] -indexing [131::asmbl_177::g.223] -indexing [132::asmbl_178::g.235] -indexing [133::asmbl_179::g.243] -indexing [12::asmbl_18::g.43] -indexing [134::asmbl_180::g.199] -indexing [136::asmbl_182::g.230] -indexing [137::asmbl_183::g.238] -indexing [138::asmbl_184::g.191] -indexing [139::asmbl_185::g.206] -indexing [140::asmbl_186::g.222] -indexing [143::asmbl_189::g.197] -indexing [12::asmbl_19::g.52] -indexing [144::asmbl_190::g.215] -indexing [145::asmbl_191::g.228] -indexing [147::asmbl_193::g.189] -indexing [148::asmbl_194::g.203] -indexing [149::asmbl_195::g.220] -indexing [150::asmbl_196::g.232] -indexing [150::asmbl_197::g.240] -indexing [151::asmbl_198::g.193] -indexing [151::asmbl_199::g.212] -indexing [2::asmbl_2::g.12] -indexing [13::asmbl_20::g.8] -indexing [151::asmbl_200::g.224] -indexing [152::asmbl_202::g.244] -indexing [153::asmbl_203::g.200] -indexing [154::asmbl_204::g.218] -indexing [155::asmbl_205::g.274] -indexing [156::asmbl_206::g.281] -indexing [156::asmbl_207::g.249] -indexing [157::asmbl_208::g.259] -indexing [13::asmbl_21::g.21] -indexing [159::asmbl_210::g.278] -indexing [162::asmbl_213::g.266] -indexing [163::asmbl_214::g.272] -indexing [164::asmbl_216::g.247] -indexing [165::asmbl_217::g.258] -indexing [165::asmbl_218::g.270] -indexing [166::asmbl_219::g.277] -indexing [13::asmbl_22::g.35] -indexing [167::asmbl_220::g.285] -indexing [167::asmbl_221::g.254] -indexing [168::asmbl_222::g.265] -indexing [170::asmbl_224::g.280] -indexing [170::asmbl_225::g.246] -indexing [171::asmbl_226::g.256] -indexing [172::asmbl_227::g.268] -indexing [172::asmbl_228::g.275] -indexing [173::asmbl_229::g.283] -indexing [14::asmbl_23::g.47] -indexing [174::asmbl_230::g.252] -indexing [174::asmbl_231::g.263] -indexing [174::asmbl_232::g.271] -indexing [175::asmbl_233::g.279] -indexing [176::asmbl_234::g.287] -indexing [176::asmbl_235::g.255] -indexing [177::asmbl_236::g.267] -indexing [179::asmbl_238::g.282] -indexing [180::asmbl_239::g.250] -indexing [15::asmbl_24::g.2] -indexing [181::asmbl_240::g.260] -indexing [182::asmbl_241::g.298] -indexing [183::asmbl_242::g.304] -indexing [184::asmbl_243::g.306] -indexing [185::asmbl_244::g.289] -indexing [186::asmbl_245::g.293] -indexing [187::asmbl_246::g.299] -indexing [189::asmbl_249::g.290] -indexing [16::asmbl_25::g.15] -indexing [190::asmbl_250::g.297] -indexing [191::asmbl_251::g.303] -indexing [192::asmbl_252::g.305] -indexing [193::asmbl_253::g.288] -indexing [194::asmbl_254::g.292] -indexing [196::asmbl_256::g.343] -indexing [197::asmbl_257::g.309] -indexing [198::asmbl_258::g.315] -indexing [198::asmbl_259::g.323] -indexing [17::asmbl_26::g.28] -indexing [198::asmbl_260::g.338] -indexing [199::asmbl_261::g.348] -indexing [200::asmbl_262::g.313] -indexing [201::asmbl_263::g.320] -indexing [202::asmbl_264::g.328] -indexing 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-indexing [546::asmbl_699::g.873] -indexing [5::asmbl_7::g.17] -indexing [547::asmbl_700::g.881] -indexing [549::asmbl_702::g.855] -indexing [550::asmbl_703::g.867] -indexing [551::asmbl_704::g.876] -indexing [553::asmbl_706::g.850] -indexing [555::asmbl_708::g.872] -indexing [556::asmbl_709::g.879] -indexing [49::asmbl_71::g.99] -indexing [557::asmbl_710::g.845] -indexing [558::asmbl_711::g.854] -indexing [559::asmbl_712::g.865] -indexing [560::asmbl_713::g.874] -indexing [560::asmbl_714::g.884] -indexing [560::asmbl_715::g.849] -indexing [561::asmbl_716::g.861] -indexing [562::asmbl_717::g.871] -indexing [563::asmbl_718::g.923] -indexing [564::asmbl_719::g.886] -indexing [50::asmbl_72::g.110] -indexing [565::asmbl_720::g.896] -indexing [566::asmbl_721::g.905] -indexing [567::asmbl_722::g.914] -indexing [568::asmbl_723::g.926] -indexing [569::asmbl_724::g.891] -indexing [569::asmbl_725::g.900] -indexing [570::asmbl_726::g.908] -indexing [571::asmbl_727::g.922] -indexing [572::asmbl_728::g.885] -indexing [50::asmbl_73::g.118] -indexing [574::asmbl_730::g.904] -indexing [574::asmbl_731::g.912] -indexing [574::asmbl_732::g.925] -indexing [574::asmbl_733::g.890] -indexing [575::asmbl_734::g.898] -indexing [576::asmbl_735::g.907] -indexing [577::asmbl_736::g.921] -indexing [578::asmbl_737::g.933] -indexing [580::asmbl_739::g.903] -indexing [50::asmbl_74::g.124] -indexing [581::asmbl_740::g.911] -indexing [581::asmbl_741::g.924] -indexing [582::asmbl_742::g.888] -indexing [583::asmbl_743::g.897] -indexing [583::asmbl_744::g.906] -indexing [584::asmbl_745::g.917] -indexing [584::asmbl_746::g.927] -indexing [586::asmbl_748::g.948] -indexing [588::asmbl_750::g.953] -indexing [588::asmbl_751::g.935] -indexing [589::asmbl_752::g.943] -indexing [590::asmbl_753::g.949] -indexing [590::asmbl_754::g.951] -indexing [590::asmbl_755::g.955] -indexing [590::asmbl_756::g.941] -indexing [590::asmbl_757::g.945] -indexing [52::asmbl_76::g.105] -indexing [593::asmbl_761::g.942] -indexing [595::asmbl_763::g.950] -indexing [596::asmbl_764::g.954] -indexing [597::asmbl_765::g.937] -indexing [597::asmbl_766::g.944] -indexing [599::asmbl_768::g.985] -indexing [600::asmbl_769::g.996] -indexing [52::asmbl_77::g.116] -indexing [601::asmbl_770::g.962] -indexing [601::asmbl_771::g.972] -indexing [602::asmbl_772::g.979] -indexing [602::asmbl_773::g.988] -indexing [603::asmbl_774::g.957] -indexing [604::asmbl_775::g.967] -indexing [605::asmbl_776::g.977] -indexing [606::asmbl_777::g.984] -indexing [607::asmbl_778::g.993] -indexing [608::asmbl_779::g.960] -indexing [53::asmbl_78::g.120] -indexing [609::asmbl_780::g.969] -indexing [611::asmbl_782::g.987] -indexing [613::asmbl_784::g.965] -indexing [614::asmbl_785::g.976] -indexing [615::asmbl_786::g.982] -indexing [615::asmbl_787::g.991] -indexing [616::asmbl_788::g.958] -indexing [617::asmbl_789::g.968] -indexing [54::asmbl_79::g.92] -indexing [618::asmbl_790::g.978] -indexing [619::asmbl_791::g.986] -indexing [620::asmbl_792::g.956] -indexing [620::asmbl_793::g.964] -indexing [621::asmbl_794::g.974] -indexing [622::asmbl_795::g.981] -indexing [623::asmbl_796::g.990] -indexing [624::asmbl_797::g.1002] -indexing [625::asmbl_798::g.1013] -indexing [626::asmbl_799::g.1024] -indexing [6::asmbl_8::g.30] -indexing [55::asmbl_80::g.98] -indexing [627::asmbl_800::g.1032] -indexing [629::asmbl_802::g.1004] -indexing [630::asmbl_803::g.1015] -indexing [631::asmbl_804::g.1028] -indexing [631::asmbl_805::g.1035] -indexing [633::asmbl_807::g.1008] -indexing [634::asmbl_808::g.1019] -indexing [635::asmbl_809::g.1030] -indexing [56::asmbl_81::g.109] -indexing [635::asmbl_810::g.1038] -indexing [636::asmbl_811::g.1003] -indexing [637::asmbl_812::g.1014] -indexing [638::asmbl_813::g.1025] -indexing [639::asmbl_814::g.1033] -indexing [640::asmbl_815::g.997] -indexing [641::asmbl_816::g.1006] -indexing [642::asmbl_817::g.1017] -indexing [643::asmbl_818::g.1029] -indexing [643::asmbl_819::g.1037] -indexing [644::asmbl_820::g.1001] -indexing [645::asmbl_821::g.1011] -indexing [646::asmbl_822::g.1021] -indexing [647::asmbl_823::g.1031] -indexing [648::asmbl_824::g.1039] -indexing [649::asmbl_825::g.1005] -indexing [650::asmbl_826::g.1016] -indexing [652::asmbl_828::g.1036] -indexing [653::asmbl_829::g.1000] -indexing [58::asmbl_83::g.122] -indexing [653::asmbl_830::g.1010] -indexing [654::asmbl_831::g.1020] -indexing [656::asmbl_833::g.1048] -indexing [656::asmbl_834::g.1042] -indexing [656::asmbl_835::g.1045] -indexing [658::asmbl_837::g.1046] -indexing [658::asmbl_838::g.1041] -indexing [658::asmbl_839::g.1043] -indexing [59::asmbl_84::g.94] -indexing [663::asmbl_844::g.1056] -indexing [664::asmbl_845::g.1061] -indexing [665::asmbl_846::g.1064] -indexing [666::asmbl_847::g.1049] -indexing [667::asmbl_848::g.1054] -indexing [668::asmbl_849::g.1058] -indexing [59::asmbl_85::g.103] -indexing [670::asmbl_851::g.1065] -indexing [671::asmbl_852::g.1052] -indexing [672::asmbl_853::g.1055] -indexing [673::asmbl_854::g.1059] -indexing [674::asmbl_855::g.1062] -indexing [675::asmbl_856::g.1066] -indexing [676::asmbl_857::g.1053] -indexing [677::asmbl_858::g.1057] -indexing [60::asmbl_86::g.115] -indexing [61::asmbl_87::g.119] -indexing [62::asmbl_88::g.91] -indexing [63::asmbl_89::g.96] -indexing [6::asmbl_9::g.44] -indexing [63::asmbl_90::g.107] -indexing [65::asmbl_93::g.93] -indexing [66::asmbl_94::g.102] -indexing [67::asmbl_95::g.112] -indexing [69::asmbl_97::g.90] -indexing [70::asmbl_99::g.106] transdecoder is finished. See output files pasa_assemblies.fasta.transdecoder.* ../../util/cdna_alignment_orf_to_genome_orf.pl pasa_assemblies.fasta.transdecoder.gff3 pasa_assemblies.gff3 pasa_assemblies.fasta > pasa_assemblies.fasta.transdecoder.genome.gff3 -indexing [1::asmbl_1::g.1] -indexing [7::asmbl_10::g.55] -indexing [71::asmbl_100::g.117] -indexing [72::asmbl_101::g.121] -indexing [73::asmbl_102::g.130] -indexing [75::asmbl_104::g.153] -indexing [75::asmbl_105::g.162] -indexing [76::asmbl_106::g.171] -indexing [77::asmbl_107::g.135] -indexing [78::asmbl_108::g.147] -indexing [79::asmbl_109::g.157] -indexing [6::asmbl_11::g.10] -indexing [79::asmbl_110::g.165] -indexing [81::asmbl_112::g.141] -indexing [83::asmbl_114::g.161] -indexing [84::asmbl_115::g.169] -indexing [84::asmbl_116::g.133] -indexing [85::asmbl_117::g.145] -indexing [86::asmbl_118::g.155] -indexing [87::asmbl_119::g.164] -indexing [8::asmbl_12::g.23] -indexing [88::asmbl_120::g.128] -indexing [89::asmbl_121::g.139] -indexing [89::asmbl_122::g.151] -indexing [90::asmbl_123::g.160] -indexing [91::asmbl_124::g.168] -indexing [91::asmbl_125::g.132] -indexing [92::asmbl_126::g.144] -indexing [93::asmbl_127::g.154] -indexing [94::asmbl_128::g.163] -indexing [95::asmbl_129::g.127] -indexing [8::asmbl_13::g.37] -indexing [97::asmbl_131::g.150] -indexing [98::asmbl_132::g.159] -indexing [97::asmbl_133::g.167] -indexing [97::asmbl_134::g.131] -indexing [99::asmbl_135::g.143] -indexing [102::asmbl_138::g.173] -indexing [103::asmbl_139::g.137] -indexing [9::asmbl_14::g.48] -indexing [104::asmbl_140::g.148] -indexing [105::asmbl_141::g.158] -indexing [106::asmbl_142::g.166] -indexing [107::asmbl_143::g.129] -indexing [108::asmbl_144::g.142] -indexing [109::asmbl_145::g.178] -indexing [109::asmbl_146::g.182] -indexing [110::asmbl_147::g.187] -indexing [111::asmbl_148::g.174] -indexing [112::asmbl_149::g.176] -indexing [9::asmbl_15::g.4] -indexing [112::asmbl_150::g.180] -indexing [112::asmbl_151::g.185] -indexing [113::asmbl_153::g.175] -indexing [114::asmbl_154::g.177] -indexing [115::asmbl_155::g.181] -indexing [116::asmbl_156::g.186] -indexing [117::asmbl_157::g.198] -indexing [117::asmbl_158::g.217] -indexing [118::asmbl_159::g.229] -indexing [10::asmbl_16::g.16] -indexing [119::asmbl_160::g.237] -indexing [120::asmbl_161::g.190] -indexing [121::asmbl_162::g.204] -indexing [121::asmbl_163::g.221] -indexing [122::asmbl_164::g.233] -indexing [122::asmbl_165::g.241] -indexing [123::asmbl_166::g.196] -indexing [123::asmbl_167::g.214] -indexing [124::asmbl_168::g.227] -indexing [125::asmbl_169::g.236] -indexing [11::asmbl_17::g.29] -indexing [126::asmbl_170::g.245] -indexing [127::asmbl_171::g.202] -indexing [127::asmbl_172::g.219] -indexing [127::asmbl_173::g.231] -indexing [128::asmbl_174::g.239] -indexing [130::asmbl_176::g.209] -indexing [131::asmbl_177::g.223] -indexing [132::asmbl_178::g.235] -indexing [133::asmbl_179::g.243] -indexing [12::asmbl_18::g.43] -indexing [134::asmbl_180::g.199] -indexing [136::asmbl_182::g.230] -indexing [137::asmbl_183::g.238] -indexing [138::asmbl_184::g.191] -indexing [139::asmbl_185::g.206] -indexing [140::asmbl_186::g.222] -indexing [143::asmbl_189::g.197] -indexing [12::asmbl_19::g.52] -indexing [144::asmbl_190::g.215] -indexing [145::asmbl_191::g.228] -indexing [147::asmbl_193::g.189] -indexing [148::asmbl_194::g.203] -indexing [149::asmbl_195::g.220] -indexing [150::asmbl_196::g.232] -indexing [150::asmbl_197::g.240] -indexing [151::asmbl_198::g.193] -indexing [151::asmbl_199::g.212] -indexing [2::asmbl_2::g.12] -indexing [13::asmbl_20::g.8] -indexing [151::asmbl_200::g.224] -indexing [152::asmbl_202::g.244] -indexing [153::asmbl_203::g.200] -indexing [154::asmbl_204::g.218] -indexing [155::asmbl_205::g.274] -indexing [156::asmbl_206::g.281] -indexing [156::asmbl_207::g.249] -indexing [157::asmbl_208::g.259] -indexing [13::asmbl_21::g.21] -indexing [159::asmbl_210::g.278] -indexing [162::asmbl_213::g.266] -indexing [163::asmbl_214::g.272] -indexing [164::asmbl_216::g.247] -indexing [165::asmbl_217::g.258] -indexing [165::asmbl_218::g.270] -indexing [166::asmbl_219::g.277] -indexing [13::asmbl_22::g.35] -indexing [167::asmbl_220::g.285] -indexing [167::asmbl_221::g.254] -indexing [168::asmbl_222::g.265] -indexing [170::asmbl_224::g.280] -indexing [170::asmbl_225::g.246] -indexing [171::asmbl_226::g.256] -indexing [172::asmbl_227::g.268] -indexing [172::asmbl_228::g.275] -indexing [173::asmbl_229::g.283] -indexing [14::asmbl_23::g.47] -indexing [174::asmbl_230::g.252] -indexing [174::asmbl_231::g.263] -indexing [174::asmbl_232::g.271] -indexing [175::asmbl_233::g.279] -indexing [176::asmbl_234::g.287] -indexing [176::asmbl_235::g.255] -indexing [177::asmbl_236::g.267] -indexing [179::asmbl_238::g.282] -indexing [180::asmbl_239::g.250] -indexing [15::asmbl_24::g.2] -indexing [181::asmbl_240::g.260] -indexing [182::asmbl_241::g.298] -indexing [183::asmbl_242::g.304] -indexing [184::asmbl_243::g.306] -indexing [185::asmbl_244::g.289] -indexing [186::asmbl_245::g.293] -indexing [187::asmbl_246::g.299] -indexing [189::asmbl_249::g.290] -indexing [16::asmbl_25::g.15] -indexing [190::asmbl_250::g.297] -indexing [191::asmbl_251::g.303] -indexing [192::asmbl_252::g.305] -indexing [193::asmbl_253::g.288] -indexing [194::asmbl_254::g.292] -indexing [196::asmbl_256::g.343] -indexing [197::asmbl_257::g.309] -indexing [198::asmbl_258::g.315] -indexing [198::asmbl_259::g.323] -indexing [17::asmbl_26::g.28] -indexing [198::asmbl_260::g.338] -indexing [199::asmbl_261::g.348] -indexing [200::asmbl_262::g.313] -indexing [201::asmbl_263::g.320] -indexing [202::asmbl_264::g.328] -indexing [203::asmbl_265::g.342] -indexing [204::asmbl_266::g.352] -indexing [207::asmbl_269::g.337] -indexing [18::asmbl_27::g.41] -indexing [208::asmbl_270::g.347] -indexing [209::asmbl_271::g.312] -indexing [211::asmbl_273::g.326] -indexing [212::asmbl_274::g.341] -indexing [213::asmbl_275::g.351] -indexing [214::asmbl_276::g.314] -indexing [215::asmbl_277::g.322] -indexing [216::asmbl_278::g.332] -indexing [217::asmbl_279::g.346] -indexing [19::asmbl_28::g.51] -indexing [216::asmbl_280::g.311] -indexing [218::asmbl_281::g.317] -indexing [219::asmbl_282::g.325] -indexing [220::asmbl_283::g.339] -indexing [220::asmbl_284::g.350] -indexing [223::asmbl_286::g.321] -indexing [222::asmbl_287::g.330] -indexing [222::asmbl_288::g.344] -indexing [224::asmbl_289::g.354] -indexing [20::asmbl_29::g.7] -indexing [224::asmbl_290::g.365] -indexing [225::asmbl_291::g.379] -indexing [225::asmbl_292::g.390] -indexing [226::asmbl_293::g.397] -indexing [227::asmbl_294::g.361] -indexing [227::asmbl_295::g.374] -indexing [228::asmbl_296::g.382] -indexing [230::asmbl_298::g.401] -indexing [231::asmbl_299::g.364] -indexing [3::asmbl_3::g.25] -indexing [20::asmbl_30::g.20] -indexing [232::asmbl_300::g.378] -indexing [233::asmbl_301::g.388] -indexing [234::asmbl_302::g.396] -indexing [234::asmbl_303::g.359] -indexing [234::asmbl_304::g.373] -indexing [234::asmbl_305::g.381] -indexing [236::asmbl_307::g.400] -indexing [237::asmbl_308::g.363] -indexing [238::asmbl_309::g.375] -indexing [20::asmbl_31::g.34] -indexing [239::asmbl_310::g.383] -indexing [239::asmbl_311::g.393] -indexing [240::asmbl_312::g.358] -indexing [241::asmbl_313::g.371] -indexing [242::asmbl_314::g.380] -indexing [243::asmbl_315::g.391] -indexing [244::asmbl_316::g.399] -indexing [245::asmbl_317::g.362] -indexing [247::asmbl_319::g.414] -indexing [20::asmbl_32::g.46] -indexing [247::asmbl_320::g.421] -indexing [248::asmbl_321::g.402] -indexing [250::asmbl_323::g.408] -indexing [251::asmbl_324::g.419] -indexing [254::asmbl_327::g.407] -indexing [254::asmbl_328::g.411] -indexing [254::asmbl_329::g.420] -indexing [254::asmbl_330::g.423] -indexing [254::asmbl_331::g.405] -indexing [255::asmbl_333::g.418] -indexing [256::asmbl_334::g.422] -indexing [256::asmbl_335::g.404] -indexing [258::asmbl_337::g.410] -indexing [260::asmbl_339::g.462] -indexing [21::asmbl_34::g.14] -indexing [261::asmbl_340::g.430] -indexing [262::asmbl_341::g.436] -indexing [263::asmbl_342::g.447] -indexing [263::asmbl_343::g.455] -indexing [264::asmbl_344::g.425] -indexing [265::asmbl_345::g.433] -indexing [266::asmbl_346::g.443] -indexing [267::asmbl_347::g.452] -indexing [268::asmbl_348::g.460] -indexing [268::asmbl_349::g.428] -indexing [21::asmbl_35::g.27] -indexing [269::asmbl_350::g.435] -indexing [270::asmbl_351::g.445] -indexing [272::asmbl_353::g.424] -indexing [274::asmbl_355::g.440] -indexing [275::asmbl_356::g.450] -indexing [276::asmbl_357::g.457] -indexing [277::asmbl_358::g.427] -indexing [278::asmbl_359::g.434] -indexing [22::asmbl_36::g.40] -indexing [279::asmbl_360::g.444] -indexing [280::asmbl_361::g.454] -indexing [281::asmbl_362::g.463] -indexing [281::asmbl_363::g.431] -indexing [282::asmbl_364::g.438] -indexing [282::asmbl_365::g.448] -indexing [283::asmbl_366::g.456] -indexing [284::asmbl_367::g.426] -indexing [285::asmbl_368::g.478] -indexing [286::asmbl_369::g.488] -indexing [23::asmbl_37::g.50] -indexing [286::asmbl_370::g.498] -indexing [287::asmbl_371::g.508] -indexing [289::asmbl_373::g.481] -indexing [290::asmbl_374::g.492] -indexing [291::asmbl_375::g.503] -indexing [292::asmbl_376::g.468] -indexing [294::asmbl_377::g.474] -indexing [293::asmbl_378::g.485] -indexing [293::asmbl_379::g.495] -indexing [24::asmbl_38::g.6] -indexing [295::asmbl_380::g.506] -indexing [296::asmbl_381::g.470] -indexing [296::asmbl_382::g.480] -indexing [297::asmbl_383::g.490] -indexing [298::asmbl_384::g.501] -indexing [299::asmbl_385::g.465] -indexing [300::asmbl_386::g.472] -indexing [301::asmbl_387::g.482] -indexing [302::asmbl_388::g.494] -indexing [303::asmbl_389::g.505] -indexing [25::asmbl_39::g.19] -indexing [304::asmbl_390::g.469] -indexing [304::asmbl_391::g.479] -indexing [305::asmbl_392::g.489] -indexing [306::asmbl_393::g.499] -indexing [307::asmbl_394::g.509] -indexing [307::asmbl_395::g.471] -indexing [309::asmbl_397::g.493] -indexing [310::asmbl_398::g.504] -indexing [4::asmbl_4::g.39] -indexing [26::asmbl_40::g.32] -indexing [312::asmbl_400::g.477] -indexing [313::asmbl_401::g.487] -indexing [314::asmbl_402::g.497] -indexing [315::asmbl_403::g.507] -indexing [320::asmbl_408::g.510] -indexing [320::asmbl_409::g.514] -indexing [320::asmbl_410::g.516] -indexing [322::asmbl_412::g.518] -indexing [322::asmbl_413::g.512] -indexing [322::asmbl_414::g.515] -indexing [324::asmbl_416::g.533] -indexing [325::asmbl_417::g.537] -indexing [326::asmbl_418::g.523] -indexing [327::asmbl_419::g.527] -indexing [328::asmbl_420::g.530] -indexing [329::asmbl_421::g.535] -indexing [330::asmbl_422::g.519] -indexing [331::asmbl_423::g.525] -indexing [333::asmbl_425::g.532] -indexing [334::asmbl_426::g.536] -indexing [335::asmbl_427::g.520] -indexing [336::asmbl_428::g.526] -indexing [337::asmbl_429::g.529] -indexing [29::asmbl_43::g.62] -indexing [338::asmbl_430::g.534] -indexing [339::asmbl_431::g.539] -indexing [340::asmbl_432::g.553] -indexing [341::asmbl_433::g.565] -indexing [342::asmbl_434::g.577] -indexing [343::asmbl_435::g.588] -indexing [344::asmbl_436::g.546] -indexing [344::asmbl_437::g.559] -indexing [345::asmbl_438::g.569] -indexing [345::asmbl_439::g.583] -indexing [30::asmbl_44::g.70] -indexing [345::asmbl_440::g.538] -indexing [345::asmbl_441::g.552] -indexing [346::asmbl_442::g.564] -indexing [347::asmbl_443::g.575] -indexing [348::asmbl_444::g.587] -indexing [349::asmbl_445::g.544] -indexing [350::asmbl_446::g.556] -indexing [351::asmbl_447::g.568] -indexing [352::asmbl_448::g.581] -indexing [352::asmbl_449::g.592] -indexing [352::asmbl_450::g.550] -indexing [353::asmbl_451::g.563] -indexing [353::asmbl_452::g.572] -indexing [354::asmbl_453::g.586] -indexing [355::asmbl_454::g.543] -indexing [356::asmbl_455::g.555] -indexing [356::asmbl_456::g.567] -indexing [357::asmbl_457::g.579] -indexing [357::asmbl_458::g.590] -indexing [358::asmbl_459::g.548] -indexing [32::asmbl_46::g.84] -indexing [358::asmbl_460::g.561] -indexing [359::asmbl_461::g.570] -indexing [358::asmbl_462::g.584] -indexing [360::asmbl_463::g.541] -indexing [361::asmbl_464::g.554] -indexing [361::asmbl_465::g.566] -indexing [361::asmbl_466::g.578] -indexing [362::asmbl_467::g.589] -indexing [363::asmbl_468::g.547] -indexing [364::asmbl_469::g.560] -indexing [33::asmbl_47::g.58] -indexing [365::asmbl_470::g.610] -indexing [365::asmbl_471::g.620] -indexing [365::asmbl_472::g.594] -indexing [370::asmbl_477::g.597] -indexing [371::asmbl_478::g.602] -indexing [372::asmbl_479::g.608] -indexing [34::asmbl_48::g.66] -indexing [373::asmbl_480::g.619] -indexing [374::asmbl_481::g.626] -indexing [375::asmbl_482::g.600] -indexing [376::asmbl_483::g.605] -indexing [376::asmbl_484::g.613] -indexing [377::asmbl_485::g.623] -indexing [378::asmbl_486::g.596] -indexing [378::asmbl_487::g.601] -indexing [378::asmbl_488::g.607] -indexing [379::asmbl_489::g.617] -indexing [34::asmbl_49::g.74] -indexing [379::asmbl_490::g.624] -indexing [379::asmbl_491::g.598] -indexing [379::asmbl_492::g.603] -indexing [380::asmbl_493::g.612] -indexing [381::asmbl_494::g.622] -indexing [384::asmbl_497::g.606] -indexing [385::asmbl_498::g.615] -indexing [4::asmbl_5::g.49] -indexing [34::asmbl_50::g.81] -indexing [388::asmbl_501::g.637] -indexing [389::asmbl_502::g.641] -indexing [390::asmbl_503::g.653] -indexing [391::asmbl_504::g.627] -indexing [393::asmbl_507::g.644] -indexing [394::asmbl_508::g.657] -indexing [395::asmbl_509::g.630] -indexing [34::asmbl_51::g.88] -indexing [397::asmbl_512::g.651] -indexing [397::asmbl_513::g.662] -indexing [398::asmbl_514::g.632] -indexing [399::asmbl_515::g.639] -indexing [400::asmbl_516::g.643] -indexing [401::asmbl_517::g.655] -indexing [401::asmbl_518::g.628] -indexing [402::asmbl_519::g.635] -indexing [35::asmbl_52::g.61] -indexing [404::asmbl_521::g.650] -indexing [405::asmbl_522::g.661] -indexing [406::asmbl_523::g.631] -indexing [407::asmbl_524::g.638] -indexing [408::asmbl_525::g.642] -indexing [408::asmbl_526::g.654] -indexing [410::asmbl_528::g.633] -indexing [410::asmbl_529::g.640] -indexing [35::asmbl_53::g.69] -indexing [410::asmbl_530::g.647] -indexing [411::asmbl_531::g.658] -indexing [412::asmbl_532::g.670] -indexing [413::asmbl_533::g.684] -indexing [414::asmbl_534::g.694] -indexing [415::asmbl_535::g.703] -indexing [416::asmbl_536::g.664] -indexing [417::asmbl_537::g.675] -indexing [418::asmbl_538::g.687] -indexing [419::asmbl_539::g.698] -indexing [35::asmbl_54::g.77] -indexing [422::asmbl_542::g.682] -indexing [423::asmbl_543::g.693] -indexing [422::asmbl_544::g.702] -indexing [422::asmbl_545::g.710] -indexing [424::asmbl_546::g.674] -indexing [426::asmbl_548::g.697] -indexing [427::asmbl_549::g.706] -indexing [36::asmbl_55::g.83] -indexing [428::asmbl_550::g.669] -indexing [429::asmbl_551::g.681] -indexing [429::asmbl_552::g.692] -indexing [430::asmbl_553::g.701] -indexing [431::asmbl_554::g.708] -indexing [431::asmbl_555::g.672] -indexing [432::asmbl_556::g.686] -indexing [433::asmbl_557::g.696] -indexing [434::asmbl_558::g.704] -indexing [435::asmbl_559::g.667] -indexing [37::asmbl_56::g.57] -indexing [436::asmbl_560::g.679] -indexing [436::asmbl_561::g.690] -indexing [437::asmbl_562::g.700] -indexing [439::asmbl_564::g.671] -indexing [440::asmbl_565::g.685] -indexing [440::asmbl_566::g.695] -indexing [442::asmbl_568::g.666] -indexing [443::asmbl_569::g.677] -indexing [37::asmbl_57::g.64] -indexing [444::asmbl_570::g.688] -indexing [445::asmbl_571::g.699] -indexing [445::asmbl_572::g.707] -indexing [447::asmbl_574::g.683] -indexing [448::asmbl_575::g.717] -indexing [449::asmbl_576::g.721] -indexing [450::asmbl_577::g.725] -indexing [451::asmbl_578::g.712] -indexing [451::asmbl_579::g.714] -indexing [38::asmbl_58::g.73] -indexing [451::asmbl_580::g.718] -indexing [452::asmbl_582::g.711] -indexing [453::asmbl_583::g.713] -indexing [454::asmbl_584::g.715] -indexing [455::asmbl_585::g.719] -indexing [455::asmbl_586::g.722] -indexing [456::asmbl_587::g.736] -indexing [457::asmbl_588::g.750] -indexing [458::asmbl_589::g.765] -indexing [39::asmbl_59::g.80] -indexing [459::asmbl_590::g.777] -indexing [459::asmbl_591::g.728] -indexing [460::asmbl_592::g.740] -indexing [460::asmbl_593::g.756] -indexing [460::asmbl_594::g.767] -indexing [461::asmbl_596::g.732] -indexing [462::asmbl_597::g.748] -indexing [463::asmbl_598::g.762] -indexing [464::asmbl_599::g.774] -indexing [4::asmbl_6::g.5] -indexing [40::asmbl_60::g.87] -indexing [466::asmbl_601::g.737] -indexing [467::asmbl_602::g.753] -indexing [470::asmbl_605::g.731] -indexing [471::asmbl_606::g.745] -indexing [472::asmbl_607::g.760] -indexing [473::asmbl_608::g.773] -indexing [474::asmbl_609::g.782] -indexing [41::asmbl_61::g.59] -indexing [476::asmbl_611::g.752] -indexing [477::asmbl_612::g.766] -indexing [478::asmbl_613::g.778] -indexing [479::asmbl_614::g.729] -indexing [480::asmbl_615::g.744] -indexing [481::asmbl_616::g.759] -indexing [481::asmbl_617::g.772] -indexing [481::asmbl_618::g.781] -indexing [482::asmbl_619::g.735] -indexing [42::asmbl_62::g.68] -indexing [484::asmbl_621::g.764] -indexing [485::asmbl_622::g.776] -indexing [486::asmbl_623::g.727] -indexing [487::asmbl_624::g.743] -indexing [487::asmbl_625::g.758] -indexing [488::asmbl_626::g.770] -indexing [488::asmbl_627::g.779] -indexing [489::asmbl_628::g.733] -indexing [489::asmbl_629::g.749] -indexing [43::asmbl_63::g.76] -indexing [490::asmbl_630::g.763] -indexing [491::asmbl_631::g.775] -indexing [492::asmbl_632::g.726] -indexing [493::asmbl_633::g.739] -indexing [493::asmbl_634::g.754] -indexing [494::asmbl_635::g.807] -indexing [495::asmbl_636::g.818] -indexing [496::asmbl_637::g.787] -indexing [498::asmbl_639::g.802] -indexing [498::asmbl_640::g.814] -indexing [499::asmbl_641::g.824] -indexing [500::asmbl_642::g.792] -indexing [501::asmbl_643::g.797] -indexing [501::asmbl_644::g.805] -indexing [501::asmbl_645::g.817] -indexing [502::asmbl_646::g.785] -indexing [503::asmbl_647::g.794] -indexing [503::asmbl_648::g.800] -indexing [504::asmbl_649::g.812] -indexing [505::asmbl_650::g.823] -indexing [505::asmbl_651::g.791] -indexing [507::asmbl_653::g.804] -indexing [508::asmbl_654::g.815] -indexing [508::asmbl_655::g.784] -indexing [509::asmbl_656::g.793] -indexing [510::asmbl_657::g.799] -indexing [510::asmbl_658::g.811] -indexing [511::asmbl_659::g.821] -indexing [512::asmbl_660::g.789] -indexing [513::asmbl_662::g.803] -indexing [515::asmbl_664::g.783] -indexing [518::asmbl_667::g.810] -indexing [519::asmbl_668::g.820] -indexing [519::asmbl_669::g.788] -indexing [47::asmbl_67::g.71] -indexing [520::asmbl_670::g.796] -indexing [522::asmbl_672::g.835] -indexing [523::asmbl_673::g.841] -indexing [524::asmbl_674::g.830] -indexing [525::asmbl_675::g.832] -indexing [526::asmbl_676::g.833] -indexing [527::asmbl_677::g.836] -indexing [528::asmbl_678::g.825] -indexing [47::asmbl_68::g.78] -indexing [531::asmbl_681::g.834] -indexing [532::asmbl_682::g.838] -indexing [533::asmbl_683::g.829] -indexing [534::asmbl_684::g.831] -indexing [535::asmbl_685::g.869] -indexing [536::asmbl_686::g.878] -indexing [535::asmbl_687::g.843] -indexing [537::asmbl_688::g.852] -indexing [537::asmbl_689::g.864] -indexing [47::asmbl_69::g.85] -indexing [539::asmbl_691::g.883] -indexing [540::asmbl_692::g.846] -indexing [541::asmbl_693::g.856] -indexing [542::asmbl_694::g.868] -indexing [541::asmbl_695::g.877] -indexing [543::asmbl_696::g.842] -indexing [544::asmbl_697::g.851] -indexing [545::asmbl_698::g.863] -indexing [546::asmbl_699::g.873] -indexing [5::asmbl_7::g.17] -indexing [547::asmbl_700::g.881] -indexing [549::asmbl_702::g.855] -indexing [550::asmbl_703::g.867] -indexing [551::asmbl_704::g.876] -indexing [553::asmbl_706::g.850] -indexing [555::asmbl_708::g.872] -indexing [556::asmbl_709::g.879] -indexing [49::asmbl_71::g.99] -indexing [557::asmbl_710::g.845] -indexing [558::asmbl_711::g.854] -indexing [559::asmbl_712::g.865] -indexing [560::asmbl_713::g.874] -indexing [560::asmbl_714::g.884] -indexing [560::asmbl_715::g.849] -indexing [561::asmbl_716::g.861] -indexing [562::asmbl_717::g.871] -indexing [563::asmbl_718::g.923] -indexing [564::asmbl_719::g.886] -indexing [50::asmbl_72::g.110] -indexing [565::asmbl_720::g.896] -indexing [566::asmbl_721::g.905] -indexing [567::asmbl_722::g.914] -indexing [568::asmbl_723::g.926] -indexing [569::asmbl_724::g.891] -indexing [569::asmbl_725::g.900] -indexing [570::asmbl_726::g.908] -indexing [571::asmbl_727::g.922] -indexing [572::asmbl_728::g.885] -indexing [50::asmbl_73::g.118] -indexing [574::asmbl_730::g.904] -indexing [574::asmbl_731::g.912] -indexing [574::asmbl_732::g.925] -indexing [574::asmbl_733::g.890] -indexing [575::asmbl_734::g.898] -indexing [576::asmbl_735::g.907] -indexing [577::asmbl_736::g.921] -indexing [578::asmbl_737::g.933] -indexing [580::asmbl_739::g.903] -indexing [50::asmbl_74::g.124] -indexing [581::asmbl_740::g.911] -indexing [581::asmbl_741::g.924] -indexing [582::asmbl_742::g.888] -indexing [583::asmbl_743::g.897] -indexing [583::asmbl_744::g.906] -indexing [584::asmbl_745::g.917] -indexing [584::asmbl_746::g.927] -indexing [586::asmbl_748::g.948] -indexing [588::asmbl_750::g.953] -indexing [588::asmbl_751::g.935] -indexing [589::asmbl_752::g.943] -indexing [590::asmbl_753::g.949] -indexing [590::asmbl_754::g.951] -indexing [590::asmbl_755::g.955] -indexing [590::asmbl_756::g.941] -indexing [590::asmbl_757::g.945] -indexing [52::asmbl_76::g.105] -indexing [593::asmbl_761::g.942] -indexing [595::asmbl_763::g.950] -indexing [596::asmbl_764::g.954] -indexing [597::asmbl_765::g.937] -indexing [597::asmbl_766::g.944] -indexing [599::asmbl_768::g.985] -indexing [600::asmbl_769::g.996] -indexing [52::asmbl_77::g.116] -indexing [601::asmbl_770::g.962] -indexing [601::asmbl_771::g.972] -indexing [602::asmbl_772::g.979] -indexing [602::asmbl_773::g.988] -indexing [603::asmbl_774::g.957] -indexing [604::asmbl_775::g.967] -indexing [605::asmbl_776::g.977] -indexing [606::asmbl_777::g.984] -indexing [607::asmbl_778::g.993] -indexing [608::asmbl_779::g.960] -indexing [53::asmbl_78::g.120] -indexing [609::asmbl_780::g.969] -indexing [611::asmbl_782::g.987] -indexing [613::asmbl_784::g.965] -indexing [614::asmbl_785::g.976] -indexing [615::asmbl_786::g.982] -indexing [615::asmbl_787::g.991] -indexing [616::asmbl_788::g.958] -indexing [617::asmbl_789::g.968] -indexing [54::asmbl_79::g.92] -indexing [618::asmbl_790::g.978] -indexing [619::asmbl_791::g.986] -indexing [620::asmbl_792::g.956] -indexing [620::asmbl_793::g.964] -indexing [621::asmbl_794::g.974] -indexing [622::asmbl_795::g.981] -indexing [623::asmbl_796::g.990] -indexing [624::asmbl_797::g.1002] -indexing [625::asmbl_798::g.1013] -indexing [626::asmbl_799::g.1024] -indexing [6::asmbl_8::g.30] -indexing [55::asmbl_80::g.98] -indexing [627::asmbl_800::g.1032] -indexing [629::asmbl_802::g.1004] -indexing [630::asmbl_803::g.1015] -indexing [631::asmbl_804::g.1028] -indexing [631::asmbl_805::g.1035] -indexing [633::asmbl_807::g.1008] -indexing [634::asmbl_808::g.1019] -indexing [635::asmbl_809::g.1030] -indexing [56::asmbl_81::g.109] -indexing [635::asmbl_810::g.1038] -indexing [636::asmbl_811::g.1003] -indexing [637::asmbl_812::g.1014] -indexing [638::asmbl_813::g.1025] -indexing [639::asmbl_814::g.1033] -indexing [640::asmbl_815::g.997] -indexing [641::asmbl_816::g.1006] -indexing [642::asmbl_817::g.1017] -indexing [643::asmbl_818::g.1029] -indexing [643::asmbl_819::g.1037] -indexing [644::asmbl_820::g.1001] -indexing [645::asmbl_821::g.1011] -indexing [646::asmbl_822::g.1021] -indexing [647::asmbl_823::g.1031] -indexing [648::asmbl_824::g.1039] -indexing [649::asmbl_825::g.1005] -indexing [650::asmbl_826::g.1016] -indexing [652::asmbl_828::g.1036] -indexing [653::asmbl_829::g.1000] -indexing [58::asmbl_83::g.122] -indexing [653::asmbl_830::g.1010] -indexing [654::asmbl_831::g.1020] -indexing [656::asmbl_833::g.1048] -indexing [656::asmbl_834::g.1042] -indexing [656::asmbl_835::g.1045] -indexing [658::asmbl_837::g.1046] -indexing [658::asmbl_838::g.1041] -indexing [658::asmbl_839::g.1043] -indexing [59::asmbl_84::g.94] -indexing [663::asmbl_844::g.1056] -indexing [664::asmbl_845::g.1061] -indexing [665::asmbl_846::g.1064] -indexing [666::asmbl_847::g.1049] -indexing [667::asmbl_848::g.1054] -indexing [668::asmbl_849::g.1058] -indexing [59::asmbl_85::g.103] -indexing [670::asmbl_851::g.1065] -indexing [671::asmbl_852::g.1052] -indexing [672::asmbl_853::g.1055] -indexing [673::asmbl_854::g.1059] -indexing [674::asmbl_855::g.1062] -indexing [675::asmbl_856::g.1066] -indexing [676::asmbl_857::g.1053] -indexing [677::asmbl_858::g.1057] -indexing [60::asmbl_86::g.115] -indexing [61::asmbl_87::g.119] -indexing [62::asmbl_88::g.91] -indexing [63::asmbl_89::g.96] -indexing [6::asmbl_9::g.44] -indexing [63::asmbl_90::g.107] -indexing [65::asmbl_93::g.93] -indexing [66::asmbl_94::g.102] -indexing [67::asmbl_95::g.112] -indexing [69::asmbl_97::g.90] -indexing [70::asmbl_99::g.106] Warning [1], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 93::asmbl_127::g.154::m.154. Warning [2], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 131::asmbl_177::g.223::m.223. Warning [3], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 184::asmbl_243::g.306::m.306. Warning [4], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 186::asmbl_245::g.293::m.293. Warning [5], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 216::asmbl_278::g.332::m.332. Warning [6], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 216::asmbl_280::g.311::m.311. Warning [7], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 224::asmbl_289::g.354::m.354. Warning [8], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 224::asmbl_290::g.365::m.365. Warning [9], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 328::asmbl_420::g.530::m.530. Warning [10], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 428::asmbl_550::g.669::m.669. Warning [11], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 480::asmbl_615::g.744::m.744. Warning [12], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 532::asmbl_682::g.838::m.838. Warning [13], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 541::asmbl_693::g.856::m.856. Warning [14], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 541::asmbl_695::g.877::m.877. Warning [15], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 584::asmbl_745::g.917::m.917. Warning [16], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 584::asmbl_746::g.927::m.927. Warning [17], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry 674::asmbl_855::g.1062::m.1062. Done. 719 / 736 transcript orfs could be propagated to the genome echo "Done. See pasa_assemblies.fasta.transdecoder.\*" Done. See pasa_assemblies.fasta.transdecoder.\* exit 0 make[4]: Leaving directory '/build/transdecoder-5.0.1/sample_data/pasa_example' Running example in $... make[4]: Entering directory '/build/transdecoder-5.0.1/sample_data/simple_transcriptome_target' ./runMe.sh -first extracting base frequencies, we'll need them later. CMD: /build/transdecoder-5.0.1/util/compute_base_probs.pl Trinity.fasta 0 > Trinity.fasta.transdecoder_dir/base_freqs.dat CMD: touch Trinity.fasta.transdecoder_dir/base_freqs.dat.ok - extracting ORFs from transcripts. -total transcripts to examine: 921 [100/921] = 10.86% done [200/921] = 21.72% done [300/921] = 32.57% done [400/921] = 43.43% done [500/921] = 54.29% done [600/921] = 65.15% done [700/921] = 76.00% done [800/921] = 86.86% done [900/921] = 97.72% done CMD: touch Trinity.fasta.transdecoder_dir/__longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: Trinity.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * Running CMD: /build/transdecoder-5.0.1/util/exclude_similar_proteins.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: comp847_c0::comp847_c0_seq2::g.357::m.357, not unique enough -skipping training candidate: comp992_c0::comp992_c0_seq2::g.523::m.523, not unique enough -skipping training candidate: comp718_c0::comp718_c0_seq2::g.213::m.213, not unique enough -skipping training candidate: comp1177_c0::comp1177_c0_seq2::g.766::m.766, not unique enough -skipping training candidate: comp999_c0::comp999_c0_seq2::g.534::m.534, not unique enough -skipping training candidate: comp989_c0::comp989_c0_seq1::g.518::m.518, not unique enough -skipping training candidate: comp836_c0::comp836_c0_seq1::g.340::m.340, not unique enough -skipping training candidate: comp621_c0::comp621_c0_seq2::g.116::m.116, not unique enough -skipping training candidate: comp844_c0::comp844_c0_seq2::g.351::m.351, not unique enough -skipping training candidate: comp594_c0::comp594_c0_seq1::g.88::m.88, not unique enough -skipping training candidate: comp956_c0::comp956_c0_seq2::g.478::m.478, not unique enough -skipping training candidate: comp1044_c0::comp1044_c0_seq1::g.607::m.607, not unique enough -skipping training candidate: comp835_c0::comp835_c0_seq2::g.339::m.339, not unique enough -skipping training candidate: comp1029_c0::comp1029_c0_seq2::g.583::m.583, not unique enough -skipping training candidate: comp1016_c0::comp1016_c0_seq2::g.559::m.559, not unique enough -skipping training candidate: comp1207_c0::comp1207_c0_seq2::g.804::m.804, not unique enough -skipping training candidate: comp862_c0::comp862_c0_seq1::g.371::m.371, not unique enough -skipping training candidate: comp703_c0::comp703_c0_seq1::g.194::m.194, not unique enough -skipping training candidate: comp1191_c0::comp1191_c0_seq1::g.783::m.783, not unique enough -skipping training candidate: comp867_c0::comp867_c0_seq1::g.378::m.378, not unique enough -skipping training candidate: comp1207_c0::comp1207_c0_seq2::g.805::m.805, not unique enough -skipping training candidate: comp905_c0::comp905_c0_seq1::g.418::m.418, not unique enough -skipping training candidate: comp784_c0::comp784_c0_seq2::g.278::m.278, not unique enough -skipping training candidate: comp674_c0::comp674_c0_seq1::g.160::m.160, not unique enough -skipping training candidate: comp924_c0::comp924_c0_seq1::g.446::m.446, not unique enough -skipping training candidate: comp1174_c0::comp1174_c0_seq2::g.761::m.761, not unique enough -skipping training candidate: comp1046_c0::comp1046_c0_seq2::g.614::m.614, not unique enough -skipping training candidate: comp1191_c0::comp1191_c0_seq2::g.786::m.786, not unique enough -skipping training candidate: comp1044_c0::comp1044_c0_seq2::g.610::m.610, not unique enough -skipping training candidate: comp873_c0::comp873_c0_seq1::g.384::m.384, not unique enough -skipping training candidate: comp1177_c0::comp1177_c0_seq2::g.767::m.767, not unique enough -skipping training candidate: comp1196_c0::comp1196_c0_seq2::g.793::m.793, not unique enough -skipping training candidate: comp999_c0::comp999_c0_seq2::g.535::m.535, not unique enough -skipping training candidate: comp985_c0::comp985_c0_seq2::g.511::m.511, not unique enough -redundancy-minimized set includes 810 / 844 = 95.97% * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 38 * Running CMD: /build/transdecoder-5.0.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest Trinity.fasta.transdecoder_dir/base_freqs.dat > Trinity.fasta.transdecoder_dir/hexamer.scores * Running CMD: /build/transdecoder-5.0.1/util/score_CDS_likelihood_all_6_frames.pl Trinity.fasta.transdecoder_dir/longest_orfs.cds Trinity.fasta.transdecoder_dir/hexamer.scores > Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores * Running CMD: /build/transdecoder-5.0.1/util/select_best_ORFs_per_transcript.pl --gff3_file Trinity.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores Trinity.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 590 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 -indexing [comp0_c0::comp0_c0_seq1::g.1] -indexing [comp1000_c0::comp1000_c0_seq1::g.536] -indexing [comp1002_c0::comp1002_c0_seq1::g.537] -indexing [comp1004_c0::comp1004_c0_seq1::g.538] -indexing [comp1004_c0::comp1004_c0_seq1::g.539] -indexing [comp1005_c0::comp1005_c0_seq1::g.540] -indexing [comp1005_c0::comp1005_c0_seq1::g.541] -indexing [comp1006_c0::comp1006_c0_seq1::g.542] -indexing [comp1007_c0::comp1007_c0_seq1::g.544] -indexing [comp1007_c0::comp1007_c0_seq1::g.545] -indexing [comp1007_c0::comp1007_c0_seq1::g.543] -indexing [comp1008_c0::comp1008_c0_seq1::g.547] -indexing [comp1008_c0::comp1008_c0_seq1::g.546] -indexing [comp1009_c0::comp1009_c0_seq1::g.551] -indexing [comp1009_c0::comp1009_c0_seq1::g.549] -indexing [comp1009_c0::comp1009_c0_seq1::g.548] -indexing [comp1009_c0::comp1009_c0_seq1::g.550] -indexing [comp1010_c0::comp1010_c0_seq1::g.552] -indexing [comp1011_c0::comp1011_c0_seq1::g.554] -indexing [comp1011_c0::comp1011_c0_seq1::g.553] -indexing [comp1012_c0::comp1012_c0_seq1::g.555] -indexing [comp1013_c0::comp1013_c0_seq1::g.556] -indexing [comp1014_c0::comp1014_c0_seq1::g.557] -indexing [comp1016_c0::comp1016_c0_seq1::g.558] -indexing [comp1016_c0::comp1016_c0_seq2::g.559] -indexing [comp1017_c0::comp1017_c0_seq1::g.560] -indexing [comp1018_c0::comp1018_c0_seq1::g.562] -indexing [comp1018_c0::comp1018_c0_seq1::g.561] -indexing [comp1019_c0::comp1019_c0_seq1::g.563] -indexing [comp1020_c0::comp1020_c0_seq1::g.564] -indexing [comp1021_c0::comp1021_c0_seq1::g.565] -indexing [comp1022_c0::comp1022_c0_seq1::g.566] -indexing [comp1022_c0::comp1022_c0_seq1::g.568] -indexing [comp1022_c0::comp1022_c0_seq1::g.567] -indexing [comp1023_c0::comp1023_c0_seq1::g.569] -indexing [comp1023_c0::comp1023_c0_seq1::g.573] -indexing [comp1023_c0::comp1023_c0_seq1::g.570] -indexing [comp1023_c0::comp1023_c0_seq1::g.571] -indexing [comp1023_c0::comp1023_c0_seq1::g.572] -indexing [comp1024_c0::comp1024_c0_seq1::g.574] -indexing [comp1025_c0::comp1025_c0_seq1::g.575] -indexing [comp1026_c0::comp1026_c0_seq1::g.577] -indexing [comp1026_c0::comp1026_c0_seq1::g.576] -indexing [comp1027_c0::comp1027_c0_seq1::g.578] -indexing [comp1027_c0::comp1027_c0_seq1::g.579] -indexing [comp1028_c0::comp1028_c0_seq1::g.580] -indexing [comp1029_c0::comp1029_c0_seq1::g.581] -indexing [comp1029_c0::comp1029_c0_seq1::g.582] -indexing [comp1029_c0::comp1029_c0_seq2::g.583] -indexing [comp1030_c0::comp1030_c0_seq1::g.586] -indexing [comp1030_c0::comp1030_c0_seq1::g.584] -indexing [comp1030_c0::comp1030_c0_seq1::g.585] -indexing [comp1031_c0::comp1031_c0_seq1::g.587] -indexing [comp1032_c0::comp1032_c0_seq1::g.588] -indexing [comp1033_c0::comp1033_c0_seq1::g.590] -indexing [comp1033_c0::comp1033_c0_seq1::g.589] -indexing [comp1034_c0::comp1034_c0_seq1::g.592] -indexing [comp1034_c0::comp1034_c0_seq1::g.591] -indexing [comp1036_c0::comp1036_c0_seq1::g.593] -indexing [comp1037_c0::comp1037_c0_seq1::g.595] -indexing [comp1037_c0::comp1037_c0_seq1::g.594] -indexing [comp1038_c0::comp1038_c0_seq1::g.597] -indexing [comp1038_c0::comp1038_c0_seq1::g.599] -indexing [comp1038_c0::comp1038_c0_seq1::g.596] -indexing [comp1038_c0::comp1038_c0_seq1::g.600] -indexing [comp1038_c0::comp1038_c0_seq1::g.598] -indexing [comp1039_c0::comp1039_c0_seq1::g.602] -indexing [comp1039_c0::comp1039_c0_seq1::g.601] -indexing [comp1042_c0::comp1042_c0_seq1::g.603] -indexing [comp1042_c0::comp1042_c0_seq1::g.604] -indexing [comp1042_c0::comp1042_c0_seq1::g.605] -indexing [comp1043_c0::comp1043_c0_seq1::g.606] -indexing [comp1044_c0::comp1044_c0_seq1::g.608] -indexing [comp1044_c0::comp1044_c0_seq1::g.607] -indexing [comp1044_c0::comp1044_c0_seq2::g.610] -indexing [comp1044_c0::comp1044_c0_seq2::g.609] -indexing [comp1045_c0::comp1045_c0_seq1::g.611] -indexing [comp1045_c0::comp1045_c0_seq1::g.612] -indexing [comp1046_c0::comp1046_c0_seq1::g.613] -indexing [comp1046_c0::comp1046_c0_seq2::g.614] -indexing [comp1047_c0::comp1047_c0_seq1::g.615] -indexing [comp1048_c0::comp1048_c0_seq1::g.616] -indexing [comp1048_c0::comp1048_c0_seq1::g.617] -indexing [comp1049_c0::comp1049_c0_seq1::g.618] -indexing [comp1050_c0::comp1050_c0_seq1::g.619] -indexing [comp1051_c1::comp1051_c1_seq1::g.620] -indexing [comp1052_c0::comp1052_c0_seq1::g.621] -indexing [comp1053_c0::comp1053_c0_seq1::g.623] -indexing [comp1053_c0::comp1053_c0_seq1::g.622] -indexing [comp1054_c0::comp1054_c0_seq1::g.625] -indexing [comp1054_c0::comp1054_c0_seq1::g.624] -indexing [comp1055_c0::comp1055_c0_seq1::g.626] -indexing [comp1056_c0::comp1056_c0_seq1::g.627] -indexing [comp1057_c0::comp1057_c0_seq1::g.628] -indexing [comp1057_c0::comp1057_c0_seq1::g.630] -indexing [comp1057_c0::comp1057_c0_seq1::g.629] -indexing [comp1058_c0::comp1058_c0_seq1::g.631] -indexing [comp1059_c0::comp1059_c0_seq1::g.632] -indexing [comp1060_c0::comp1060_c0_seq1::g.633] -indexing [comp1061_c0::comp1061_c0_seq1::g.634] -indexing [comp1062_c0::comp1062_c0_seq1::g.635] -indexing [comp1063_c0::comp1063_c0_seq1::g.636] -indexing [comp1065_c0::comp1065_c0_seq1::g.637] -indexing [comp1065_c0::comp1065_c0_seq1::g.638] -indexing [comp1068_c0::comp1068_c0_seq1::g.639] -indexing [comp1069_c0::comp1069_c0_seq1::g.640] -indexing [comp1069_c0::comp1069_c0_seq1::g.641] -indexing [comp1070_c0::comp1070_c0_seq1::g.642] -indexing [comp1071_c0::comp1071_c0_seq1::g.644] -indexing [comp1071_c0::comp1071_c0_seq1::g.643] -indexing [comp1072_c0::comp1072_c0_seq1::g.645] -indexing [comp1074_c0::comp1074_c0_seq1::g.647] -indexing [comp1074_c0::comp1074_c0_seq1::g.646] -indexing [comp1074_c1::comp1074_c1_seq1::g.649] -indexing [comp1074_c1::comp1074_c1_seq1::g.648] -indexing [comp1075_c0::comp1075_c0_seq1::g.650] -indexing [comp1075_c0::comp1075_c0_seq1::g.651] -indexing [comp1075_c0::comp1075_c0_seq1::g.652] -indexing [comp1076_c0::comp1076_c0_seq2::g.653] -indexing [comp1077_c0::comp1077_c0_seq1::g.654] -indexing [comp1078_c0::comp1078_c0_seq1::g.655] -indexing [comp1079_c0::comp1079_c0_seq1::g.656] -indexing [comp1080_c0::comp1080_c0_seq1::g.657] -indexing [comp1081_c0::comp1081_c0_seq1::g.658] -indexing [comp1081_c0::comp1081_c0_seq1::g.659] -indexing [comp1082_c0::comp1082_c0_seq1::g.660] -indexing [comp1083_c0::comp1083_c0_seq1::g.662] -indexing [comp1083_c0::comp1083_c0_seq1::g.661] -indexing [comp1084_c0::comp1084_c0_seq1::g.663] -indexing [comp1085_c0::comp1085_c0_seq1::g.664] -indexing [comp1086_c0::comp1086_c0_seq1::g.665] -indexing [comp1087_c0::comp1087_c0_seq1::g.666] -indexing [comp1089_c0::comp1089_c0_seq1::g.667] -indexing [comp1090_c0::comp1090_c0_seq1::g.670] -indexing [comp1090_c0::comp1090_c0_seq1::g.669] -indexing [comp1090_c0::comp1090_c0_seq1::g.668] -indexing [comp1090_c0::comp1090_c0_seq1::g.671] -indexing [comp1091_c0::comp1091_c0_seq1::g.672] -indexing [comp1092_c0::comp1092_c0_seq1::g.673] -indexing [comp1093_c0::comp1093_c0_seq1::g.674] -indexing [comp1094_c0::comp1094_c0_seq1::g.675] -indexing [comp1095_c0::comp1095_c0_seq1::g.676] -indexing [comp1096_c0::comp1096_c0_seq1::g.677] -indexing [comp1097_c0::comp1097_c0_seq1::g.678] -indexing [comp1098_c0::comp1098_c0_seq1::g.679] -indexing [comp1099_c0::comp1099_c0_seq1::g.680] -indexing [comp1099_c0::comp1099_c0_seq1::g.682] -indexing [comp1099_c0::comp1099_c0_seq1::g.681] -indexing [comp1100_c0::comp1100_c0_seq1::g.683] -indexing [comp1100_c0::comp1100_c0_seq1::g.684] -indexing [comp1101_c0::comp1101_c0_seq1::g.685] -indexing [comp1102_c0::comp1102_c0_seq1::g.686] -indexing [comp1103_c0::comp1103_c0_seq1::g.687] -indexing [comp1104_c0::comp1104_c0_seq1::g.688] -indexing [comp1105_c0::comp1105_c0_seq1::g.689] -indexing [comp1106_c0::comp1106_c0_seq1::g.690] -indexing [comp1108_c0::comp1108_c0_seq1::g.691] -indexing [comp1110_c0::comp1110_c0_seq1::g.692] -indexing [comp1112_c0::comp1112_c0_seq1::g.693] -indexing [comp1114_c0::comp1114_c0_seq1::g.694] -indexing [comp1115_c0::comp1115_c0_seq1::g.696] -indexing [comp1115_c0::comp1115_c0_seq1::g.697] -indexing [comp1115_c0::comp1115_c0_seq1::g.695] -indexing [comp1115_c0::comp1115_c0_seq1::g.698] -indexing [comp1117_c0::comp1117_c0_seq1::g.699] -indexing [comp1118_c0::comp1118_c0_seq1::g.701] -indexing [comp1118_c0::comp1118_c0_seq1::g.700] -indexing [comp111_c0::comp111_c0_seq1::g.11] -indexing [comp1120_c0::comp1120_c0_seq1::g.702] -indexing [comp1121_c0::comp1121_c0_seq1::g.704] -indexing [comp1121_c0::comp1121_c0_seq1::g.703] -indexing [comp1122_c0::comp1122_c0_seq1::g.705] -indexing [comp1123_c0::comp1123_c0_seq1::g.706] -indexing [comp1124_c0::comp1124_c0_seq1::g.707] -indexing [comp1125_c0::comp1125_c0_seq1::g.708] -indexing [comp1126_c0::comp1126_c0_seq1::g.709] -indexing [comp1127_c0::comp1127_c0_seq1::g.710] -indexing [comp1128_c0::comp1128_c0_seq1::g.711] -indexing [comp1129_c0::comp1129_c0_seq1::g.712] -indexing [comp1129_c1::comp1129_c1_seq1::g.713] -indexing [comp1129_c1::comp1129_c1_seq1::g.714] -indexing [comp1130_c0::comp1130_c0_seq1::g.715] -indexing [comp1132_c0::comp1132_c0_seq1::g.716] -indexing [comp1133_c0::comp1133_c0_seq1::g.717] -indexing [comp1134_c0::comp1134_c0_seq1::g.718] -indexing [comp1135_c0::comp1135_c0_seq1::g.719] -indexing [comp1136_c0::comp1136_c0_seq1::g.721] -indexing [comp1136_c0::comp1136_c0_seq1::g.720] -indexing [comp1137_c0::comp1137_c0_seq1::g.722] -indexing [comp1138_c0::comp1138_c0_seq1::g.723] -indexing [comp1138_c0::comp1138_c0_seq1::g.724] -indexing [comp1140_c0::comp1140_c0_seq1::g.725] -indexing [comp1141_c0::comp1141_c0_seq1::g.726] -indexing [comp1142_c0::comp1142_c0_seq1::g.727] -indexing [comp1142_c0::comp1142_c0_seq1::g.728] -indexing [comp1142_c1::comp1142_c1_seq1::g.729] -indexing [comp1143_c0::comp1143_c0_seq1::g.730] -indexing [comp1144_c0::comp1144_c0_seq1::g.731] -indexing [comp1146_c0::comp1146_c0_seq1::g.732] -indexing [comp1147_c0::comp1147_c0_seq1::g.733] -indexing [comp1148_c0::comp1148_c0_seq1::g.735] -indexing [comp1148_c0::comp1148_c0_seq1::g.734] -indexing [comp1149_c0::comp1149_c0_seq1::g.736] -indexing [comp1150_c0::comp1150_c0_seq1::g.737] -indexing [comp1151_c0::comp1151_c0_seq1::g.738] -indexing [comp1154_c0::comp1154_c0_seq1::g.739] -indexing [comp1156_c0::comp1156_c0_seq1::g.740] -indexing [comp1157_c0::comp1157_c0_seq1::g.741] -indexing [comp1157_c0::comp1157_c0_seq1::g.742] -indexing [comp1158_c0::comp1158_c0_seq1::g.743] -indexing [comp1159_c0::comp1159_c0_seq1::g.744] -indexing [comp1161_c0::comp1161_c0_seq1::g.745] -indexing [comp1161_c0::comp1161_c0_seq1::g.746] -indexing [comp1162_c0::comp1162_c0_seq1::g.747] -indexing [comp1165_c0::comp1165_c0_seq1::g.748] -indexing [comp1165_c0::comp1165_c0_seq1::g.749] -indexing [comp1166_c0::comp1166_c0_seq1::g.750] -indexing [comp1167_c0::comp1167_c0_seq1::g.752] -indexing [comp1167_c0::comp1167_c0_seq1::g.753] -indexing [comp1167_c0::comp1167_c0_seq1::g.751] -indexing [comp1168_c0::comp1168_c0_seq1::g.754] -indexing [comp1170_c0::comp1170_c0_seq1::g.755] -indexing [comp1171_c0::comp1171_c0_seq1::g.756] -indexing [comp1172_c0::comp1172_c0_seq1::g.757] -indexing 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[comp978_c0::comp978_c0_seq1::g.501] -indexing [comp978_c0::comp978_c0_seq1::g.502] -indexing [comp979_c0::comp979_c0_seq1::g.503] -indexing [comp980_c0::comp980_c0_seq1::g.504] -indexing [comp981_c0::comp981_c0_seq1::g.505] -indexing [comp982_c0::comp982_c0_seq2::g.506] -indexing [comp983_c0::comp983_c0_seq1::g.508] -indexing [comp983_c0::comp983_c0_seq1::g.507] -indexing [comp984_c0::comp984_c0_seq1::g.509] -indexing [comp985_c0::comp985_c0_seq1::g.510] -indexing [comp985_c0::comp985_c0_seq2::g.511] -indexing [comp986_c0::comp986_c0_seq1::g.512] -indexing [comp987_c0::comp987_c0_seq1::g.513] -indexing [comp987_c0::comp987_c0_seq1::g.514] -indexing [comp988_c0::comp988_c0_seq1::g.516] -indexing [comp988_c0::comp988_c0_seq1::g.517] -indexing [comp988_c0::comp988_c0_seq1::g.515] -indexing [comp989_c0::comp989_c0_seq1::g.518] -indexing [comp989_c0::comp989_c0_seq2::g.519] -indexing [comp98_c0::comp98_c0_seq1::g.10] -indexing [comp990_c0::comp990_c0_seq1::g.520] -indexing [comp991_c0::comp991_c0_seq1::g.521] -indexing [comp992_c0::comp992_c0_seq1::g.522] -indexing [comp992_c0::comp992_c0_seq2::g.523] -indexing [comp993_c0::comp993_c0_seq1::g.524] -indexing [comp993_c0::comp993_c0_seq1::g.525] -indexing [comp994_c0::comp994_c0_seq1::g.526] -indexing [comp995_c0::comp995_c0_seq1::g.527] -indexing [comp996_c0::comp996_c0_seq1::g.528] -indexing [comp997_c0::comp997_c0_seq1::g.529] -indexing [comp998_c0::comp998_c0_seq1::g.530] -indexing [comp998_c0::comp998_c0_seq1::g.531] -indexing [comp999_c0::comp999_c0_seq1::g.532] -indexing [comp999_c0::comp999_c0_seq1::g.533] -indexing [comp999_c0::comp999_c0_seq2::g.535] -indexing [comp999_c0::comp999_c0_seq2::g.534] * Running CMD: /build/transdecoder-5.0.1/util/train_start_PWM.pl --transcripts Trinity.fasta --selected_orfs Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.fasta.transdecoder_dir/start_refinement * Running CMD: /build/transdecoder-5.0.1/util/PWM/build_atgPWM_+-.pl --transcripts Trinity.fasta --selected_orfs Trinity.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix Trinity.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.+.features --features_minus Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl Trinity.fasta.transdecoder_dir/start_refinement.feature.scores > Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl Trinity.fasta.transdecoder_dir/start_refinement.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript Trinity.fasta.transdecoder_dir/start_refinement.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript Trinity.fasta.transdecoder_dir/start_refinement.-.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/deplete_feature_noise.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus Trinity.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix Trinity.fasta.transdecoder_dir/start_refinement.enhanced num features: 358 num_incorporate: 107 -feature swap of score: 2.01860755745774 instead of -2.43253294753209 -feature swap of score: 2.34732451463516 instead of -2.03515280104856 -feature swap of score: 2.42600756963178 instead of -1.88586714183678 -feature swap of score: 4.04692570560011 instead of -2.07838396233827 -feature swap of score: -2.10349049055208 instead of -2.14357898216183 -feature swap of score: 3.34270681682176 instead of -1.68919591401722 -feature swap of score: 0.785638027271692 instead of -1.75537844488172 -feature swap of score: 0.124937617546208 instead of -1.42423447927029 -feature swap of score: 3.80360939610757 instead of -1.25581956645478 -feature swap of score: 2.22972790847055 instead of -1.43724022198391 -feature swap of score: 1.87223224767761 instead of -1.39134963935408 -feature swap of score: -0.869196741065359 instead of -1.45437592553593 -feature swap of score: 2.61126122082178 instead of -1.4644389491732 -feature swap of score: 0.041614898233897 instead of -1.38236698907653 -feature swap of score: 5.23702512832804 instead of -1.06647647854364 -feature swap of score: 0.489018424262898 instead of -0.95713076184448 -feature swap of score: 1.06810458576389 instead of -0.894284983683669 -feature swap of score: -0.226298629660561 instead of -0.948994050642804 -feature swap of score: 0.450699974271914 instead of -0.959497695240219 -feature swap of score: 4.28695919068754 instead of -0.978907600609435 -feature swap of score: 2.14133448495559 instead of -0.753180766675387 -feature swap of score: 4.12202729113471 instead of -0.76828282708309 -feature swap of score: -0.104946382094106 instead of -0.628776084467911 -feature swap of score: 0.000572807808514326 instead of -0.53263942949094 -feature swap of score: 0.198006134044188 instead of -0.34106805075173 -feature swap of score: 3.6047163749624 instead of -0.51212082035361 -feature swap of score: 0.814286538900709 instead of -0.339061555243772 -feature swap of score: 4.97523538835402 instead of -0.219644205392414 -feature swap of score: 1.97045125499639 instead of -0.113036838336636 -feature swap of score: 4.13053733045551 instead of -0.170052581383971 -feature swap of score: 0.00206436128981199 instead of -0.181062974960661 -feature swap of score: 1.604245252388 instead of 0.0517161275151237 -feature swap of score: 4.3932806981529 instead of 0.0860431565952234 -feature swap of score: 1.72957229182765 instead of 0.221968210457067 -feature swap of score: 1.57263236697426 instead of 0.288968311790631 -feature swap of score: 0.203166281459456 instead of 0.10534662338876 -feature swap of score: 4.38190400149154 instead of 0.196370432457334 -feature swap of score: 5.04613038233112 instead of 0.150614918926321 -feature swap of score: 2.26071953474249 instead of 0.230526386115092 -feature swap of score: 5.13639850152629 instead of 0.252892697647447 -feature swap of score: 1.17098382473728 instead of 0.282995900530861 -feature swap of score: 4.34776268138483 instead of 0.41430990147474 -feature swap of score: 2.15329616437699 instead of 0.429451771590664 -feature swap of score: 5.09229418476461 instead of 0.297828956020416 -feature swap of score: 1.13675328930652 instead of 0.171694593520241 -feature swap of score: 2.02231900226323 instead of 0.206703978994726 -feature swap of score: 2.66734827613583 instead of 0.443525927859022 -feature swap of score: 3.77684820014943 instead of 0.599510264128007 -feature swap of score: 1.29789971226826 instead of 0.51658385615187 -feature swap of score: 3.74256664801257 instead of 0.445260647950643 -feature swap of score: 4.32680419305246 instead of 0.596611075477652 -feature swap of score: 1.77920876164079 instead of 0.52605377488021 -feature swap of score: 1.61583261588263 instead of 0.65317830698915 -feature swap of score: 4.10400531839299 instead of 0.789843632233928 -feature swap of score: 1.83659343125585 instead of 0.716731928502843 -feature swap of score: 1.6438027810344 instead of 0.767790779444299 -feature swap of score: 2.51637019194037 instead of 0.699527206449989 -feature swap of score: 1.60560873858958 instead of 1.07464412670026 -feature swap of score: 2.89883210321421 instead of 1.07157389032513 -feature swap of score: 2.93101514977772 instead of 0.988616846801185 -feature swap of score: 3.72069918320373 instead of 0.868454192870146 -feature swap of score: 1.03519107357972 instead of 0.753010048444791 -feature swap of score: 4.01020820806659 instead of 0.886358064075704 -feature swap of score: 0.879618323769624 instead of 0.61109819149034 -feature swap of score: 7.15234940921215 instead of 1.03360771341683 -feature swap of score: 1.83921458905268 instead of 1.02334035960285 -feature swap of score: 2.23998772164463 instead of 0.834483027752134 -feature swap of score: 2.16522830829353 instead of 1.1968190751818 -feature swap of score: 3.565902255058 instead of 1.04816444694555 -feature swap of score: 1.1156878707122 instead of 0.972785593550388 -feature swap of score: 1.63015648897591 instead of 1.12916093095551 -feature swap of score: 3.15623525707792 instead of 1.19443129843577 -feature swap of score: 1.75064193312005 instead of 1.22439213990375 -feature swap of score: 2.22558017270471 instead of 1.41095670579146 -feature swap of score: 1.69472767650654 instead of 1.47090708539632 -feature swap of score: 5.71675848798316 instead of 1.54417528485585 -feature swap of score: 2.36834513989863 instead of 1.56065511814006 -feature swap of score: 4.72132107671951 instead of 1.39108914413569 -feature swap of score: 2.98996061269645 instead of 1.4726797291019 -feature swap of score: 2.30202014931778 instead of 1.35942459345001 -feature swap of score: 6.94448025054924 instead of 1.53071141968655 -feature swap of score: 2.02147832129674 instead of 1.39293685217156 -feature swap of score: 3.0540382236436 instead of 1.47682791921283 -feature swap of score: 8.35170655675059 instead of 1.54271367706925 -feature swap of score: 2.3591087448739 instead of 1.62983627612991 -feature swap of score: 3.33896220987853 instead of 1.74551832680512 -feature swap of score: 4.47931807129169 instead of 1.65656837994906 -feature swap of score: 6.43889512650897 instead of 1.63523856658065 -feature swap of score: 4.44139726355316 instead of 1.62413947257281 -feature swap of score: 4.3934217091148 instead of 1.5563895897064 -feature swap of score: 2.4178749161712 instead of 1.53540854291086 -feature swap of score: 4.50084537762944 instead of 1.99813615680005 -feature swap of score: 4.36085158331683 instead of 1.81509165074822 -feature swap of score: 3.50540200807125 instead of 1.84763588301182 -feature swap of score: 2.14307301177581 instead of 1.58943578807425 -feature swap of score: 2.80249705432441 instead of 2.03323063135445 -feature swap of score: 2.51995823874979 instead of 1.80649830131556 -feature swap of score: 2.18546699630314 instead of 2.01678734343503 -feature swap of score: 6.02870360838808 instead of 2.11230538713769 -feature swap of score: 4.79559537621424 instead of 1.93041915648434 -feature swap of score: 8.43445355562363 instead of 2.187388349484 -feature swap of score: 3.43057432858564 instead of 2.04524276099259 -feature swap of score: 2.64567534439595 instead of 1.91708045098195 -num feature swaps: 103 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus Trinity.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl Trinity.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript Trinity.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/start_codon_refinement.pl --transcripts Trinity.fasta --gff3_file Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 > Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 -indexing [comp0_c0::comp0_c0_seq1::g.1] -indexing [comp1000_c0::comp1000_c0_seq1::g.536] -indexing [comp1002_c0::comp1002_c0_seq1::g.537] -indexing [comp1004_c0::comp1004_c0_seq1::g.538] -indexing [comp1005_c0::comp1005_c0_seq1::g.540] -indexing [comp1006_c0::comp1006_c0_seq1::g.542] -indexing [comp1007_c0::comp1007_c0_seq1::g.543] -indexing [comp1008_c0::comp1008_c0_seq1::g.546] -indexing [comp1009_c0::comp1009_c0_seq1::g.548] -indexing [comp1010_c0::comp1010_c0_seq1::g.552] -indexing [comp1011_c0::comp1011_c0_seq1::g.553] -indexing [comp1012_c0::comp1012_c0_seq1::g.555] -indexing [comp1013_c0::comp1013_c0_seq1::g.556] -indexing [comp1014_c0::comp1014_c0_seq1::g.557] -indexing [comp1016_c0::comp1016_c0_seq1::g.558] -indexing [comp1016_c0::comp1016_c0_seq2::g.559] -indexing [comp1017_c0::comp1017_c0_seq1::g.560] -indexing [comp1018_c0::comp1018_c0_seq1::g.561] -indexing [comp1019_c0::comp1019_c0_seq1::g.563] -indexing [comp1020_c0::comp1020_c0_seq1::g.564] -indexing [comp1021_c0::comp1021_c0_seq1::g.565] -indexing [comp1022_c0::comp1022_c0_seq1::g.566] -indexing [comp1023_c0::comp1023_c0_seq1::g.569] -indexing [comp1024_c0::comp1024_c0_seq1::g.574] -indexing [comp1025_c0::comp1025_c0_seq1::g.575] -indexing [comp1026_c0::comp1026_c0_seq1::g.577] -indexing [comp1027_c0::comp1027_c0_seq1::g.578] -indexing [comp1028_c0::comp1028_c0_seq1::g.580] -indexing [comp1029_c0::comp1029_c0_seq1::g.582] -indexing [comp1029_c0::comp1029_c0_seq2::g.583] -indexing [comp1030_c0::comp1030_c0_seq1::g.584] -indexing [comp1031_c0::comp1031_c0_seq1::g.587] -indexing [comp1032_c0::comp1032_c0_seq1::g.588] -indexing [comp1033_c0::comp1033_c0_seq1::g.590] -indexing [comp1034_c0::comp1034_c0_seq1::g.591] -indexing [comp1037_c0::comp1037_c0_seq1::g.594] -indexing [comp1038_c0::comp1038_c0_seq1::g.596] -indexing [comp1039_c0::comp1039_c0_seq1::g.601] -indexing [comp1042_c0::comp1042_c0_seq1::g.603] -indexing [comp1043_c0::comp1043_c0_seq1::g.606] -indexing [comp1044_c0::comp1044_c0_seq1::g.607] -indexing [comp1044_c0::comp1044_c0_seq2::g.609] -indexing [comp1045_c0::comp1045_c0_seq1::g.611] -indexing [comp1046_c0::comp1046_c0_seq1::g.613] -indexing [comp1046_c0::comp1046_c0_seq2::g.614] -indexing [comp1047_c0::comp1047_c0_seq1::g.615] -indexing 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[comp924_c0::comp924_c0_seq1::g.445] -indexing [comp926_c0::comp926_c0_seq1::g.448] -indexing [comp927_c0::comp927_c0_seq1::g.449] -indexing [comp928_c0::comp928_c0_seq1::g.450] -indexing [comp929_c0::comp929_c0_seq1::g.451] -indexing [comp930_c0::comp930_c0_seq1::g.452] -indexing [comp931_c0::comp931_c0_seq1::g.453] -indexing [comp932_c0::comp932_c0_seq1::g.454] -indexing [comp934_c0::comp934_c0_seq1::g.456] -indexing [comp935_c0::comp935_c0_seq1::g.457] -indexing [comp939_c0::comp939_c0_seq1::g.458] -indexing [comp940_c0::comp940_c0_seq1::g.459] -indexing [comp942_c0::comp942_c0_seq1::g.460] -indexing [comp943_c0::comp943_c0_seq1::g.461] -indexing [comp944_c0::comp944_c0_seq1::g.463] -indexing [comp945_c0::comp945_c0_seq1::g.466] -indexing [comp946_c0::comp946_c0_seq1::g.467] -indexing [comp947_c0::comp947_c0_seq1::g.468] -indexing [comp948_c0::comp948_c0_seq1::g.469] -indexing [comp950_c0::comp950_c0_seq1::g.470] -indexing [comp951_c0::comp951_c0_seq1::g.471] -indexing [comp952_c0::comp952_c0_seq1::g.472] -indexing [comp953_c0::comp953_c0_seq1::g.474] -indexing [comp954_c0::comp954_c0_seq1::g.475] -indexing [comp955_c0::comp955_c0_seq1::g.476] -indexing [comp956_c0::comp956_c0_seq1::g.477] -indexing [comp956_c0::comp956_c0_seq2::g.478] -indexing [comp959_c0::comp959_c0_seq1::g.479] -indexing [comp960_c0::comp960_c0_seq1::g.480] -indexing [comp961_c0::comp961_c0_seq1::g.483] -indexing [comp962_c0::comp962_c0_seq1::g.484] -indexing [comp963_c0::comp963_c0_seq1::g.485] -indexing [comp964_c0::comp964_c0_seq1::g.487] -indexing [comp965_c0::comp965_c0_seq1::g.488] -indexing [comp966_c0::comp966_c0_seq1::g.489] -indexing [comp967_c0::comp967_c0_seq1::g.490] -indexing [comp968_c0::comp968_c0_seq1::g.491] -indexing [comp969_c0::comp969_c0_seq1::g.492] -indexing [comp970_c0::comp970_c0_seq1::g.494] -indexing [comp972_c0::comp972_c0_seq1::g.496] -indexing [comp973_c0::comp973_c0_seq1::g.497] -indexing [comp974_c0::comp974_c0_seq1::g.498] -indexing [comp976_c0::comp976_c0_seq1::g.499] -indexing [comp977_c0::comp977_c0_seq1::g.500] -indexing [comp978_c0::comp978_c0_seq1::g.501] -indexing [comp979_c0::comp979_c0_seq1::g.503] -indexing [comp980_c0::comp980_c0_seq1::g.504] -indexing [comp981_c0::comp981_c0_seq1::g.505] -indexing [comp982_c0::comp982_c0_seq2::g.506] -indexing [comp983_c0::comp983_c0_seq1::g.507] -indexing [comp984_c0::comp984_c0_seq1::g.509] -indexing [comp985_c0::comp985_c0_seq1::g.510] -indexing [comp985_c0::comp985_c0_seq2::g.511] -indexing [comp986_c0::comp986_c0_seq1::g.512] -indexing [comp987_c0::comp987_c0_seq1::g.513] -indexing [comp988_c0::comp988_c0_seq1::g.515] -indexing [comp989_c0::comp989_c0_seq1::g.518] -indexing [comp989_c0::comp989_c0_seq2::g.519] -indexing [comp98_c0::comp98_c0_seq1::g.10] -indexing [comp990_c0::comp990_c0_seq1::g.520] -indexing [comp991_c0::comp991_c0_seq1::g.521] -indexing [comp992_c0::comp992_c0_seq1::g.522] -indexing [comp992_c0::comp992_c0_seq2::g.523] -indexing [comp993_c0::comp993_c0_seq1::g.524] -indexing [comp994_c0::comp994_c0_seq1::g.526] -indexing [comp995_c0::comp995_c0_seq1::g.527] -indexing [comp996_c0::comp996_c0_seq1::g.528] -indexing [comp997_c0::comp997_c0_seq1::g.529] -indexing [comp998_c0::comp998_c0_seq1::g.530] -indexing [comp999_c0::comp999_c0_seq1::g.532] -indexing [comp999_c0::comp999_c0_seq2::g.534] -number of revised start positions: 42 CMD: cp Trinity.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 Trinity.fasta.transdecoder.gff3 CMD: /build/transdecoder-5.0.1/util/gff3_file_to_bed.pl Trinity.fasta.transdecoder.gff3 > Trinity.fasta.transdecoder.bed -indexing [comp0_c0::comp0_c0_seq1::g.1] -indexing [comp1000_c0::comp1000_c0_seq1::g.536] -indexing [comp1002_c0::comp1002_c0_seq1::g.537] -indexing [comp1004_c0::comp1004_c0_seq1::g.538] -indexing [comp1005_c0::comp1005_c0_seq1::g.540] -indexing [comp1006_c0::comp1006_c0_seq1::g.542] -indexing [comp1007_c0::comp1007_c0_seq1::g.543] -indexing [comp1008_c0::comp1008_c0_seq1::g.546] -indexing [comp1009_c0::comp1009_c0_seq1::g.548] -indexing [comp1010_c0::comp1010_c0_seq1::g.552] -indexing [comp1011_c0::comp1011_c0_seq1::g.553] -indexing [comp1012_c0::comp1012_c0_seq1::g.555] -indexing [comp1013_c0::comp1013_c0_seq1::g.556] -indexing [comp1014_c0::comp1014_c0_seq1::g.557] -indexing [comp1016_c0::comp1016_c0_seq1::g.558] -indexing [comp1016_c0::comp1016_c0_seq2::g.559] -indexing [comp1017_c0::comp1017_c0_seq1::g.560] -indexing [comp1018_c0::comp1018_c0_seq1::g.561] -indexing [comp1019_c0::comp1019_c0_seq1::g.563] -indexing [comp1020_c0::comp1020_c0_seq1::g.564] -indexing [comp1021_c0::comp1021_c0_seq1::g.565] -indexing [comp1022_c0::comp1022_c0_seq1::g.566] -indexing [comp1023_c0::comp1023_c0_seq1::g.569] -indexing [comp1024_c0::comp1024_c0_seq1::g.574] -indexing [comp1025_c0::comp1025_c0_seq1::g.575] -indexing [comp1026_c0::comp1026_c0_seq1::g.577] -indexing [comp1027_c0::comp1027_c0_seq1::g.578] -indexing [comp1028_c0::comp1028_c0_seq1::g.580] -indexing [comp1029_c0::comp1029_c0_seq1::g.582] -indexing [comp1029_c0::comp1029_c0_seq2::g.583] -indexing [comp1030_c0::comp1030_c0_seq1::g.584] -indexing [comp1031_c0::comp1031_c0_seq1::g.587] -indexing [comp1032_c0::comp1032_c0_seq1::g.588] -indexing [comp1033_c0::comp1033_c0_seq1::g.590] -indexing [comp1034_c0::comp1034_c0_seq1::g.591] -indexing [comp1037_c0::comp1037_c0_seq1::g.594] -indexing [comp1038_c0::comp1038_c0_seq1::g.596] -indexing [comp1039_c0::comp1039_c0_seq1::g.601] -indexing [comp1042_c0::comp1042_c0_seq1::g.603] -indexing [comp1043_c0::comp1043_c0_seq1::g.606] -indexing [comp1044_c0::comp1044_c0_seq1::g.607] -indexing [comp1044_c0::comp1044_c0_seq2::g.609] -indexing [comp1045_c0::comp1045_c0_seq1::g.611] -indexing [comp1046_c0::comp1046_c0_seq1::g.613] -indexing [comp1046_c0::comp1046_c0_seq2::g.614] -indexing [comp1047_c0::comp1047_c0_seq1::g.615] -indexing [comp1048_c0::comp1048_c0_seq1::g.616] -indexing [comp1049_c0::comp1049_c0_seq1::g.618] -indexing [comp1050_c0::comp1050_c0_seq1::g.619] -indexing [comp1051_c1::comp1051_c1_seq1::g.620] -indexing [comp1052_c0::comp1052_c0_seq1::g.621] -indexing [comp1053_c0::comp1053_c0_seq1::g.622] -indexing [comp1054_c0::comp1054_c0_seq1::g.624] -indexing [comp1055_c0::comp1055_c0_seq1::g.626] -indexing [comp1056_c0::comp1056_c0_seq1::g.627] -indexing [comp1057_c0::comp1057_c0_seq1::g.628] -indexing [comp1058_c0::comp1058_c0_seq1::g.631] -indexing [comp1059_c0::comp1059_c0_seq1::g.632] -indexing [comp1060_c0::comp1060_c0_seq1::g.633] -indexing [comp1061_c0::comp1061_c0_seq1::g.634] -indexing [comp1062_c0::comp1062_c0_seq1::g.635] -indexing [comp1063_c0::comp1063_c0_seq1::g.636] -indexing [comp1065_c0::comp1065_c0_seq1::g.637] -indexing [comp1068_c0::comp1068_c0_seq1::g.639] -indexing [comp1069_c0::comp1069_c0_seq1::g.640] -indexing [comp1070_c0::comp1070_c0_seq1::g.642] -indexing [comp1071_c0::comp1071_c0_seq1::g.643] -indexing [comp1072_c0::comp1072_c0_seq1::g.645] -indexing [comp1074_c0::comp1074_c0_seq1::g.646] -indexing [comp1074_c1::comp1074_c1_seq1::g.648] -indexing [comp1075_c0::comp1075_c0_seq1::g.650] -indexing [comp1076_c0::comp1076_c0_seq2::g.653] -indexing [comp1077_c0::comp1077_c0_seq1::g.654] -indexing [comp1078_c0::comp1078_c0_seq1::g.655] -indexing [comp1079_c0::comp1079_c0_seq1::g.656] -indexing [comp1080_c0::comp1080_c0_seq1::g.657] -indexing [comp1081_c0::comp1081_c0_seq1::g.658] -indexing [comp1082_c0::comp1082_c0_seq1::g.660] -indexing [comp1083_c0::comp1083_c0_seq1::g.661] -indexing [comp1084_c0::comp1084_c0_seq1::g.663] -indexing [comp1085_c0::comp1085_c0_seq1::g.664] -indexing [comp1086_c0::comp1086_c0_seq1::g.665] -indexing [comp1087_c0::comp1087_c0_seq1::g.666] -indexing [comp1089_c0::comp1089_c0_seq1::g.667] -indexing [comp1090_c0::comp1090_c0_seq1::g.668] -indexing [comp1091_c0::comp1091_c0_seq1::g.672] -indexing [comp1092_c0::comp1092_c0_seq1::g.673] -indexing [comp1093_c0::comp1093_c0_seq1::g.674] -indexing [comp1094_c0::comp1094_c0_seq1::g.675] -indexing [comp1095_c0::comp1095_c0_seq1::g.676] -indexing [comp1096_c0::comp1096_c0_seq1::g.677] -indexing [comp1097_c0::comp1097_c0_seq1::g.678] -indexing [comp1098_c0::comp1098_c0_seq1::g.679] -indexing [comp1099_c0::comp1099_c0_seq1::g.680] -indexing [comp1100_c0::comp1100_c0_seq1::g.683] -indexing [comp1101_c0::comp1101_c0_seq1::g.685] -indexing [comp1102_c0::comp1102_c0_seq1::g.686] -indexing [comp1103_c0::comp1103_c0_seq1::g.687] -indexing [comp1104_c0::comp1104_c0_seq1::g.688] -indexing [comp1105_c0::comp1105_c0_seq1::g.689] -indexing [comp1106_c0::comp1106_c0_seq1::g.690] -indexing [comp1108_c0::comp1108_c0_seq1::g.691] -indexing [comp1110_c0::comp1110_c0_seq1::g.692] -indexing [comp1112_c0::comp1112_c0_seq1::g.693] -indexing [comp1114_c0::comp1114_c0_seq1::g.694] -indexing [comp1115_c0::comp1115_c0_seq1::g.695] -indexing [comp1117_c0::comp1117_c0_seq1::g.699] -indexing 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[comp1138_c0::comp1138_c0_seq1::g.723] -indexing [comp1140_c0::comp1140_c0_seq1::g.725] -indexing [comp1141_c0::comp1141_c0_seq1::g.726] -indexing [comp1142_c0::comp1142_c0_seq1::g.727] -indexing [comp1142_c1::comp1142_c1_seq1::g.729] -indexing [comp1143_c0::comp1143_c0_seq1::g.730] -indexing [comp1144_c0::comp1144_c0_seq1::g.731] -indexing [comp1146_c0::comp1146_c0_seq1::g.732] -indexing [comp1147_c0::comp1147_c0_seq1::g.733] -indexing [comp1148_c0::comp1148_c0_seq1::g.734] -indexing [comp1149_c0::comp1149_c0_seq1::g.736] -indexing [comp1150_c0::comp1150_c0_seq1::g.737] -indexing [comp1151_c0::comp1151_c0_seq1::g.738] -indexing [comp1154_c0::comp1154_c0_seq1::g.739] -indexing [comp1156_c0::comp1156_c0_seq1::g.740] -indexing [comp1157_c0::comp1157_c0_seq1::g.741] -indexing [comp1158_c0::comp1158_c0_seq1::g.743] -indexing [comp1159_c0::comp1159_c0_seq1::g.744] -indexing [comp1161_c0::comp1161_c0_seq1::g.745] -indexing [comp1162_c0::comp1162_c0_seq1::g.747] -indexing [comp1165_c0::comp1165_c0_seq1::g.748] -indexing [comp1166_c0::comp1166_c0_seq1::g.750] -indexing [comp1167_c0::comp1167_c0_seq1::g.751] -indexing [comp1168_c0::comp1168_c0_seq1::g.754] -indexing [comp1170_c0::comp1170_c0_seq1::g.755] -indexing [comp1171_c0::comp1171_c0_seq1::g.756] -indexing [comp1172_c0::comp1172_c0_seq1::g.757] -indexing [comp1173_c0::comp1173_c0_seq1::g.759] -indexing [comp1174_c0::comp1174_c0_seq1::g.760] -indexing [comp1174_c0::comp1174_c0_seq2::g.761] -indexing [comp1175_c0::comp1175_c0_seq1::g.762] -indexing [comp1177_c0::comp1177_c0_seq1::g.764] -indexing [comp1177_c0::comp1177_c0_seq2::g.766] -indexing [comp1178_c0::comp1178_c0_seq1::g.768] -indexing [comp1179_c0::comp1179_c0_seq1::g.769] -indexing [comp117_c0::comp117_c0_seq1::g.12] -indexing [comp117_c1::comp117_c1_seq1::g.13] -indexing [comp1180_c0::comp1180_c0_seq1::g.771] -indexing [comp1181_c0::comp1181_c0_seq1::g.773] -indexing [comp1182_c0::comp1182_c0_seq1::g.774] -indexing [comp1183_c0::comp1183_c0_seq1::g.775] -indexing [comp1185_c0::comp1185_c0_seq1::g.776] -indexing [comp1185_c1::comp1185_c1_seq1::g.777] -indexing [comp1186_c0::comp1186_c0_seq1::g.778] -indexing [comp1187_c0::comp1187_c0_seq1::g.779] -indexing [comp1188_c0::comp1188_c0_seq1::g.780] -indexing [comp1189_c0::comp1189_c0_seq1::g.781] -indexing [comp1190_c0::comp1190_c0_seq1::g.782] -indexing [comp1191_c0::comp1191_c0_seq1::g.783] -indexing [comp1191_c0::comp1191_c0_seq2::g.785] -indexing [comp1193_c0::comp1193_c0_seq1::g.787] -indexing [comp1194_c0::comp1194_c0_seq1::g.788] -indexing [comp1195_c0::comp1195_c0_seq1::g.791] -indexing [comp1196_c0::comp1196_c0_seq1::g.792] -indexing [comp1196_c0::comp1196_c0_seq2::g.793] -indexing [comp1197_c0::comp1197_c0_seq1::g.794] -indexing [comp1198_c0::comp1198_c0_seq1::g.795] -indexing [comp1200_c0::comp1200_c0_seq1::g.796] -indexing [comp1201_c0::comp1201_c0_seq1::g.797] -indexing [comp1202_c0::comp1202_c0_seq1::g.798] -indexing [comp1203_c0::comp1203_c0_seq1::g.800] -indexing [comp1206_c0::comp1206_c0_seq1::g.801] -indexing [comp1207_c0::comp1207_c0_seq1::g.802] -indexing [comp1207_c0::comp1207_c0_seq2::g.804] -indexing [comp1209_c0::comp1209_c0_seq1::g.806] -indexing [comp1210_c0::comp1210_c0_seq1::g.807] -indexing [comp1211_c0::comp1211_c0_seq1::g.808] -indexing [comp1212_c0::comp1212_c0_seq1::g.810] -indexing [comp1213_c0::comp1213_c0_seq1::g.811] -indexing [comp1214_c0::comp1214_c0_seq1::g.812] -indexing [comp1215_c0::comp1215_c0_seq1::g.813] -indexing [comp1216_c0::comp1216_c0_seq1::g.815] -indexing [comp1217_c0::comp1217_c0_seq1::g.817] -indexing [comp1218_c0::comp1218_c0_seq1::g.820] -indexing [comp1220_c0::comp1220_c0_seq1::g.821] -indexing [comp1222_c0::comp1222_c0_seq1::g.822] -indexing [comp1223_c0::comp1223_c0_seq1::g.823] -indexing [comp1224_c0::comp1224_c0_seq1::g.824] -indexing [comp1225_c0::comp1225_c0_seq2::g.827] -indexing [comp1226_c0::comp1226_c0_seq1::g.828] -indexing [comp1227_c0::comp1227_c0_seq1::g.829] -indexing [comp1228_c0::comp1228_c0_seq1::g.830] -indexing [comp1229_c0::comp1229_c0_seq1::g.831] -indexing [comp1231_c0::comp1231_c0_seq1::g.832] -indexing [comp1232_c0::comp1232_c0_seq1::g.834] -indexing [comp1233_c0::comp1233_c0_seq1::g.836] -indexing [comp1234_c0::comp1234_c0_seq1::g.837] -indexing [comp1236_c0::comp1236_c0_seq1::g.838] -indexing [comp1239_c0::comp1239_c0_seq1::g.840] -indexing [comp1240_c0::comp1240_c0_seq1::g.841] -indexing [comp1241_c0::comp1241_c0_seq1::g.842] -indexing [comp1242_c0::comp1242_c0_seq1::g.843] -indexing [comp1243_c0::comp1243_c0_seq1::g.844] -indexing [comp1244_c0::comp1244_c0_seq1::g.845] -indexing [comp133_c1::comp133_c1_seq1::g.14] -indexing [comp180_c0::comp180_c0_seq1::g.15] -indexing [comp190_c0::comp190_c0_seq1::g.16] -indexing [comp201_c0::comp201_c0_seq1::g.18] -indexing [comp209_c0::comp209_c0_seq1::g.19] -indexing [comp213_c0::comp213_c0_seq1::g.20] -indexing [comp217_c0::comp217_c0_seq1::g.21] 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[comp977_c0::comp977_c0_seq1::g.500] -indexing [comp978_c0::comp978_c0_seq1::g.501] -indexing [comp979_c0::comp979_c0_seq1::g.503] -indexing [comp980_c0::comp980_c0_seq1::g.504] -indexing [comp981_c0::comp981_c0_seq1::g.505] -indexing [comp982_c0::comp982_c0_seq2::g.506] -indexing [comp983_c0::comp983_c0_seq1::g.507] -indexing [comp984_c0::comp984_c0_seq1::g.509] -indexing [comp985_c0::comp985_c0_seq1::g.510] -indexing [comp985_c0::comp985_c0_seq2::g.511] -indexing [comp986_c0::comp986_c0_seq1::g.512] -indexing [comp987_c0::comp987_c0_seq1::g.513] -indexing [comp988_c0::comp988_c0_seq1::g.515] -indexing [comp989_c0::comp989_c0_seq1::g.518] -indexing [comp989_c0::comp989_c0_seq2::g.519] -indexing [comp98_c0::comp98_c0_seq1::g.10] -indexing [comp990_c0::comp990_c0_seq1::g.520] -indexing [comp991_c0::comp991_c0_seq1::g.521] -indexing [comp992_c0::comp992_c0_seq1::g.522] -indexing [comp992_c0::comp992_c0_seq2::g.523] -indexing [comp993_c0::comp993_c0_seq1::g.524] -indexing [comp994_c0::comp994_c0_seq1::g.526] -indexing [comp995_c0::comp995_c0_seq1::g.527] -indexing [comp996_c0::comp996_c0_seq1::g.528] -indexing [comp997_c0::comp997_c0_seq1::g.529] -indexing [comp998_c0::comp998_c0_seq1::g.530] -indexing [comp999_c0::comp999_c0_seq1::g.532] -indexing [comp999_c0::comp999_c0_seq2::g.534] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 Trinity.fasta.transdecoder.gff3 --fasta Trinity.fasta > Trinity.fasta.transdecoder.pep -indexing [comp0_c0::comp0_c0_seq1::g.1] -indexing [comp1000_c0::comp1000_c0_seq1::g.536] -indexing [comp1002_c0::comp1002_c0_seq1::g.537] -indexing [comp1004_c0::comp1004_c0_seq1::g.538] -indexing [comp1005_c0::comp1005_c0_seq1::g.540] -indexing [comp1006_c0::comp1006_c0_seq1::g.542] -indexing [comp1007_c0::comp1007_c0_seq1::g.543] -indexing [comp1008_c0::comp1008_c0_seq1::g.546] -indexing [comp1009_c0::comp1009_c0_seq1::g.548] -indexing [comp1010_c0::comp1010_c0_seq1::g.552] -indexing 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[comp999_c0::comp999_c0_seq2::g.534] transdecoder is finished. See output files Trinity.fasta.transdecoder.* -indexing [comp0_c0::comp0_c0_seq1::g.1] -indexing [comp1000_c0::comp1000_c0_seq1::g.536] -indexing [comp1002_c0::comp1002_c0_seq1::g.537] -indexing [comp1004_c0::comp1004_c0_seq1::g.538] -indexing [comp1005_c0::comp1005_c0_seq1::g.540] -indexing [comp1006_c0::comp1006_c0_seq1::g.542] -indexing [comp1007_c0::comp1007_c0_seq1::g.543] -indexing [comp1008_c0::comp1008_c0_seq1::g.546] -indexing [comp1009_c0::comp1009_c0_seq1::g.548] -indexing [comp1010_c0::comp1010_c0_seq1::g.552] -indexing [comp1011_c0::comp1011_c0_seq1::g.553] -indexing [comp1012_c0::comp1012_c0_seq1::g.555] -indexing [comp1013_c0::comp1013_c0_seq1::g.556] -indexing [comp1014_c0::comp1014_c0_seq1::g.557] -indexing [comp1016_c0::comp1016_c0_seq1::g.558] -indexing [comp1016_c0::comp1016_c0_seq2::g.559] -indexing [comp1017_c0::comp1017_c0_seq1::g.560] -indexing [comp1018_c0::comp1018_c0_seq1::g.561] -indexing [comp1019_c0::comp1019_c0_seq1::g.563] -indexing 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[comp943_c0::comp943_c0_seq1::g.461] -indexing [comp944_c0::comp944_c0_seq1::g.463] -indexing [comp945_c0::comp945_c0_seq1::g.466] -indexing [comp946_c0::comp946_c0_seq1::g.467] -indexing [comp947_c0::comp947_c0_seq1::g.468] -indexing [comp948_c0::comp948_c0_seq1::g.469] -indexing [comp950_c0::comp950_c0_seq1::g.470] -indexing [comp951_c0::comp951_c0_seq1::g.471] -indexing [comp952_c0::comp952_c0_seq1::g.472] -indexing [comp953_c0::comp953_c0_seq1::g.474] -indexing [comp954_c0::comp954_c0_seq1::g.475] -indexing [comp955_c0::comp955_c0_seq1::g.476] -indexing [comp956_c0::comp956_c0_seq1::g.477] -indexing [comp956_c0::comp956_c0_seq2::g.478] -indexing [comp959_c0::comp959_c0_seq1::g.479] -indexing [comp960_c0::comp960_c0_seq1::g.480] -indexing [comp961_c0::comp961_c0_seq1::g.483] -indexing [comp962_c0::comp962_c0_seq1::g.484] -indexing [comp963_c0::comp963_c0_seq1::g.485] -indexing [comp964_c0::comp964_c0_seq1::g.487] -indexing [comp965_c0::comp965_c0_seq1::g.488] -indexing [comp966_c0::comp966_c0_seq1::g.489] -indexing [comp967_c0::comp967_c0_seq1::g.490] -indexing [comp968_c0::comp968_c0_seq1::g.491] -indexing [comp969_c0::comp969_c0_seq1::g.492] -indexing [comp970_c0::comp970_c0_seq1::g.494] -indexing [comp972_c0::comp972_c0_seq1::g.496] -indexing [comp973_c0::comp973_c0_seq1::g.497] -indexing [comp974_c0::comp974_c0_seq1::g.498] -indexing [comp976_c0::comp976_c0_seq1::g.499] -indexing [comp977_c0::comp977_c0_seq1::g.500] -indexing [comp978_c0::comp978_c0_seq1::g.501] -indexing [comp979_c0::comp979_c0_seq1::g.503] -indexing [comp980_c0::comp980_c0_seq1::g.504] -indexing [comp981_c0::comp981_c0_seq1::g.505] -indexing [comp982_c0::comp982_c0_seq2::g.506] -indexing [comp983_c0::comp983_c0_seq1::g.507] -indexing [comp984_c0::comp984_c0_seq1::g.509] -indexing [comp985_c0::comp985_c0_seq1::g.510] -indexing [comp985_c0::comp985_c0_seq2::g.511] -indexing [comp986_c0::comp986_c0_seq1::g.512] -indexing [comp987_c0::comp987_c0_seq1::g.513] -indexing [comp988_c0::comp988_c0_seq1::g.515] -indexing [comp989_c0::comp989_c0_seq1::g.518] -indexing [comp989_c0::comp989_c0_seq2::g.519] -indexing [comp98_c0::comp98_c0_seq1::g.10] -indexing [comp990_c0::comp990_c0_seq1::g.520] -indexing [comp991_c0::comp991_c0_seq1::g.521] -indexing [comp992_c0::comp992_c0_seq1::g.522] -indexing [comp992_c0::comp992_c0_seq2::g.523] -indexing [comp993_c0::comp993_c0_seq1::g.524] -indexing [comp994_c0::comp994_c0_seq1::g.526] -indexing [comp995_c0::comp995_c0_seq1::g.527] -indexing [comp996_c0::comp996_c0_seq1::g.528] -indexing [comp997_c0::comp997_c0_seq1::g.529] -indexing [comp998_c0::comp998_c0_seq1::g.530] -indexing [comp999_c0::comp999_c0_seq1::g.532] -indexing [comp999_c0::comp999_c0_seq2::g.534] -WARNING, comp1008_c0_seq1 has no genome representation... skipping -WARNING, comp1021_c0_seq1 has no genome representation... skipping -WARNING, comp1053_c0_seq1 has no genome representation... skipping -WARNING, comp1075_c0_seq1 has no genome representation... skipping Error, comp1112_c0::comp1112_c0_seq1::g.693 couldn't be fully propagated: $VAR1 = { 'contig' => 'III', 'asmbl' => 'comp1112_c0_seq1', 'orient' => '-', 'trans_id' => '', 'coords' => [ [ 2380416, '2380466' ], [ 2379717, '2380336' ] ], 'gene_id' => '' }; num_exons: 1 gene_type: protein-coding mid_pt: 1041 is_pseudogene: 0 gene_length: 2081 is_3prime_partial: 0 strand: + Model_feat_name: comp1112_c0::comp1112_c0_seq1::g.693::m.693 source: transdecoder asmbl_id: comp1112_c0_seq1 com_name: ORF type:complete len:513 (+),score=155.28 TU_feat_name: comp1112_c0::comp1112_c0_seq1::g.693 is_5prime_partial: 0 classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 2081 CDS-exon: 365, 1903 gene_span: 1-2081 model_span: 365-1903 Error, couldn't localize pt 1903 within coordsets: $VAR1 = [ [ 2379717, '2380336' ], [ 2380416, '2380466' ] ]; -WARNING, comp1124_c0_seq1 has no genome representation... skipping Error, comp1198_c0::comp1198_c0_seq1::g.795 couldn't be fully propagated: $VAR1 = { 'coords' => [ [ 402195, '402246' ], [ 402017, '402141' ], [ 401844, '401910' ], [ 401352, '401683' ] ], 'trans_id' => '', 'asmbl' => 'comp1198_c0_seq1', 'orient' => '-', 'contig' => 'II', 'gene_id' => '' }; is_pseudogene: 0 mid_pt: 299 gene_type: protein-coding num_exons: 1 is_3prime_partial: 0 source: transdecoder Model_feat_name: comp1198_c0::comp1198_c0_seq1::g.795::m.795 strand: + gene_length: 597 com_name: ORF type:internal len:199 (+),score=37.56 is_5prime_partial: 0 TU_feat_name: comp1198_c0::comp1198_c0_seq1::g.795 asmbl_id: comp1198_c0_seq1 classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 597 CDS-exon: 2, 595 gene_span: 1-597 model_span: 2-595 Error, couldn't localize pt 595 within coordsets: $VAR1 = [ [ 401352, '401683' ], [ 401844, '401910' ], [ 402017, '402141' ], [ 402195, '402246' ] ]; Error, comp242_c0::comp242_c0_seq1::g.25 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ '2213051', '2213441' ] ], 'asmbl' => 'comp242_c0_seq1', 'orient' => '-', 'contig' => 'I', 'gene_id' => '' }; asmbl_id: comp242_c0_seq1 com_name: ORF type:internal len:131 (+),score=23.76 TU_feat_name: comp242_c0::comp242_c0_seq1::g.25 is_5prime_partial: 0 classification: annotated_genes num_exons: 1 mid_pt: 196 gene_type: protein-coding is_pseudogene: 0 gene_length: 392 is_3prime_partial: 0 source: transdecoder Model_feat_name: comp242_c0::comp242_c0_seq1::g.25::m.25 strand: + gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 392 CDS-exon: 3, 392 gene_span: 1-392 model_span: 3-392 Error, couldn't localize pt 392 within coordsets: $VAR1 = [ [ '2213051', '2213441' ] ]; Error, comp366_c0::comp366_c0_seq1::g.41 couldn't be fully propagated: $VAR1 = { 'trans_id' => '', 'coords' => [ [ '3840968', '3841303' ] ], 'orient' => '-', 'asmbl' => 'comp366_c0_seq1', 'contig' => 'II', 'gene_id' => '' }; com_name: ORF type:internal len:114 (-),score=12.83 TU_feat_name: comp366_c0::comp366_c0_seq1::g.41 is_5prime_partial: 0 asmbl_id: comp366_c0_seq1 classification: annotated_genes is_pseudogene: 0 gene_type: protein-coding mid_pt: 170 num_exons: 1 is_3prime_partial: 0 strand: - source: transdecoder Model_feat_name: comp366_c0::comp366_c0_seq1::g.41::m.41 gene_length: 340 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 340, 1 CDS-exon: 339, 1 gene_span: 340-1 model_span: 339-1 Error, couldn't localize pt 339 within coordsets: $VAR1 = [ [ '3840968', '3841303' ] ]; -WARNING, comp504_c0_seq1 has no genome representation... skipping -WARNING, comp576_c0_seq1 has no genome representation... skipping Warning [1], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry comp591_c0::comp591_c0_seq1::g.86::m.86. Warning [2], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry comp642_c0::comp642_c0_seq1::g.133::m.133. Error, comp688_c0::comp688_c0_seq1::g.176 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', 'asmbl' => 'comp688_c0_seq1', 'orient' => '+', 'coords' => [ [ 380308, '380560' ], [ 380624, '381243' ] ], 'trans_id' => '', 'contig' => 'II' }; num_exons: 1 mid_pt: 1392 gene_type: protein-coding is_pseudogene: 0 gene_length: 2784 is_3prime_partial: 0 Model_feat_name: comp688_c0::comp688_c0_seq1::g.176::m.176 source: transdecoder strand: + asmbl_id: comp688_c0_seq1 com_name: ORF type:complete len:832 (+),score=172.54 TU_feat_name: comp688_c0::comp688_c0_seq1::g.176 is_5prime_partial: 0 classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 2784 CDS-exon: 83, 2578 gene_span: 1-2784 model_span: 83-2578 Error, couldn't localize pt [2578] within coordsets: $VAR1 = [ [ 380308, '380560' ], [ 380624, '381243' ] ]; -WARNING, comp701_c0_seq1 has no genome representation... skipping Error, comp765_c1::comp765_c1_seq1::g.257 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', 'contig' => 'I', 'coords' => [ [ '4506216', '4506869' ] ], 'trans_id' => '', 'asmbl' => 'comp765_c1_seq1', 'orient' => '-' }; gene_length: 655 source: transdecoder Model_feat_name: comp765_c1::comp765_c1_seq1::g.257::m.257 strand: + is_3prime_partial: 0 num_exons: 1 mid_pt: 328 gene_type: protein-coding is_pseudogene: 0 classification: annotated_genes asmbl_id: comp765_c1_seq1 TU_feat_name: comp765_c1::comp765_c1_seq1::g.257 is_5prime_partial: 0 com_name: ORF type:3prime_partial len:210 (+),score=22.04 gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 655 CDS-exon: 29, 655 gene_span: 1-655 model_span: 29-655 Error, couldn't localize pt 655 within coordsets: $VAR1 = [ [ '4506216', '4506869' ] ]; -WARNING, comp831_c0_seq1 has no genome representation... skipping Error, comp856_c0::comp856_c0_seq1::g.365 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', 'coords' => [ [ 3753910, '3754392' ], [ 3754438, '3755057' ] ], 'trans_id' => '', 'asmbl' => 'comp856_c0_seq1', 'orient' => '+', 'contig' => 'II' }; is_pseudogene: 0 num_exons: 1 gene_type: protein-coding mid_pt: 785 strand: + source: transdecoder Model_feat_name: comp856_c0::comp856_c0_seq1::g.365::m.365 is_3prime_partial: 0 gene_length: 1569 is_5prime_partial: 0 TU_feat_name: comp856_c0::comp856_c0_seq1::g.365 com_name: ORF type:complete len:448 (+),score=71.94 asmbl_id: comp856_c0_seq1 classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 1569 CDS-exon: 161, 1504 gene_span: 1-1569 model_span: 161-1504 Error, couldn't localize pt [1504] within coordsets: $VAR1 = [ [ 3753910, '3754392' ], [ 3754438, '3755057' ] ]; -WARNING, comp932_c0_seq1 has no genome representation... skipping Error, comp940_c0::comp940_c0_seq1::g.459 couldn't be fully propagated: $VAR1 = { 'gene_id' => '', 'orient' => '+', 'asmbl' => 'comp940_c0_seq1', 'coords' => [ [ 105641, '105736' ], [ 105785, '106404' ] ], 'trans_id' => '', 'contig' => 'III' }; is_pseudogene: 0 num_exons: 1 mid_pt: 1065 gene_type: protein-coding is_3prime_partial: 0 source: transdecoder Model_feat_name: comp940_c0::comp940_c0_seq1::g.459::m.459 strand: + gene_length: 2129 com_name: ORF type:complete len:577 (+),score=94.37 TU_feat_name: comp940_c0::comp940_c0_seq1::g.459 is_5prime_partial: 0 asmbl_id: comp940_c0_seq1 classification: annotated_genes gene_synonyms: mRNA_coords CDS_coords RNA-exon: 1, 2129 CDS-exon: 40, 1731 gene_span: 1-2129 model_span: 40-1731 Error, couldn't localize pt [1731] within coordsets: $VAR1 = [ [ 105641, '105736' ], [ 105785, '106404' ] ]; -WARNING, comp995_c0_seq1 has no genome representation... skipping Done. 635 / 656 transcript orfs could be propagated to the genome make[4]: Leaving directory '/build/transdecoder-5.0.1/sample_data/simple_transcriptome_target' Running example in $... make[4]: Entering directory '/build/transdecoder-5.0.1/sample_data/stringtie_example' ./runMe.sh #!/bin/bash -ve export PERL_HASH_SEED=0 ## generate alignment gff3 formatted output ../../util/cufflinks_gtf_to_alignment_gff3.pl stringtie_merged.gtf > stringtie_merged.gff3 ## generate transcripts fasta file # not including the genome here... too big, but here's how you'd do it. #../../util/cufflinks_gtf_genome_to_cdna_fasta.pl stringtie_merged.gtf genome.fasta > stringtie_merged.transcripts.fasta ## Extract the long ORFs ../../TransDecoder.LongOrfs -t stringtie_merged.transcripts.fasta -S -first extracting base frequencies, we'll need them later. CMD: /build/transdecoder-5.0.1/util/compute_base_probs.pl stringtie_merged.transcripts.fasta 1 > stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat CMD: touch stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat.ok - extracting ORFs from transcripts. -total transcripts to examine: 3501 [100/3501] = 2.86% done [200/3501] = 5.71% done [300/3501] = 8.57% done [400/3501] = 11.43% done [500/3501] = 14.28% done [600/3501] = 17.14% done [700/3501] = 19.99% done [800/3501] = 22.85% done [900/3501] = 25.71% done [1000/3501] = 28.56% done [1100/3501] = 31.42% done [1200/3501] = 34.28% done [1300/3501] = 37.13% done [1400/3501] = 39.99% done [1500/3501] = 42.84% done [1600/3501] = 45.70% done [1700/3501] = 48.56% done [1800/3501] = 51.41% done [1900/3501] = 54.27% done [2000/3501] = 57.13% done [2100/3501] = 59.98% done [2200/3501] = 62.84% done [2300/3501] = 65.70% done [2400/3501] = 68.55% done [2500/3501] = 71.41% done [2600/3501] = 74.26% done [2700/3501] = 77.12% done [2800/3501] = 79.98% done [2900/3501] = 82.83% done [3000/3501] = 85.69% done [3100/3501] = 88.55% done [3200/3501] = 91.40% done [3300/3501] = 94.26% done [3400/3501] = 97.12% done [3500/3501] = 99.97% done CMD: touch stringtie_merged.transcripts.fasta.transdecoder_dir/__longorfs.ok ################################# ### Done preparing long ORFs. ### ################################## Use file: stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.pep for Pfam and/or BlastP searches to enable homology-based coding region identification. Then, run TransDecoder.Predict for your final coding region predictions. ## Predict likely ORFs ../../TransDecoder.Predict -t stringtie_merged.transcripts.fasta * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds 5000 5000 > stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 * Running CMD: /build/transdecoder-5.0.1/util/exclude_similar_proteins.pl stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000 > stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr -skipping training candidate: Gene.974::NM_198270::g.974::m.974, not unique enough -skipping training candidate: Gene.2410::NR_104391::g.2410::m.2410, not unique enough -skipping training candidate: Gene.2394::NR_104395::g.2394::m.2394, not unique enough -skipping training candidate: Gene.138::NM_001282622::g.138::m.138, not unique enough -skipping training candidate: Gene.146::MSTRG.376.1::g.146::m.146, not unique enough -skipping training candidate: Gene.2124::MSTRG.839.3::g.2124::m.2124, not unique enough -skipping training candidate: Gene.2414::NR_104394::g.2414::m.2414, not unique enough -skipping training candidate: Gene.743::MSTRG.397.18::g.743::m.743, not unique enough -skipping training candidate: Gene.4236::NM_020717::g.4236::m.4236, not unique enough -skipping training candidate: Gene.2393::MSTRG.505.14::g.2393::m.2393, not unique enough -skipping training candidate: Gene.3630::NM_001136024::g.3630::m.3630, not unique enough -skipping training candidate: Gene.1226::MSTRG.538.2::g.1226::m.1226, not unique enough -skipping training candidate: Gene.1865::NM_001291868::g.1865::m.1865, not unique enough -skipping training candidate: Gene.879::MSTRG.236.1::g.879::m.879, not unique enough -skipping training candidate: Gene.3478::MSTRG.404.8::g.3478::m.3478, not unique enough -skipping training candidate: Gene.3403::NM_001555::g.3403::m.3403, not unique enough -skipping training candidate: Gene.2623::NM_001282224::g.2623::m.2623, not unique enough -skipping training candidate: Gene.3285::NM_001170962::g.3285::m.3285, not unique enough -skipping training candidate: Gene.3696::NM_001291416::g.3696::m.3696, not unique enough -skipping training candidate: Gene.3689::NM_021140::g.3689::m.3689, not unique enough -skipping training candidate: Gene.131::MSTRG.376.9::g.131::m.131, not unique enough -skipping training candidate: Gene.1193::NM_014710::g.1193::m.1193, not unique enough -skipping training candidate: Gene.1194::NM_001099411::g.1194::m.1194, not unique enough -skipping training candidate: Gene.1195::NM_001184727::g.1195::m.1195, not unique enough -skipping training candidate: Gene.148::NM_001146702::g.148::m.148, not unique enough -skipping training candidate: Gene.3681::MSTRG.258.8::g.3681::m.3681, not unique enough -skipping training candidate: Gene.1558::NM_005096::g.1558::m.1558, not unique enough -skipping training candidate: Gene.3691::MSTRG.258.9::g.3691::m.3691, not unique enough -skipping training candidate: Gene.1553::MSTRG.502.3::g.1553::m.1553, not unique enough -skipping training candidate: Gene.1556::NM_001171162::g.1556::m.1556, not unique enough -skipping training candidate: Gene.1560::MSTRG.502.2::g.1560::m.1560, not unique enough -skipping training candidate: Gene.1562::MSTRG.502.1::g.1562::m.1562, not unique enough -skipping training candidate: Gene.3687::NM_001291417::g.3687::m.3687, not unique enough -skipping training candidate: Gene.3633::NM_001168360::g.3633::m.3633, not unique enough -skipping training candidate: Gene.3638::NM_032969::g.3638::m.3638, not unique enough -skipping training candidate: Gene.3639::NM_001168363::g.3639::m.3639, not unique enough -skipping training candidate: Gene.877::MSTRG.236.3::g.877::m.877, not unique enough -skipping training candidate: Gene.3634::NM_001168362::g.3634::m.3634, not unique enough -skipping training candidate: Gene.3694::NM_001291418::g.3694::m.3694, not unique enough -skipping training candidate: Gene.833::NM_001169123::g.833::m.833, not unique enough -skipping training candidate: Gene.2152::MSTRG.570.10::g.2152::m.2152, not unique enough -skipping training candidate: Gene.3679::NR_111960::g.3679::m.3679, not unique enough -skipping training candidate: Gene.842::NM_001169122::g.842::m.842, not unique enough -skipping training candidate: Gene.845::NM_001169124::g.845::m.845, not unique enough -skipping training candidate: Gene.839::NM_001169125::g.839::m.839, not unique enough -skipping training candidate: Gene.3754::MSTRG.848.14::g.3754::m.3754, not unique enough -skipping training candidate: Gene.3757::NM_001042749::g.3757::m.3757, not unique enough -skipping training candidate: Gene.3759::MSTRG.848.13::g.3759::m.3759, not unique enough -skipping training candidate: Gene.3760::MSTRG.848.7::g.3760::m.3760, not unique enough -skipping training candidate: Gene.3761::MSTRG.848.12::g.3761::m.3761, not unique enough -skipping training candidate: Gene.1629::NM_000425::g.1629::m.1629, not unique enough -skipping training candidate: Gene.1635::NM_024003::g.1635::m.1635, not unique enough -skipping training candidate: Gene.1641::NM_001143963::g.1641::m.1641, not unique enough -skipping training candidate: Gene.2143::MSTRG.477.3::g.2143::m.2143, not unique enough -skipping training candidate: Gene.2144::NM_012310::g.2144::m.2144, not unique enough -skipping training candidate: Gene.3748::MSTRG.848.11::g.3748::m.3748, not unique enough -skipping training candidate: Gene.3750::NM_001042751::g.3750::m.3750, not unique enough -skipping training candidate: Gene.3751::NM_006603::g.3751::m.3751, not unique enough -skipping training candidate: Gene.3752::MSTRG.848.1::g.3752::m.3752, not unique enough -skipping training candidate: Gene.3753::MSTRG.848.4::g.3753::m.3753, not unique enough -skipping training candidate: Gene.3755::MSTRG.848.2::g.3755::m.3755, not unique enough -skipping training candidate: Gene.3756::NM_001282418::g.3756::m.3756, not unique enough -skipping training candidate: Gene.3758::MSTRG.848.6::g.3758::m.3758, not unique enough -skipping training candidate: Gene.2234::NM_004022::g.2234::m.2234, not unique enough -skipping training candidate: Gene.2233::NM_004013::g.2233::m.2233, not unique enough -skipping training candidate: Gene.2154::MSTRG.570.9::g.2154::m.2154, not unique enough -skipping training candidate: Gene.1723::MSTRG.147.2::g.1723::m.1723, not unique enough -skipping training candidate: Gene.888::NM_006044::g.888::m.888, not unique enough -skipping training candidate: Gene.890::MSTRG.331.3::g.890::m.890, not unique enough -skipping training candidate: Gene.894::MSTRG.331.2::g.894::m.894, not unique enough -skipping training candidate: Gene.896::MSTRG.331.4::g.896::m.896, not unique enough -skipping training candidate: Gene.3394::NM_001281463::g.3394::m.3394, not unique enough -skipping training candidate: Gene.1311::NM_001122670::g.1311::m.1311, not unique enough -skipping training candidate: Gene.1727::MSTRG.147.3::g.1727::m.1727, not unique enough -skipping training candidate: Gene.2069::NM_021949::g.2069::m.2069, not unique enough -skipping training candidate: Gene.2820::MSTRG.456.2::g.2820::m.2820, not unique enough -skipping training candidate: Gene.2807::NM_001130860::g.2807::m.2807, not unique enough -skipping training candidate: Gene.1315::NM_001172436::g.1315::m.1315, not unique enough -skipping training candidate: Gene.348::MSTRG.442.1::g.348::m.348, not unique enough -skipping training candidate: Gene.2223::NM_004023::g.2223::m.2223, not unique enough -skipping training candidate: Gene.380::MSTRG.945.2::g.380::m.380, not unique enough -skipping training candidate: Gene.384::MSTRG.945.3::g.384::m.384, not unique enough -skipping training candidate: Gene.386::MSTRG.945.8::g.386::m.386, not unique enough -skipping training candidate: Gene.4270::MSTRG.518.1::g.4270::m.4270, not unique enough -skipping training candidate: Gene.391::NM_001010986::g.391::m.391, not unique enough -skipping training candidate: Gene.387::MSTRG.945.1::g.387::m.387, not unique enough -skipping training candidate: Gene.2227::NM_004020::g.2227::m.2227, not unique enough -skipping training candidate: Gene.2501::NM_153280::g.2501::m.2501, not unique enough -skipping training candidate: Gene.3684::NM_001291421::g.3684::m.3684, not unique enough -skipping training candidate: Gene.3353::NM_001105243::g.3353::m.3353, not unique enough -skipping training candidate: Gene.2865::NM_020766::g.2865::m.2865, not unique enough -skipping training candidate: Gene.3086::NM_007309::g.3086::m.3086, not unique enough -skipping training candidate: Gene.2901::NM_005756::g.2901::m.2901, not unique enough -skipping training candidate: Gene.3015::NM_001113490::g.3015::m.3015, not unique enough -skipping training candidate: Gene.676::NM_001079859::g.676::m.676, not unique enough -skipping training candidate: Gene.1::NM_001184833::g.1::m.1, not unique enough -skipping training candidate: Gene.383::MSTRG.945.6::g.383::m.383, not unique enough -skipping training candidate: Gene.3635::NM_001168361::g.3635::m.3635, not unique enough -skipping training candidate: Gene.1993::NM_001079860::g.1993::m.1993, not unique enough -skipping training candidate: Gene.3189::NM_001184836::g.3189::m.3189, not unique enough -skipping training candidate: Gene.3661::NM_001184837::g.3661::m.3661, not unique enough -skipping training candidate: Gene.81::NM_001257231::g.81::m.81, not unique enough -skipping training candidate: Gene.674::NM_001184835::g.674::m.674, not unique enough -skipping training candidate: Gene.1369::NM_001282875::g.1369::m.1369, not unique enough -skipping training candidate: Gene.1367::NM_003069::g.1367::m.1367, not unique enough -skipping training candidate: Gene.886::MSTRG.88.1::g.886::m.886, not unique enough -skipping training candidate: Gene.3727::MSTRG.387.2::g.3727::m.3727, not unique enough -skipping training candidate: Gene.3740::MSTRG.387.1::g.3740::m.3740, not unique enough -skipping training candidate: Gene.1933::MSTRG.860.6::g.1933::m.1933, not unique enough -skipping training candidate: Gene.2745::NM_001184834::g.2745::m.2745, not unique enough -skipping training candidate: Gene.3345::NM_138636::g.3345::m.3345, not unique enough -skipping training candidate: Gene.2655::NM_181673::g.2655::m.2655, not unique enough -skipping training candidate: Gene.3481::NM_001271184::g.3481::m.3481, not unique enough -skipping training candidate: Gene.64::MSTRG.759.13::g.64::m.64, not unique enough -skipping training candidate: Gene.66::MSTRG.759.12::g.66::m.66, not unique enough -skipping training candidate: Gene.2753::NM_001037343::g.2753::m.2753, not unique enough -skipping training candidate: Gene.3731::NM_015107::g.3731::m.3731, not unique enough -skipping training candidate: Gene.2581::NM_014725::g.2581::m.2581, not unique enough -skipping training candidate: Gene.2878::NM_001142504::g.2878::m.2878, not unique enough -skipping training candidate: Gene.389::MSTRG.945.7::g.389::m.389, not unique enough -skipping training candidate: Gene.2916::NM_001168647::g.2916::m.2916, not unique enough -skipping training candidate: Gene.127::NM_001099855::g.127::m.127, not unique enough -skipping training candidate: Gene.2229::NM_004014::g.2229::m.2229, not unique enough -skipping training candidate: Gene.433::MSTRG.110.1::g.433::m.433, not unique enough -skipping training candidate: Gene.2815::NM_001282141::g.2815::m.2815, not unique enough -skipping training candidate: Gene.4036::NM_001666::g.4036::m.4036, not unique enough -skipping training candidate: Gene.3476::NM_001271183::g.3476::m.3476, not unique enough -skipping training candidate: Gene.63::NM_001257237::g.63::m.63, not unique enough -skipping training candidate: Gene.65::NM_001257230::g.65::m.65, not unique enough -skipping training candidate: Gene.80::NM_001257234::g.80::m.80, not unique enough -skipping training candidate: Gene.832::NM_001170628::g.832::m.832, not unique enough -skipping training candidate: Gene.2675::NM_015075::g.2675::m.2675, not unique enough -skipping training candidate: Gene.3398::NM_001587::g.3398::m.3398, not unique enough -skipping training candidate: Gene.3729::NM_001184897::g.3729::m.3729, not unique enough -skipping training candidate: Gene.3017::NM_001171879::g.3017::m.3017, not unique enough -skipping training candidate: Gene.77::MSTRG.759.11::g.77::m.77, not unique enough -skipping training candidate: Gene.426::MSTRG.110.4::g.426::m.426, not unique enough -skipping training candidate: Gene.2000::NM_005676::g.2000::m.2000, not unique enough -skipping training candidate: Gene.422::MSTRG.110.5::g.422::m.422, not unique enough -skipping training candidate: Gene.1996::NM_001204467::g.1996::m.1996, not unique enough -skipping training candidate: Gene.1223::NM_031276::g.1223::m.1223, not unique enough -skipping training candidate: Gene.3611::NM_005369::g.3611::m.3611, not unique enough -skipping training candidate: Gene.1576::MSTRG.250.1::g.1576::m.1576, not unique enough -skipping training candidate: Gene.3734::MSTRG.387.3::g.3734::m.3734, not unique enough -skipping training candidate: Gene.4046::MSTRG.1005.1::g.4046::m.4046, not unique enough -skipping training candidate: Gene.1262::NM_001300788::g.1262::m.1262, not unique enough -skipping training candidate: Gene.2650::MSTRG.508.1::g.2650::m.2650, not unique enough -skipping training candidate: Gene.1580::NM_001126054::g.1580::m.1580, not unique enough -skipping training candidate: Gene.3862::NM_003588::g.3862::m.3862, not unique enough -skipping training candidate: Gene.1578::NM_001126055::g.1578::m.1578, not unique enough -skipping training candidate: Gene.434::MSTRG.110.7::g.434::m.434, not unique enough -skipping training candidate: Gene.3646::NM_001184965::g.3646::m.3646, not unique enough -skipping training candidate: Gene.1022::NM_001085354::g.1022::m.1022, not unique enough -skipping training candidate: Gene.2907::NM_001168648::g.2907::m.2907, not unique enough -skipping training candidate: Gene.3861::NM_001079872::g.3861::m.3861, not unique enough -skipping training candidate: Gene.2850::NM_007325::g.2850::m.2850, not unique enough -skipping training candidate: Gene.2812::NM_014799::g.2812::m.2812, not unique enough -skipping training candidate: Gene.424::MSTRG.110.8::g.424::m.424, not unique enough -skipping training candidate: Gene.3397::MSTRG.855.3::g.3397::m.3397, not unique enough -skipping training candidate: Gene.2891::NM_001171184::g.2891::m.2891, not unique enough -skipping training candidate: Gene.432::MSTRG.110.6::g.432::m.432, not unique enough -skipping training candidate: Gene.3742::NM_001184898::g.3742::m.3742, not unique enough -skipping training candidate: Gene.1810::MSTRG.276.2::g.1810::m.1810, not unique enough -skipping training candidate: Gene.3548::NM_024597::g.3548::m.3548, not unique enough -skipping training candidate: Gene.2119::MSTRG.839.4::g.2119::m.2119, not unique enough -skipping training candidate: Gene.3898::NM_007156::g.3898::m.3898, not unique enough -skipping training candidate: Gene.68::MSTRG.759.1::g.68::m.68, not unique enough -skipping training candidate: Gene.75::MSTRG.759.21::g.75::m.75, not unique enough -skipping training candidate: Gene.86::MSTRG.759.22::g.86::m.86, not unique enough -skipping training candidate: Gene.1483::NM_182540::g.1483::m.1483, not unique enough -skipping training candidate: Gene.984::NM_001171878::g.984::m.984, not unique enough -skipping training candidate: Gene.2236::NM_152633::g.2236::m.2236, not unique enough -skipping training candidate: Gene.347::MSTRG.442.2::g.347::m.347, not unique enough -skipping training candidate: Gene.3546::NM_001173516::g.3546::m.3546, not unique enough -skipping training candidate: Gene.1501::MSTRG.921.2::g.1501::m.1501, not unique enough -skipping training candidate: Gene.2004::NM_001204466::g.2004::m.2004, not unique enough -skipping training candidate: Gene.2011::NM_152856::g.2011::m.2011, not unique enough -skipping training candidate: Gene.60::MSTRG.759.20::g.60::m.60, not unique enough -skipping training candidate: Gene.3399::MSTRG.855.4::g.3399::m.3399, not unique enough -skipping training candidate: Gene.2909::NM_001168649::g.2909::m.2909, not unique enough -skipping training candidate: Gene.1831::NM_001077445::g.1831::m.1831, not unique enough -skipping training candidate: Gene.2115::MSTRG.839.6::g.2115::m.2115, not unique enough -skipping training candidate: Gene.875::NM_001144004::g.875::m.875, not unique enough -skipping training candidate: Gene.930::NM_001144010::g.930::m.930, not unique enough -skipping training candidate: Gene.1534::NM_001144003::g.1534::m.1534, not unique enough -skipping training candidate: Gene.2951::NM_001144009::g.2951::m.2951, not unique enough -skipping training candidate: Gene.3231::NM_001144005::g.3231::m.3231, not unique enough -skipping training candidate: Gene.3347::NM_001144006::g.3347::m.3347, not unique enough -skipping training candidate: Gene.3667::NM_032539::g.3667::m.3667, not unique enough -skipping training candidate: Gene.3896::NM_139289::g.3896::m.3896, not unique enough -skipping training candidate: Gene.2121::MSTRG.839.5::g.2121::m.2121, not unique enough -skipping training candidate: Gene.3543::NM_001173517::g.3543::m.3543, not unique enough -skipping training candidate: Gene.585::NM_001184875::g.585::m.585, not unique enough -skipping training candidate: Gene.591::NM_138437::g.591::m.591, not unique enough -skipping training candidate: Gene.595::NM_001199818::g.595::m.595, not unique enough -skipping training candidate: Gene.602::NM_001004051::g.602::m.602, not unique enough -skipping training candidate: Gene.606::NM_001184874::g.606::m.606, not unique enough -skipping training candidate: Gene.425::MSTRG.110.11::g.425::m.425, not unique enough -skipping training candidate: Gene.642::NM_001184749::g.642::m.642, not unique enough -skipping training candidate: Gene.647::NM_173078::g.647::m.647, not unique enough -skipping training candidate: Gene.84::MSTRG.759.24::g.84::m.84, not unique enough -skipping training candidate: Gene.3310::NM_018977::g.3310::m.3310, not unique enough -skipping training candidate: Gene.3650::NM_001184966::g.3650::m.3650, not unique enough -skipping training candidate: Gene.1833::NM_014735::g.1833::m.1833, not unique enough -skipping training candidate: Gene.3612::NM_001171877::g.3612::m.3612, not unique enough -skipping training candidate: Gene.1068::NM_001282146::g.1068::m.1068, not unique enough -skipping training candidate: Gene.1087::NM_001282145::g.1087::m.1087, not unique enough -skipping training candidate: Gene.3302::NM_020742::g.3302::m.3302, not unique enough -skipping training candidate: Gene.4088::NM_001127898::g.4088::m.4088, not unique enough -skipping training candidate: Gene.3816::NM_001005332::g.3816::m.3816, not unique enough -skipping training candidate: Gene.3309::NM_001166660::g.3309::m.3309, not unique enough -skipping training candidate: Gene.1130::MSTRG.189.10::g.1130::m.1130, not unique enough -skipping training candidate: Gene.1131::NM_001178085::g.1131::m.1131, not unique enough -skipping training candidate: Gene.1132::MSTRG.189.1::g.1132::m.1132, not unique enough -skipping training candidate: Gene.1135::NM_001178084::g.1135::m.1135, not unique enough -skipping training candidate: Gene.1138::NM_003410::g.1138::m.1138, not unique enough -skipping training candidate: Gene.1141::MSTRG.189.7::g.1141::m.1141, not unique enough -skipping training candidate: Gene.1489::MSTRG.921.3::g.1489::m.1489, not unique enough -skipping training candidate: Gene.431::MSTRG.110.10::g.431::m.431, not unique enough -skipping training candidate: Gene.3962::NM_001287242::g.3962::m.3962, not unique enough -skipping training candidate: Gene.3210::MSTRG.76.2::g.3210::m.3210, not unique enough -skipping training candidate: Gene.240::MSTRG.279.6::g.240::m.240, not unique enough -skipping training candidate: Gene.248::MSTRG.279.1::g.248::m.248, not unique enough -skipping training candidate: Gene.1129::MSTRG.189.11::g.1129::m.1129, not unique enough -skipping training candidate: Gene.1134::MSTRG.189.9::g.1134::m.1134, not unique enough -skipping training candidate: Gene.232::NM_153380::g.232::m.232, not unique enough -skipping training candidate: Gene.238::MSTRG.279.11::g.238::m.238, not unique enough -skipping training candidate: Gene.242::MSTRG.279.2::g.242::m.242, not unique enough -skipping training candidate: Gene.244::MSTRG.279.3::g.244::m.244, not unique enough -skipping training candidate: Gene.246::NM_007130::g.246::m.246, not unique enough -skipping training candidate: Gene.252::MSTRG.279.10::g.252::m.252, not unique enough -skipping training candidate: Gene.3810::NM_006986::g.3810::m.3810, not unique enough -skipping training candidate: Gene.4038::MSTRG.1005.3::g.4038::m.4038, not unique enough -skipping training candidate: Gene.511::NM_001271696::g.511::m.511, not unique enough -skipping training candidate: Gene.234::MSTRG.279.8::g.234::m.234, not unique enough -skipping training candidate: Gene.236::MSTRG.279.7::g.236::m.236, not unique enough -skipping training candidate: Gene.4347::NM_024778::g.4347::m.4347, not unique enough -skipping training candidate: Gene.3503::NM_032591::g.3503::m.3503, not unique enough -skipping training candidate: Gene.2722::NM_152780::g.2722::m.2722, not unique enough -skipping training candidate: Gene.3957::NM_013423::g.3957::m.3957, not unique enough -skipping training candidate: Gene.3291::NM_032512::g.3291::m.3291, not unique enough -skipping training candidate: Gene.2911::MSTRG.166.5::g.2911::m.2911, not unique enough -skipping training candidate: Gene.4085::NM_001282163::g.4085::m.4085, not unique enough -skipping training candidate: Gene.3959::NM_006125::g.3959::m.3959, not unique enough -skipping training candidate: Gene.1080::MSTRG.604.2::g.1080::m.1080, not unique enough -skipping training candidate: Gene.1439::NM_001243963::g.1439::m.1439, not unique enough -skipping training candidate: Gene.2511::NM_001184782::g.2511::m.2511, not unique enough -skipping training candidate: Gene.3808::NM_001272061_dup1::g.3808::m.3808, not unique enough -skipping training candidate: Gene.1879::MSTRG.654.4::g.1879::m.1879, not unique enough -skipping training candidate: Gene.1883::NM_006733::g.1883::m.1883, not unique enough -skipping training candidate: Gene.1885::MSTRG.654.1::g.1885::m.1885, not unique enough -skipping training candidate: Gene.1852::MSTRG.925.2::g.1852::m.1852, not unique enough -skipping training candidate: Gene.1855::NM_001163280::g.1855::m.1855, not unique enough -skipping training candidate: Gene.2068::NR_033717::g.2068::m.2068, not unique enough -skipping training candidate: Gene.2435::NM_001177466::g.2435::m.2435, not unique enough -skipping training candidate: Gene.507::NM_001271698::g.507::m.507, not unique enough -skipping training candidate: Gene.4086::NM_000084::g.4086::m.4086, not unique enough -skipping training candidate: Gene.1887::MSTRG.654.3::g.1887::m.1887, not unique enough -skipping training candidate: Gene.2181::NM_001272062::g.2181::m.2181, not unique enough -skipping training candidate: Gene.2184::NM_001272063::g.2184::m.2184, not unique enough -skipping training candidate: Gene.3136::MSTRG.308.3::g.3136::m.3136, not unique enough -skipping training candidate: Gene.3811::NM_030801_dup1::g.3811::m.3811, not unique enough -skipping training candidate: Gene.3813::NM_177535_dup1::g.3813::m.3813, not unique enough -skipping training candidate: Gene.2186::NM_177537::g.2186::m.2186, not unique enough -skipping training candidate: Gene.3817::NM_177537_dup1::g.3817::m.3817, not unique enough -skipping training candidate: Gene.2620::MSTRG.572.4::g.2620::m.2620, not unique enough -skipping training candidate: Gene.510::NM_001271699::g.510::m.510, not unique enough -skipping training candidate: Gene.509::NM_001271697::g.509::m.509, not unique enough -skipping training candidate: Gene.3139::MSTRG.308.4::g.3139::m.3139, not unique enough -skipping training candidate: Gene.47::NM_001163335::g.47::m.47, not unique enough -skipping training candidate: Gene.2348::NM_138780::g.2348::m.2348, not unique enough -skipping training candidate: Gene.3172::NM_001271835::g.3172::m.3172, not unique enough -skipping training candidate: Gene.3181::NM_001163323::g.3181::m.3181, not unique enough -skipping training candidate: Gene.2727::NM_001168466::g.2727::m.2727, not unique enough -skipping training candidate: Gene.1724::MSTRG.147.4::g.1724::m.1724, not unique enough -skipping training candidate: Gene.2624::MSTRG.572.5::g.2624::m.2624, not unique enough -skipping training candidate: Gene.61::MSTRG.759.10::g.61::m.61, not unique enough -skipping training candidate: Gene.70::MSTRG.759.2::g.70::m.70, not unique enough -skipping training candidate: Gene.72::MSTRG.759.9::g.72::m.72, not unique enough -skipping training candidate: Gene.449::NM_001166221::g.449::m.449, not unique enough -skipping training candidate: Gene.1199::NM_019117::g.1199::m.1199, not unique enough -skipping training candidate: Gene.1892::NM_001170649::g.1892::m.1892, not unique enough -skipping training candidate: Gene.1894::MSTRG.451.1::g.1894::m.1894, not unique enough -skipping training candidate: Gene.2527::MSTRG.929.1::g.2527::m.2527, not unique enough -skipping training candidate: Gene.140::MSTRG.376.2::g.140::m.140, not unique enough -skipping training candidate: Gene.2729::MSTRG.161.3::g.2729::m.2729, not unique enough -skipping training candidate: Gene.4177::NM_152787::g.4177::m.4177, not unique enough -skipping training candidate: Gene.4180::MSTRG.208.2::g.4180::m.4180, not unique enough -skipping training candidate: Gene.2730::MSTRG.161.2::g.2730::m.2730, not unique enough -skipping training candidate: Gene.133::MSTRG.376.4::g.133::m.133, not unique enough -skipping training candidate: Gene.3480::NM_177556::g.3480::m.3480, not unique enough -skipping training candidate: Gene.3483::NM_016157::g.3483::m.3483, not unique enough -skipping training candidate: Gene.865::NM_001173487::g.865::m.865, not unique enough -skipping training candidate: Gene.2074::NM_052817::g.2074::m.2074, not unique enough -skipping training candidate: Gene.358::MSTRG.215.2::g.358::m.358, not unique enough -skipping training candidate: Gene.955::NM_001306193::g.955::m.955, not unique enough -skipping training candidate: Gene.3011::NM_152423::g.3011::m.3011, not unique enough -skipping training candidate: Gene.3183::NM_001163321::g.3183::m.3183, not unique enough -skipping training candidate: Gene.2619::MSTRG.572.6::g.2619::m.2619, not unique enough -skipping training candidate: Gene.3941::NM_001282754::g.3941::m.3941, not unique enough -skipping training candidate: Gene.259::NM_001171135::g.259::m.259, not unique enough -skipping training candidate: Gene.260::NM_001171136::g.260::m.260, not unique enough -skipping training candidate: Gene.2962::NM_001303515::g.2962::m.2962, not unique enough -skipping training candidate: Gene.4213::MSTRG.922.1::g.4213::m.4213, not unique enough -skipping training candidate: Gene.250::MSTRG.279.5::g.250::m.250, not unique enough -skipping training candidate: Gene.1010::NM_022117::g.1010::m.1010, not unique enough -skipping training candidate: Gene.2025::NM_001178107::g.2025::m.2025, not unique enough -skipping training candidate: Gene.864::NM_001173488::g.864::m.864, not unique enough -skipping training candidate: Gene.917::NM_144657::g.917::m.917, not unique enough -skipping training candidate: Gene.2031::NM_001178108::g.2031::m.2031, not unique enough -skipping training candidate: Gene.3966::NR_109776::g.3966::m.3966, not unique enough -skipping training candidate: Gene.2028::NM_007150::g.2028::m.2028, not unique enough -skipping training candidate: Gene.2139::NM_001303516::g.2139::m.2139, not unique enough -skipping training candidate: Gene.466::NM_198881::g.466::m.466, not unique enough -skipping training candidate: Gene.128::MSTRG.376.3::g.128::m.128, not unique enough -skipping training candidate: Gene.143::MSTRG.376.8::g.143::m.143, not unique enough -skipping training candidate: Gene.4175::MSTRG.208.3::g.4175::m.4175, not unique enough -skipping training candidate: Gene.1919::NM_001025242::g.1919::m.1919, not unique enough -skipping training candidate: Gene.4334::MSTRG.345.1::g.4334::m.4334, not unique enough -skipping training candidate: Gene.3473::NR_073148::g.3473::m.3473, not unique enough -skipping training candidate: Gene.2723::NM_001168467::g.2723::m.2723, not unique enough -skipping training candidate: Gene.3137::MSTRG.308.1::g.3137::m.3137, not unique enough -skipping training candidate: Gene.1895::NM_001170650::g.1895::m.1895, not unique enough -skipping training candidate: Gene.2380::NM_001721::g.2380::m.2380, not unique enough -skipping training candidate: Gene.3014::NM_133265::g.3014::m.3014, not unique enough -skipping training candidate: Gene.3227::NM_001303513::g.3227::m.3227, not unique enough -skipping training candidate: Gene.2806::NM_006777::g.2806::m.2806, not unique enough -skipping training candidate: Gene.690::NM_001129896::g.690::m.690, not unique enough -skipping training candidate: Gene.2863::NM_001174068::g.2863::m.2863, not unique enough -skipping training candidate: Gene.12::MSTRG.732.1::g.12::m.12, not unique enough -skipping training candidate: Gene.13::NM_004458::g.13::m.13, not unique enough -skipping training candidate: Gene.15::MSTRG.732.2::g.15::m.15, not unique enough -skipping training candidate: Gene.3322::NM_133499::g.3322::m.3322, not unique enough -skipping training candidate: Gene.4214::NM_006359::g.4214::m.4214, not unique enough -skipping training candidate: Gene.720::NM_033290::g.720::m.720, not unique enough -skipping training candidate: Gene.2264::NM_001098624::g.2264::m.2264, not unique enough -skipping training candidate: Gene.3431::NM_001193277::g.3431::m.3431, not unique enough -skipping training candidate: Gene.1072::NM_001256944::g.1072::m.1072, not unique enough -skipping training candidate: Gene.4256::NM_004192::g.4256::m.4256, not unique enough -skipping training candidate: Gene.500::NM_031892::g.500::m.500, not unique enough -skipping training candidate: Gene.1454::NM_003828::g.1454::m.1454, not unique enough -skipping training candidate: Gene.2652::MSTRG.508.2::g.2652::m.2652, not unique enough -skipping training candidate: Gene.4346::NR_110311::g.4346::m.4346, not unique enough -skipping training candidate: Gene.103::NM_001127197::g.103::m.103, not unique enough -skipping training candidate: Gene.106::MSTRG.862.3::g.106::m.106, not unique enough -skipping training candidate: Gene.109::NM_001421::g.109::m.109, not unique enough -skipping training candidate: Gene.112::MSTRG.862.4::g.112::m.112, not unique enough -skipping training candidate: Gene.3088::MSTRG.641.6::g.3088::m.3088, not unique enough -skipping training candidate: Gene.3606::NM_001356::g.3606::m.3606, not unique enough -skipping training candidate: Gene.2195::NM_007137::g.2195::m.2195, not unique enough -skipping training candidate: Gene.2197::MSTRG.292.4::g.2197::m.2197, not unique enough -skipping training candidate: Gene.2215::NM_004016::g.2215::m.2215, not unique enough -skipping training candidate: Gene.3599::NM_001193416::g.3599::m.3599, not unique enough -skipping training candidate: Gene.610::NM_001303514::g.610::m.610, not unique enough -skipping training candidate: Gene.2033::NM_001178109::g.2033::m.2033, not unique enough -skipping training candidate: Gene.859::NM_000061::g.859::m.859, not unique enough -skipping training candidate: Gene.1656::NM_001080975::g.1656::m.1656, not unique enough -skipping training candidate: Gene.983::NM_001168299::g.983::m.983, not unique enough -skipping training candidate: Gene.2282::MSTRG.468.4::g.2282::m.2282, not unique enough -skipping training candidate: Gene.1528::NM_001282201::g.1528::m.1528, not unique enough -skipping training candidate: Gene.979::NM_033495::g.979::m.979, not unique enough -skipping training candidate: Gene.2238::MSTRG.113.1::g.2238::m.2238, not unique enough -skipping training candidate: Gene.4261::NM_001173474::g.4261::m.4261, not unique enough -skipping training candidate: Gene.497::MSTRG.151.7::g.497::m.497, not unique enough -skipping training candidate: Gene.978::NM_001168300::g.978::m.978, not unique enough -skipping training candidate: Gene.4211::NM_001177651::g.4211::m.4211, not unique enough -skipping training candidate: Gene.916::MSTRG.601.4::g.916::m.916, not unique enough -skipping training candidate: Gene.2222::NM_004018::g.2222::m.2222, not unique enough -skipping training candidate: Gene.3604::NM_001193417::g.3604::m.3604, not unique enough -skipping training candidate: Gene.79::MSTRG.759.25::g.79::m.79, not unique enough -skipping training candidate: Gene.3872::NM_001184767::g.3872::m.3872, not unique enough -skipping training candidate: Gene.1530::NM_001190255::g.1530::m.1530, not unique enough -skipping training candidate: Gene.2226::NM_004015::g.2226::m.2226, not unique enough -skipping training candidate: Gene.2284::NM_145119::g.2284::m.2284, not unique enough -skipping training candidate: Gene.977::NM_001168301::g.977::m.977, not unique enough -skipping training candidate: Gene.981::NM_001168302::g.981::m.981, not unique enough -skipping training candidate: Gene.1142::NM_001178086::g.1142::m.1142, not unique enough -skipping training candidate: Gene.2698::NM_006962::g.2698::m.2698, not unique enough -skipping training candidate: Gene.2701::MSTRG.294.4::g.2701::m.2701, not unique enough -skipping training candidate: Gene.4258::NM_001173473::g.4258::m.4258, not unique enough -skipping training candidate: Gene.3964::MSTRG.82.6::g.3964::m.3964, not unique enough -skipping training candidate: Gene.1922::NM_001025243::g.1922::m.1922, not unique enough -skipping training candidate: Gene.915::NM_001177478::g.915::m.915, not unique enough -skipping training candidate: Gene.1747::NM_002024::g.1747::m.1747, not unique enough -skipping training candidate: Gene.2639::MSTRG.669.2::g.2639::m.2639, not unique enough -skipping training candidate: Gene.2640::MSTRG.669.1::g.2640::m.2640, not unique enough -skipping training candidate: Gene.2641::NM_177949::g.2641::m.2641, not unique enough -skipping training candidate: Gene.2642::MSTRG.669.10::g.2642::m.2642, not unique enough -skipping training candidate: Gene.2643::MSTRG.669.3::g.2643::m.2643, not unique enough -skipping training candidate: Gene.2644::NM_014782::g.2644::m.2644, not unique enough -skipping training candidate: Gene.2645::MSTRG.669.9::g.2645::m.2645, not unique enough -skipping training candidate: Gene.2646::MSTRG.669.4::g.2646::m.2646, not unique enough -skipping training candidate: Gene.2647::NM_001282231::g.2647::m.2647, not unique enough -skipping training candidate: Gene.2810::MSTRG.456.6::g.2810::m.2810, not unique enough -skipping training candidate: Gene.1759::MSTRG.306.3::g.1759::m.1759, not unique enough -skipping training candidate: Gene.2032::NM_001178110::g.2032::m.2032, not unique enough -skipping training candidate: Gene.2224::NM_004017::g.2224::m.2224, not unique enough -skipping training candidate: Gene.3176::NM_033626::g.3176::m.3176, not unique enough -skipping training candidate: Gene.3179::NM_001271836::g.3179::m.3179, not unique enough -skipping training candidate: Gene.3280::NM_005032::g.3280::m.3280, not unique enough -skipping training candidate: Gene.2954::NM_033289::g.2954::m.2954, not unique enough -skipping training candidate: Gene.505::NM_001024666::g.505::m.505, not unique enough -skipping training candidate: Gene.33::NM_001099686_dup1::g.33::m.33, not unique enough -skipping training candidate: Gene.129::MSTRG.376.3::g.129::m.129, not unique enough -skipping training candidate: Gene.134::MSTRG.376.4::g.134::m.134, not unique enough -skipping training candidate: Gene.144::MSTRG.376.8::g.144::m.144, not unique enough -skipping training candidate: Gene.620::NM_022053::g.620::m.620, not unique enough -skipping training candidate: Gene.621::NM_022053_dup1::g.621::m.621, not unique enough -skipping training candidate: Gene.1746::MSTRG.957.10::g.1746::m.1746, not unique enough -skipping training candidate: Gene.34::NM_001142805::g.34::m.34, not unique enough -skipping training candidate: Gene.141::MSTRG.376.2::g.141::m.141, not unique enough -skipping training candidate: Gene.1740::MSTRG.957.8::g.1740::m.1740, not unique enough -skipping training candidate: Gene.3201::NM_152224::g.3201::m.3201, not unique enough -skipping training candidate: Gene.503::MSTRG.151.5::g.503::m.503, not unique enough -skipping training candidate: Gene.712::NM_016120::g.712::m.712, not unique enough -skipping training candidate: Gene.714::MSTRG.537.1::g.714::m.714, not unique enough -skipping training candidate: Gene.716::NM_183353::g.716::m.716, not unique enough -skipping training candidate: Gene.1742::MSTRG.957.13::g.1742::m.1742, not unique enough -skipping training candidate: Gene.3795::NM_001307979::g.3795::m.3795, not unique enough -skipping training candidate: Gene.2523::NM_001306177::g.2523::m.2523, not unique enough -skipping training candidate: Gene.2695::NM_001007088::g.2695::m.2695, not unique enough -skipping training candidate: Gene.3947::NM_001048164::g.3947::m.3947, not unique enough -skipping training candidate: Gene.3276::NM_001282337::g.3276::m.3276, not unique enough -skipping training candidate: Gene.1745::NM_001185076::g.1745::m.1745, not unique enough -skipping training candidate: Gene.427::MSTRG.110.2::g.427::m.427, not unique enough -skipping training candidate: Gene.1251::NM_145812::g.1251::m.1251, not unique enough -skipping training candidate: Gene.502::MSTRG.151.1::g.502::m.502, not unique enough -skipping training candidate: Gene.2171::NM_001654::g.2171::m.2171, not unique enough -skipping training candidate: Gene.3922::NM_201222::g.3922::m.3922, not unique enough -skipping training candidate: Gene.3923::NM_014599::g.3923::m.3923, not unique enough -skipping training candidate: Gene.3924::NM_177433::g.3924::m.3924, not unique enough -skipping training candidate: Gene.468::MSTRG.717.1::g.468::m.468, not unique enough -skipping training candidate: Gene.3055::NM_080612::g.3055::m.3055, not unique enough -skipping training candidate: Gene.3669::NM_147175::g.3669::m.3669, not unique enough -skipping training candidate: Gene.1355::NM_030624::g.1355::m.1355, not unique enough -skipping training candidate: Gene.1733::MSTRG.957.12::g.1733::m.1733, not unique enough -skipping training candidate: Gene.3277::NM_001172335::g.3277::m.3277, not unique enough -skipping training candidate: Gene.2748::NM_001325::g.2748::m.2748, not unique enough -skipping training candidate: Gene.3424::NM_001037967::g.3424::m.3424, not unique enough -skipping training candidate: Gene.2648::NM_001282631::g.2648::m.2648, not unique enough -skipping training candidate: Gene.2512::MSTRG.714.3::g.2512::m.2512, not unique enough -skipping training candidate: Gene.3807::MSTRG.365.2::g.3807::m.3807, not unique enough -skipping training candidate: Gene.352::NM_152226::g.352::m.352, not unique enough -skipping training candidate: Gene.1621::NM_001145933::g.1621::m.1621, not unique enough -skipping training candidate: Gene.1974::MSTRG.62.1::g.1974::m.1974, not unique enough -skipping training candidate: Gene.3350::NM_001201539::g.3350::m.3350, not unique enough -skipping training candidate: Gene.3359::NM_004042::g.3359::m.3359, not unique enough -skipping training candidate: Gene.622::NM_024921::g.622::m.622, not unique enough -skipping training candidate: Gene.1358::NM_000047::g.1358::m.1358, not unique enough -skipping training candidate: Gene.429::MSTRG.110.9::g.429::m.429, not unique enough -skipping training candidate: Gene.3038::MSTRG.338.5::g.3038::m.3038, not unique enough -skipping training candidate: Gene.99::MSTRG.862.1::g.99::m.99, not unique enough -skipping training candidate: Gene.1202::NM_019857::g.1202::m.1202, not unique enough -skipping training candidate: Gene.1204::NM_001144002::g.1204::m.1204, not unique enough -skipping training candidate: Gene.1734::NM_001185082::g.1734::m.1734, not unique enough -skipping training candidate: Gene.3030::NM_001136158::g.3030::m.3030, not unique enough -skipping training candidate: Gene.3033::MSTRG.338.7::g.3033::m.3033, not unique enough -skipping training candidate: Gene.3036::NM_001136157::g.3036::m.3036, not unique enough -skipping training candidate: Gene.3034::MSTRG.338.6::g.3034::m.3034, not unique enough -skipping training candidate: Gene.3275::NM_001282338::g.3275::m.3275, not unique enough -skipping training candidate: Gene.1970::NM_000351::g.1970::m.1970, not unique enough -skipping training candidate: Gene.3999::NM_001142463::g.3999::m.3999, not unique enough -skipping training candidate: Gene.2468::NM_001184819::g.2468::m.2468, not unique enough -skipping training candidate: Gene.2933::NM_006375::g.2933::m.2933, not unique enough -skipping training candidate: Gene.2934::NM_001281736::g.2934::m.2934, not unique enough -skipping training candidate: Gene.2095::NM_004484::g.2095::m.2095, not unique enough -skipping training candidate: Gene.2721::MSTRG.159.5::g.2721::m.2721, not unique enough -skipping training candidate: Gene.2936::MSTRG.872.2::g.2936::m.2936, not unique enough -skipping training candidate: Gene.2747::NM_001306209::g.2747::m.2747, not unique enough -skipping training candidate: Gene.1606::MSTRG.75.10::g.1606::m.1606, not unique enough -skipping training candidate: Gene.1608::MSTRG.75.6::g.1608::m.1608, not unique enough -skipping training candidate: Gene.1610::MSTRG.75.9::g.1610::m.1610, not unique enough -skipping training candidate: Gene.1611::NM_001139466::g.1611::m.1611, not unique enough -skipping training candidate: Gene.4126::NM_001190417::g.4126::m.4126, not unique enough -skipping training candidate: Gene.4128::NM_001146291::g.4128::m.4128, not unique enough -skipping training candidate: Gene.1158::NM_001037968::g.1158::m.1158, not unique enough -skipping training candidate: Gene.4008::NM_001139514::g.4008::m.4008, not unique enough -skipping training candidate: Gene.807::NM_001170460::g.807::m.807, not unique enough -skipping training candidate: Gene.3056::NM_001282283::g.3056::m.3056, not unique enough -skipping training candidate: Gene.291::NM_001170760::g.291::m.291, not unique enough -skipping training candidate: Gene.3057::NM_001128172::g.3057::m.3057, not unique enough -skipping training candidate: Gene.2099::NM_001164618::g.2099::m.2099, not unique enough -skipping training candidate: Gene.3859::NM_001079855::g.3859::m.3859, not unique enough -skipping training candidate: Gene.1040::MSTRG.305.6::g.1040::m.1040, not unique enough -skipping training candidate: Gene.2858::NM_001184702::g.2858::m.2858, not unique enough -skipping training candidate: Gene.643::NM_001128173::g.643::m.643, not unique enough -skipping training candidate: Gene.589::NM_001168479::g.589::m.589, not unique enough -skipping training candidate: Gene.590::NM_001168480::g.590::m.590, not unique enough -skipping training candidate: Gene.598::MSTRG.680.5::g.598::m.598, not unique enough -skipping training candidate: Gene.599::NM_001168485::g.599::m.599, not unique enough -skipping training candidate: Gene.600::NM_022838::g.600::m.600, not unique enough -skipping training candidate: Gene.601::NM_001168482::g.601::m.601, not unique enough -skipping training candidate: Gene.2575::NM_001145140_dup1::g.2575::m.2575, not unique enough -skipping training candidate: Gene.4294::NM_001145139_dup1::g.4294::m.4294, not unique enough -skipping training candidate: Gene.4298::NM_001145139::g.4298::m.4298, not unique enough -skipping training candidate: Gene.382::MSTRG.945.9::g.382::m.382, not unique enough -skipping training candidate: Gene.4204::NM_001448::g.4204::m.4204, not unique enough -skipping training candidate: Gene.3794::MSTRG.340.2::g.3794::m.3794, not unique enough -skipping training candidate: Gene.2968::NM_001128127::g.2968::m.2968, not unique enough -skipping training candidate: Gene.4183::NM_015507::g.4183::m.4183, not unique enough -skipping training candidate: Gene.4317::NM_001167::g.4317::m.4317, not unique enough -skipping training candidate: Gene.3060::NM_001142529::g.3060::m.3060, not unique enough -skipping training candidate: Gene.3062::NM_030639::g.3062::m.3062, not unique enough -skipping training candidate: Gene.3064::NM_001142528::g.3064::m.3064, not unique enough -skipping training candidate: Gene.3066::NM_001142530::g.3066::m.3066, not unique enough -skipping training candidate: Gene.3068::NM_001142526::g.3068::m.3068, not unique enough -skipping training candidate: Gene.3070::NM_001142527::g.3070::m.3070, not unique enough -skipping training candidate: Gene.3072::NM_001142524::g.3072::m.3072, not unique enough -skipping training candidate: Gene.1948::NM_001142391::g.1948::m.1948, not unique enough -skipping training candidate: Gene.3219::NM_000402::g.3219::m.3219, not unique enough -skipping training candidate: Gene.461::NM_001128166::g.461::m.461, not unique enough -skipping training candidate: Gene.2672::NM_001128167::g.2672::m.2672, not unique enough -skipping training candidate: Gene.3484::NM_002578::g.3484::m.3484, not unique enough -skipping training candidate: Gene.810::MSTRG.275.2::g.810::m.810, not unique enough -skipping training candidate: Gene.406::NM_001145934::g.406::m.406, not unique enough -skipping training candidate: Gene.1143::NM_017711::g.1143::m.1143, not unique enough -skipping training candidate: Gene.4318::NM_001204401::g.4318::m.4318, not unique enough -skipping training candidate: Gene.3534::MSTRG.326.1::g.3534::m.3534, not unique enough -skipping training candidate: Gene.1744::MSTRG.957.16::g.1744::m.1744, not unique enough -skipping training candidate: Gene.3710::NM_001282607::g.3710::m.3710, not unique enough -skipping training candidate: Gene.294::NM_001170761::g.294::m.294, not unique enough -skipping training candidate: Gene.1532::NM_001282202::g.1532::m.1532, not unique enough -skipping training candidate: Gene.1940::NR_033348::g.1940::m.1940, not unique enough -skipping training candidate: Gene.2803::NM_001172743::g.2803::m.2803, not unique enough -skipping training candidate: Gene.2974::NM_203391::g.2974::m.2974, not unique enough -skipping training candidate: Gene.3540::NR_033349::g.3540::m.3540, not unique enough -skipping training candidate: Gene.3834::NM_001172739::g.3834::m.3834, not unique enough -skipping training candidate: Gene.124::NM_001271815::g.124::m.124, not unique enough -skipping training candidate: Gene.1254::MSTRG.865.1::g.1254::m.1254, not unique enough -skipping training candidate: Gene.1598::MSTRG.75.4::g.1598::m.1598, not unique enough -skipping training candidate: Gene.1601::NM_001139467::g.1601::m.1601, not unique enough -skipping training candidate: Gene.1607::NM_001139468::g.1607::m.1607, not unique enough -skipping training candidate: Gene.1609::MSTRG.75.8::g.1609::m.1609, not unique enough -skipping training candidate: Gene.1613::MSTRG.75.7::g.1613::m.1613, not unique enough -skipping training candidate: Gene.2097::NM_001164619::g.2097::m.2097, not unique enough -skipping training candidate: Gene.848::NM_001184703::g.848::m.848, not unique enough -skipping training candidate: Gene.2973::NM_000167::g.2973::m.2973, not unique enough -skipping training candidate: Gene.1043::NM_203475::g.1043::m.1043, not unique enough -skipping training candidate: Gene.3410::NM_002186::g.3410::m.3410, not unique enough -skipping training candidate: Gene.3533::NM_000377::g.3533::m.3533, not unique enough -skipping training candidate: Gene.36::NM_001142806::g.36::m.36, not unique enough -skipping training candidate: Gene.798::NM_001109878::g.798::m.798, not unique enough -skipping training candidate: Gene.3217::MSTRG.1040.3::g.3217::m.3217, not unique enough -skipping training candidate: Gene.3992::NM_145802::g.3992::m.3992, not unique enough -skipping training candidate: Gene.1045::NM_203473::g.1045::m.1045, not unique enough -skipping training candidate: Gene.1743::NM_001185081::g.1743::m.1743, not unique enough -skipping training candidate: Gene.1910::NM_015185::g.1910::m.1910, not unique enough -skipping training candidate: Gene.126::NM_013955::g.126::m.126, not unique enough -skipping training candidate: Gene.3988::NM_145799::g.3988::m.3988, not unique enough -skipping training candidate: Gene.3991::NM_145800::g.3991::m.3991, not unique enough -skipping training candidate: Gene.4121::MSTRG.266.5::g.4121::m.4121, not unique enough -skipping training candidate: Gene.4130::MSTRG.266.4::g.4130::m.4130, not unique enough -skipping training candidate: Gene.1967::NM_020730::g.1967::m.1967, not unique enough -skipping training candidate: Gene.4253::MSTRG.17.2::g.4253::m.4253, not unique enough -skipping training candidate: Gene.4263::MSTRG.17.6::g.4263::m.4263, not unique enough -skipping training candidate: Gene.1035::NM_022825::g.1035::m.1035, not unique enough -skipping training candidate: Gene.1338::NM_007131::g.1338::m.1338, not unique enough -skipping training candidate: Gene.304::NM_001193270::g.304::m.304, not unique enough -skipping training candidate: Gene.4119::MSTRG.496.3::g.4119::m.4119, not unique enough -skipping training candidate: Gene.4162::NM_001167972::g.4162::m.4162, not unique enough -skipping training candidate: Gene.4164::NM_001167970::g.4164::m.4164, not unique enough -skipping training candidate: Gene.4167::NM_024917::g.4167::m.4167, not unique enough -skipping training candidate: Gene.1949::MSTRG.1036.1::g.1949::m.1949, not unique enough -skipping training candidate: Gene.2622::NR_104109::g.2622::m.2622, not unique enough -skipping training candidate: Gene.4348::NM_001289109::g.4348::m.4348, not unique enough -skipping training candidate: Gene.799::NM_033018::g.799::m.799, not unique enough -skipping training candidate: Gene.3532::MSTRG.326.2::g.3532::m.3532, not unique enough -skipping training candidate: Gene.4116::MSTRG.496.5::g.4116::m.4116, not unique enough -skipping training candidate: Gene.91::NM_001166460::g.91::m.91, not unique enough -skipping training candidate: Gene.3109::MSTRG.137.3::g.3109::m.3109, not unique enough -skipping training candidate: Gene.92::NM_001166461::g.92::m.92, not unique enough -skipping training candidate: Gene.2544::NM_005089::g.2544::m.2544, not unique enough -skipping training candidate: Gene.4321::MSTRG.838.6::g.4321::m.4321, not unique enough -skipping training candidate: Gene.802::MSTRG.275.3::g.802::m.802, not unique enough -skipping training candidate: Gene.813::MSTRG.275.4::g.813::m.813, not unique enough -skipping training candidate: Gene.818::MSTRG.275.7::g.818::m.818, not unique enough -skipping training candidate: Gene.821::MSTRG.275.6::g.821::m.821, not unique enough -skipping training candidate: Gene.1105::MSTRG.961.3::g.1105::m.1105, not unique enough -skipping training candidate: Gene.2036::MSTRG.991.7::g.2036::m.2036, not unique enough -skipping training candidate: Gene.1555::NM_001171163::g.1555::m.1555, not unique enough -skipping training candidate: Gene.1896::MSTRG.443.4::g.1896::m.1896, not unique enough -skipping training candidate: Gene.1898::MSTRG.443.1::g.1898::m.1898, not unique enough -skipping training candidate: Gene.1904::MSTRG.443.2::g.1904::m.1904, not unique enough -skipping training candidate: Gene.1912::MSTRG.443.5::g.1912::m.1912, not unique enough -skipping training candidate: Gene.4001::NM_001288747::g.4001::m.4001, not unique enough -skipping training candidate: Gene.2429::NM_001184745::g.2429::m.2429, not unique enough -skipping training candidate: Gene.4118::MSTRG.496.4::g.4118::m.4118, not unique enough -skipping training candidate: Gene.922::NM_001193279::g.922::m.922, not unique enough -skipping training candidate: Gene.3091::NM_198511::g.3091::m.3091, not unique enough -skipping training candidate: Gene.3297::MSTRG.431.1::g.3297::m.3297, not unique enough -skipping training candidate: Gene.439::NM_004992::g.439::m.439, not unique enough -skipping training candidate: Gene.2090::NM_017883::g.2090::m.2090, not unique enough -skipping training candidate: Gene.1456::MSTRG.977.4::g.1456::m.1456, not unique enough -skipping training candidate: Gene.857::NM_001287345::g.857::m.857, not unique enough -skipping training candidate: Gene.3652::NM_001172732::g.3652::m.3652, not unique enough -skipping training candidate: Gene.1946::NM_019848::g.1946::m.1946, not unique enough -skipping training candidate: Gene.2146::MSTRG.570.8::g.2146::m.2146, not unique enough -skipping training candidate: Gene.2967::MSTRG.209.8::g.2967::m.2967, not unique enough -skipping training candidate: Gene.2597::NM_033518::g.2597::m.2597, not unique enough -skipping training candidate: Gene.2599::MSTRG.301.2::g.2599::m.2599, not unique enough -skipping training candidate: Gene.1982::MSTRG.503.1::g.1982::m.1982, not unique enough -skipping training candidate: Gene.1983::NM_001145409::g.1983::m.1983, not unique enough -skipping training candidate: Gene.1987::NM_007363::g.1987::m.1987, not unique enough -skipping training candidate: Gene.1989::MSTRG.503.2::g.1989::m.1989, not unique enough -skipping training candidate: Gene.4117::MSTRG.496.7::g.4117::m.4117, not unique enough -skipping training candidate: Gene.867::NM_023010::g.867::m.867, not unique enough -skipping training candidate: Gene.2037::NM_001282142::g.2037::m.2037, not unique enough -skipping training candidate: Gene.3826::NM_001145252::g.3826::m.3826, not unique enough -skipping training candidate: Gene.2027::NM_001178113::g.2027::m.2027, not unique enough -skipping training candidate: Gene.1033::NM_203474::g.1033::m.1033, not unique enough -skipping training candidate: Gene.3622::NM_001282401::g.3622::m.3622, not unique enough -skipping training candidate: Gene.3626::MSTRG.672.4::g.3626::m.3626, not unique enough -skipping training candidate: Gene.3627::NM_001282400::g.3627::m.3627, not unique enough -skipping training candidate: Gene.3990::MSTRG.804.4::g.3990::m.3990, not unique enough -skipping training candidate: Gene.4112::MSTRG.496.6::g.4112::m.4112, not unique enough -skipping training candidate: Gene.3858::NM_006140::g.3858::m.3858, not unique enough -skipping training candidate: Gene.1906::NM_001173479::g.1906::m.1906, not unique enough -skipping training candidate: Gene.1111::NM_001166550::g.1111::m.1111, not unique enough -skipping training candidate: Gene.2361::NM_001171193::g.2361::m.2361, not unique enough -skipping training candidate: Gene.2963::NM_001171191::g.2963::m.2963, not unique enough -skipping training candidate: Gene.1737::MSTRG.957.9::g.1737::m.1737, not unique enough -skipping training candidate: Gene.4159::NM_001167971::g.4159::m.4159, not unique enough -skipping training candidate: Gene.1445::NM_001114377::g.1445::m.1445, not unique enough -skipping training candidate: Gene.1958::NM_000868::g.1958::m.1958, not unique enough -skipping training candidate: Gene.1004::NM_001143982::g.1004::m.1004, not unique enough -skipping training candidate: Gene.3016::NM_001271804::g.3016::m.3016, not unique enough -skipping training candidate: Gene.2364::NM_145234::g.2364::m.2364, not unique enough -skipping training candidate: Gene.2542::MSTRG.128.4::g.2542::m.2542, not unique enough -skipping training candidate: Gene.3522::NM_172245::g.3522::m.3522, not unique enough -skipping training candidate: Gene.1583::NM_001177475::g.1583::m.1583, not unique enough -skipping training candidate: Gene.2281::NM_022368::g.2281::m.2281, not unique enough -skipping training candidate: Gene.3582::NM_001282535::g.3582::m.3582, not unique enough -skipping training candidate: Gene.1362::NM_000240::g.1362::m.1362, not unique enough -skipping training candidate: Gene.1508::NM_016608::g.1508::m.1508, not unique enough -skipping training candidate: Gene.2900::NM_002063::g.2900::m.2900, not unique enough -skipping training candidate: Gene.3915::NM_001118886::g.3915::m.3915, not unique enough -skipping training candidate: Gene.305::MSTRG.91.1::g.305::m.305, not unique enough -skipping training candidate: Gene.309::NM_078628::g.309::m.309, not unique enough -skipping training candidate: Gene.1908::MSTRG.443.9::g.1908::m.1908, not unique enough -skipping training candidate: Gene.3286::NM_001193280::g.3286::m.3286, not unique enough -skipping training candidate: Gene.4006::NM_001139515::g.4006::m.4006, not unique enough -skipping training candidate: Gene.2734::NM_001170931::g.2734::m.2734, not unique enough -skipping training candidate: Gene.3986::MSTRG.804.5::g.3986::m.3986, not unique enough -skipping training candidate: Gene.1736::NR_033699::g.1736::m.1736, not unique enough -skipping training candidate: Gene.3328::NM_001199974::g.3328::m.3328, not unique enough -skipping training candidate: Gene.3332::NM_001032393::g.3332::m.3332, not unique enough -skipping training candidate: Gene.3333::NM_001199973::g.3333::m.3333, not unique enough -skipping training candidate: Gene.1185::NM_001103151::g.1185::m.1185, not unique enough -skipping training candidate: Gene.2840::NM_001103150::g.2840::m.2840, not unique enough -skipping training candidate: Gene.4215::NM_052926::g.4215::m.4215, not unique enough -skipping training candidate: Gene.1738::MSTRG.957.14::g.1738::m.1738, not unique enough -skipping training candidate: Gene.4277::MSTRG.32.1::g.4277::m.4277, not unique enough -skipping training candidate: Gene.3005::NM_001173455::g.3005::m.3005, not unique enough -skipping training candidate: Gene.4309::NM_001170750::g.4309::m.4309, not unique enough -skipping training candidate: Gene.2167::MSTRG.284.1::g.2167::m.2167, not unique enough -skipping training candidate: Gene.2175::MSTRG.284.5::g.2175::m.2175, not unique enough -skipping training candidate: Gene.4014::MSTRG.178.6::g.4014::m.4014, not unique enough -skipping training candidate: Gene.4293::NM_001161530::g.4293::m.4293, not unique enough -skipping training candidate: Gene.1277::NM_172246::g.1277::m.1277, not unique enough -skipping training candidate: Gene.20::NM_182607::g.20::m.20, not unique enough -skipping training candidate: Gene.4013::NM_001033583::g.4013::m.4013, not unique enough -skipping training candidate: Gene.3004::NM_000284::g.3004::m.3004, not unique enough -skipping training candidate: Gene.4332::MSTRG.345.2::g.4332::m.4332, not unique enough -skipping training candidate: Gene.89::NM_001166462::g.89::m.89, not unique enough -skipping training candidate: Gene.1761::MSTRG.306.1::g.1761::m.1761, not unique enough -skipping training candidate: Gene.990::NM_001313913::g.990::m.990, not unique enough -skipping training candidate: Gene.1136::NM_001178095::g.1136::m.1136, not unique enough -skipping training candidate: Gene.4012::MSTRG.178.5::g.4012::m.4012, not unique enough -skipping training candidate: Gene.1205::MSTRG.131.4::g.1205::m.1205, not unique enough -skipping training candidate: Gene.1741::NR_033700::g.1741::m.1741, not unique enough -skipping training candidate: Gene.3025::NM_001114123::g.3025::m.3025, not unique enough -skipping training candidate: Gene.499::NM_001184960::g.499::m.499, not unique enough -skipping training candidate: Gene.3993::MSTRG.804.3::g.3993::m.3993, not unique enough -skipping training candidate: Gene.42::NM_002893::g.42::m.42, not unique enough -skipping training candidate: Gene.2436::NM_001177466::g.2436::m.2436, not unique enough -skipping training candidate: Gene.3356::NM_005491::g.3356::m.3356, not unique enough -skipping training candidate: Gene.1777::NM_001171080::g.1777::m.1777, not unique enough -skipping training candidate: Gene.3261::NM_001164415_dup1::g.3261::m.3261, not unique enough -skipping training candidate: Gene.3523::NM_016153::g.3523::m.3523, not unique enough -skipping training candidate: Gene.3524::NM_016153_dup1::g.3524::m.3524, not unique enough -skipping training candidate: Gene.3039::NM_001136159::g.3039::m.3039, not unique enough -skipping training candidate: Gene.3158::NM_003639::g.3158::m.3158, not unique enough -skipping training candidate: Gene.3160::NM_001099857::g.3160::m.3160, not unique enough -skipping training candidate: Gene.1497::MSTRG.921.6::g.1497::m.1497, not unique enough -skipping training candidate: Gene.2705::NM_016542::g.2705::m.2705, not unique enough -skipping training candidate: Gene.1333::NM_001185063::g.1333::m.1333, not unique enough -skipping training candidate: Gene.1339::MSTRG.912.2::g.1339::m.1339, not unique enough -skipping training candidate: Gene.1351::NM_001168474::g.1351::m.1351, not unique enough -skipping training candidate: Gene.1900::NM_001173480::g.1900::m.1900, not unique enough -skipping training candidate: Gene.3108::NM_001168683::g.3108::m.3108, not unique enough -skipping training candidate: Gene.1520::NM_003173::g.1520::m.1520, not unique enough -skipping training candidate: Gene.2207::NM_013995::g.2207::m.2207, not unique enough -skipping training candidate: Gene.2208::NM_002294::g.2208::m.2208, not unique enough -skipping training candidate: Gene.3283::NM_001586::g.3283::m.3283, not unique enough -skipping training candidate: Gene.3973::NM_032227::g.3973::m.3973, not unique enough -skipping training candidate: Gene.2103::NM_031274::g.2103::m.2103, not unique enough -skipping training candidate: Gene.4042::MSTRG.1005.2::g.4042::m.4042, not unique enough -skipping training candidate: Gene.3081::MSTRG.641.4::g.3081::m.3081, not unique enough -skipping training candidate: Gene.1137::NM_001178095::g.1137::m.1137, not unique enough -skipping training candidate: Gene.2248::NM_001277423_dup1::g.2248::m.2248, not unique enough -skipping training candidate: Gene.3006::NM_001173456::g.3006::m.3006, not unique enough -skipping training candidate: Gene.3615::MSTRG.320.4::g.3615::m.3615, not unique enough -skipping training candidate: Gene.1221::NM_001271805::g.1221::m.1221, not unique enough -skipping training candidate: Gene.2605::MSTRG.336.9::g.2605::m.2605, not unique enough -skipping training candidate: Gene.2608::NM_001282650::g.2608::m.2608, not unique enough -skipping training candidate: Gene.2681::NM_005391::g.2681::m.2681, not unique enough -skipping training candidate: Gene.1684::NM_001170751::g.1684::m.1684, not unique enough -skipping training candidate: Gene.3401::NM_001195553::g.3401::m.3401, not unique enough -skipping training candidate: Gene.1154::NM_178152::g.1154::m.1154, not unique enough -skipping training candidate: Gene.2147::MSTRG.570.8::g.2147::m.2147, not unique enough -skipping training candidate: Gene.2456::NM_173798::g.2456::m.2456, not unique enough -skipping training candidate: Gene.1492::MSTRG.921.5::g.1492::m.1492, not unique enough -skipping training candidate: Gene.3082::MSTRG.641.2::g.3082::m.3082, not unique enough -skipping training candidate: Gene.3229::NM_001303475::g.3229::m.3229, not unique enough -skipping training candidate: Gene.3281::NM_001109879::g.3281::m.3281, not unique enough -skipping training candidate: Gene.3417::NM_001011544::g.3417::m.3417, not unique enough -skipping training candidate: Gene.4172::NM_001161529::g.4172::m.4172, not unique enough -skipping training candidate: Gene.2507::NM_178153::g.2507::m.2507, not unique enough -skipping training candidate: Gene.2607::NM_005660::g.2607::m.2607, not unique enough -skipping training candidate: Gene.961::NM_001270458::g.961::m.961, not unique enough -skipping training candidate: Gene.442::NM_001316337::g.442::m.442, not unique enough -skipping training candidate: Gene.908::NM_004135::g.908::m.908, not unique enough -skipping training candidate: Gene.2079::NR_029427::g.2079::m.2079, not unique enough -skipping training candidate: Gene.2083::MSTRG.325.4::g.2083::m.2083, not unique enough -skipping training candidate: Gene.2086::NM_001166426::g.2086::m.2086, not unique enough -skipping training candidate: Gene.2606::MSTRG.336.10::g.2606::m.2606, not unique enough -skipping training candidate: Gene.2611::NM_001042498::g.2611::m.2611, not unique enough -skipping training candidate: Gene.1209::NM_000513::g.1209::m.1209, not unique enough -skipping training candidate: Gene.1211::NM_000513_dup2::g.1211::m.1211, not unique enough -skipping training candidate: Gene.2495::NM_001048181_dup1::g.2495::m.2495, not unique enough -skipping training candidate: Gene.2496::NM_001048181::g.2496::m.2496, not unique enough -skipping training candidate: Gene.2497::NM_001048181_dup2::g.2497::m.2497, not unique enough -skipping training candidate: Gene.670::NM_001504::g.670::m.670, not unique enough -skipping training candidate: Gene.3084::MSTRG.641.5::g.3084::m.3084, not unique enough -skipping training candidate: Gene.1197::NM_001170574::g.1197::m.1197, not unique enough -skipping training candidate: Gene.4192::NM_001005609::g.4192::m.4192, not unique enough -skipping training candidate: Gene.2138::NM_001011549::g.2138::m.2138, not unique enough -skipping training candidate: Gene.3418::NM_001011645::g.3418::m.3418, not unique enough -skipping training candidate: Gene.4002::NR_110023::g.4002::m.4002, not unique enough -skipping training candidate: Gene.4197::NM_001005612::g.4197::m.4197, not unique enough -skipping training candidate: Gene.452::NM_001011550::g.452::m.452, not unique enough -skipping training candidate: Gene.4273::NR_027383::g.4273::m.4273, not unique enough -skipping training candidate: Gene.4289::MSTRG.32.4::g.4289::m.4289, not unique enough -skipping training candidate: Gene.3802::NM_020061::g.3802::m.3802, not unique enough -skipping training candidate: Gene.2943::MSTRG.1070.2::g.2943::m.2943, not unique enough -skipping training candidate: Gene.1985::NM_001145410::g.1985::m.1985, not unique enough -skipping training candidate: Gene.1683::NM_005300::g.1683::m.1683, not unique enough -skipping training candidate: Gene.906::NM_174869::g.906::m.906, not unique enough -skipping training candidate: Gene.1029::MSTRG.305.1::g.1029::m.1029, not unique enough -skipping training candidate: Gene.1050::NM_001282167::g.1050::m.1050, not unique enough -skipping training candidate: Gene.1543::NM_001170752::g.1543::m.1543, not unique enough -skipping training candidate: Gene.1617::NM_177947::g.1617::m.1617, not unique enough -skipping training candidate: Gene.1618::MSTRG.666.2::g.1618::m.1618, not unique enough -skipping training candidate: Gene.1619::NM_016607::g.1619::m.1619, not unique enough -skipping training candidate: Gene.1620::NM_177948::g.1620::m.1620, not unique enough -skipping training candidate: Gene.4015::MSTRG.178.4::g.4015::m.4015, not unique enough -skipping training candidate: Gene.4016::MSTRG.178.3::g.4016::m.4016, not unique enough -skipping training candidate: Gene.672::MSTRG.507.1::g.672::m.672, not unique enough -skipping training candidate: Gene.1716::MSTRG.9.5::g.1716::m.1716, not unique enough -skipping training candidate: Gene.2438::NM_001143983::g.2438::m.2438, not unique enough -skipping training candidate: Gene.1150::MSTRG.2.1::g.1150::m.1150, not unique enough -skipping training candidate: Gene.1712::MSTRG.9.4::g.1712::m.1712, not unique enough -skipping training candidate: Gene.1717::MSTRG.9.3::g.1717::m.1717, not unique enough -skipping training candidate: Gene.1477::NM_012151::g.1477::m.1477, not unique enough -skipping training candidate: Gene.2320::NM_012151_dup1::g.2320::m.2320, not unique enough -skipping training candidate: Gene.2944::NM_001184797::g.2944::m.2944, not unique enough -skipping training candidate: Gene.3537::MSTRG.976.2::g.3537::m.3537, not unique enough -skipping training candidate: Gene.3563::NM_001129765::g.3563::m.3563, not unique enough -skipping training candidate: Gene.4287::NM_001171038::g.4287::m.4287, not unique enough -skipping training candidate: Gene.302::NM_001282174::g.302::m.302, not unique enough -skipping training candidate: Gene.342::NM_001007524_dup2::g.342::m.342, not unique enough -skipping training candidate: Gene.1479::NM_001007523::g.1479::m.1479, not unique enough -skipping training candidate: Gene.2322::NM_001007523_dup1::g.2322::m.2322, not unique enough -skipping training candidate: Gene.1094::MSTRG.961.2::g.1094::m.1094, not unique enough -skipping training candidate: Gene.4023::NM_001278000::g.4023::m.4023, not unique enough -skipping training candidate: Gene.1089::NM_021048::g.1089::m.1089, not unique enough -skipping training candidate: Gene.1177::NM_001011543::g.1177::m.1177, not unique enough -skipping training candidate: Gene.3168::MSTRG.1041.9::g.3168::m.3168, not unique enough -skipping training candidate: Gene.3767::NM_017518::g.3767::m.3767, not unique enough -skipping training candidate: Gene.1965::MSTRG.480.4::g.1965::m.1965, not unique enough -skipping training candidate: Gene.2022::NM_001135740::g.2022::m.2022, not unique enough -skipping training candidate: Gene.2219::MSTRG.222.1::g.2219::m.2219, not unique enough -skipping training candidate: Gene.2221::NM_004019::g.2221::m.2221, not unique enough -skipping training candidate: Gene.2230::MSTRG.222.2::g.2230::m.2230, not unique enough -skipping training candidate: Gene.4249::MSTRG.17.7::g.4249::m.4249, not unique enough -skipping training candidate: Gene.1592::NM_032458::g.1592::m.1592, not unique enough -skipping training candidate: Gene.1593::NM_001015877::g.1593::m.1593, not unique enough -skipping training candidate: Gene.3265::NM_002765::g.3265::m.3265, not unique enough -skipping training candidate: Gene.3704::NM_032946::g.3704::m.3704, not unique enough -skipping training candidate: Gene.2888::NM_001008222::g.2888::m.2888, not unique enough -skipping training candidate: Gene.1449::NM_001306145::g.1449::m.1449, not unique enough -skipping training candidate: Gene.1582::NM_001171942::g.1582::m.1582, not unique enough -skipping training candidate: Gene.3613::MSTRG.320.5::g.3613::m.3613, not unique enough -skipping training candidate: Gene.3614::NM_007075::g.3614::m.3614, not unique enough -skipping training candidate: Gene.3619::MSTRG.320.2::g.3619::m.3619, not unique enough -skipping training candidate: Gene.1614::NM_178151::g.1614::m.1614, not unique enough -skipping training candidate: Gene.3049::NR_045864::g.3049::m.3049, not unique enough -skipping training candidate: Gene.3617::NM_001029896::g.3617::m.3617, not unique enough -skipping training candidate: Gene.2492::NM_007250::g.2492::m.2492, not unique enough -skipping training candidate: Gene.3238::NM_178129::g.3238::m.3238, not unique enough -skipping training candidate: Gene.3513::MSTRG.268.2::g.3513::m.3513, not unique enough -skipping training candidate: Gene.3515::MSTRG.268.1::g.3515::m.3515, not unique enough -skipping training candidate: Gene.494::NM_153488::g.494::m.494, not unique enough -skipping training candidate: Gene.999::MSTRG.51.1::g.999::m.999, not unique enough -skipping training candidate: Gene.1487::MSTRG.921.7::g.1487::m.1487, not unique enough -skipping training candidate: Gene.2711::NM_001042452::g.2711::m.2711, not unique enough -skipping training candidate: Gene.1062::MSTRG.1042.3::g.1062::m.1062, not unique enough -skipping training candidate: Gene.300::MSTRG.91.8::g.300::m.300, not unique enough -skipping training candidate: Gene.301::NM_006800::g.301::m.301, not unique enough -skipping training candidate: Gene.2676::NM_015075::g.2676::m.2676, not unique enough -skipping training candidate: Gene.159::MSTRG.889.3::g.159::m.159, not unique enough -skipping training candidate: Gene.161::MSTRG.889.13::g.161::m.161, not unique enough -skipping training candidate: Gene.168::NM_018388::g.168::m.168, not unique enough -skipping training candidate: Gene.176::MSTRG.889.1::g.176::m.176, not unique enough -skipping training candidate: Gene.3590::NM_001171132::g.3590::m.3590, not unique enough -skipping training candidate: Gene.4156::MSTRG.651.11::g.4156::m.4156, not unique enough -skipping training candidate: Gene.4166::MSTRG.651.10::g.4166::m.4166, not unique enough -skipping training candidate: Gene.4168::MSTRG.651.14::g.4168::m.4168, not unique enough -skipping training candidate: Gene.4169::MSTRG.651.9::g.4169::m.4169, not unique enough -skipping training candidate: Gene.3425::NM_012069::g.3425::m.3425, not unique enough -skipping training candidate: Gene.3718::NR_028477::g.3718::m.3718, not unique enough -skipping training candidate: Gene.361::NM_001163264::g.361::m.361, not unique enough -skipping training candidate: Gene.1013::NM_001297564::g.1013::m.1013, not unique enough -skipping training candidate: Gene.1017::NM_001297563::g.1017::m.1017, not unique enough -skipping training candidate: Gene.1787::MSTRG.4.4::g.1787::m.1787, not unique enough -skipping training candidate: Gene.2718::NR_027760::g.2718::m.2718, not unique enough -skipping training candidate: Gene.52::MSTRG.668.1::g.52::m.52, not unique enough -skipping training candidate: Gene.2970::MSTRG.209.6::g.2970::m.2970, not unique enough -skipping training candidate: Gene.3048::NR_045861::g.3048::m.3048, not unique enough -skipping training candidate: Gene.1173::NM_002363::g.1173::m.1173, not unique enough -skipping training candidate: Gene.2741::NM_001257403::g.2741::m.2741, not unique enough -skipping training candidate: Gene.2956::NM_001271748::g.2956::m.2956, not unique enough -skipping training candidate: Gene.3009::NM_177415::g.3009::m.3009, not unique enough -skipping training candidate: Gene.2387::NM_006064::g.2387::m.2387, not unique enough -skipping training candidate: Gene.2548::MSTRG.128.1::g.2548::m.2548, not unique enough -skipping training candidate: Gene.1104::NM_006123::g.1104::m.1104, not unique enough -skipping training candidate: Gene.1113::MSTRG.961.1::g.1113::m.1113, not unique enough -skipping training candidate: Gene.4074::MSTRG.108.1::g.4074::m.4074, not unique enough -skipping training candidate: Gene.2719::NM_001172285::g.2719::m.2719, not unique enough -skipping training candidate: Gene.2961::NM_172247::g.2961::m.2961, not unique enough -skipping training candidate: Gene.512::MSTRG.549.1::g.512::m.512, not unique enough -skipping training candidate: Gene.2029::NM_001178115::g.2029::m.2029, not unique enough -skipping training candidate: Gene.2128::MSTRG.583.5::g.2128::m.2128, not unique enough -skipping training candidate: Gene.2129::MSTRG.583.4::g.2129::m.2129, not unique enough -skipping training candidate: Gene.2130::MSTRG.583.2::g.2130::m.2130, not unique enough -skipping training candidate: Gene.2131::NM_198333::g.2131::m.2131, not unique enough -skipping training candidate: Gene.2132::NM_014499::g.2132::m.2132, not unique enough -skipping training candidate: Gene.2134::MSTRG.583.1::g.2134::m.2134, not unique enough -skipping training candidate: Gene.2708::NM_001042453::g.2708::m.2708, not unique enough -skipping training candidate: Gene.3314::NM_001551::g.3314::m.3314, not unique enough -skipping training candidate: Gene.3501::MSTRG.268.4::g.3501::m.3501, not unique enough -skipping training candidate: Gene.1651::MSTRG.705.2::g.1651::m.1651, not unique enough -skipping training candidate: Gene.1962::NM_001282187::g.1962::m.1962, not unique enough -skipping training candidate: Gene.1963::NM_001282188::g.1963::m.1963, not unique enough -skipping training candidate: Gene.1964::NM_001282186::g.1964::m.1964, not unique enough -skipping training candidate: Gene.1084::NM_205833::g.1084::m.1084, not unique enough -skipping training candidate: Gene.2056::NM_178270::g.2056::m.2056, not unique enough -skipping training candidate: Gene.537::MSTRG.302.7::g.537::m.537, not unique enough -skipping training candidate: Gene.538::MSTRG.302.4::g.538::m.538, not unique enough -skipping training candidate: Gene.910::MSTRG.1001.1::g.910::m.910, not unique enough -skipping training candidate: Gene.2885::MSTRG.858.4::g.2885::m.2885, not unique enough -skipping training candidate: Gene.3967::NR_109776::g.3967::m.3967, not unique enough -skipping training candidate: Gene.165::NM_133486::g.165::m.165, not unique enough -skipping training candidate: Gene.2585::MSTRG.586.1::g.2585::m.2585, not unique enough -skipping training candidate: Gene.2604::NM_001282649::g.2604::m.2604, not unique enough -skipping training candidate: Gene.3339::NM_001171186::g.3339::m.3339, not unique enough -skipping training candidate: Gene.2969::MSTRG.209.7::g.2969::m.2969, not unique enough -skipping training candidate: Gene.349::NM_001163265::g.349::m.349, not unique enough -skipping training candidate: Gene.2932::NM_001169574::g.2932::m.2932, not unique enough -skipping training candidate: Gene.519::NM_001080485::g.519::m.519, not unique enough -skipping training candidate: Gene.535::NM_012280::g.535::m.535, not unique enough -skipping training candidate: Gene.2021::NM_001282198::g.2021::m.2021, not unique enough -skipping training candidate: Gene.2853::NM_001242640::g.2853::m.2853, not unique enough -skipping training candidate: Gene.4091::NM_001146256::g.4091::m.4091, not unique enough -skipping training candidate: Gene.531::NM_177439::g.531::m.531, not unique enough -skipping training candidate: Gene.2854::NM_001018055::g.2854::m.2854, not unique enough -skipping training candidate: Gene.4072::NM_001042479::g.4072::m.4072, not unique enough -skipping training candidate: Gene.1064::MSTRG.1042.1::g.1064::m.1064, not unique enough -skipping training candidate: Gene.900::NM_001104544::g.900::m.900, not unique enough -skipping training candidate: Gene.2019::NM_001282195::g.2019::m.2019, not unique enough -skipping training candidate: Gene.3616::MSTRG.320.3::g.3616::m.3616, not unique enough -skipping training candidate: Gene.3934::NR_037859::g.3934::m.3934, not unique enough -skipping training candidate: Gene.1246::NM_001130847::g.1246::m.1246, not unique enough -skipping training candidate: Gene.1835::NM_001166418::g.1835::m.1835, not unique enough -skipping training candidate: Gene.1658::MSTRG.1023.3::g.1658::m.1658, not unique enough -skipping training candidate: Gene.1800::MSTRG.4.6::g.1800::m.1800, not unique enough -skipping training candidate: Gene.1802::NM_018390::g.1802::m.1802, not unique enough -skipping training candidate: Gene.1808::NR_028057::g.1808::m.1808, not unique enough -skipping training candidate: Gene.2015::NM_001282196::g.2015::m.2015, not unique enough -skipping training candidate: Gene.2237::MSTRG.113.4::g.2237::m.2237, not unique enough -skipping training candidate: Gene.2054::MSTRG.725.3::g.2054::m.2054, not unique enough -skipping training candidate: Gene.2482::NM_001242310::g.2482::m.2482, not unique enough -skipping training candidate: Gene.3653::NM_001184830::g.3653::m.3653, not unique enough -skipping training candidate: Gene.3151::NM_001145255::g.3151::m.3151, not unique enough -skipping training candidate: Gene.4274::NR_027383::g.4274::m.4274, not unique enough -skipping training candidate: Gene.54::MSTRG.668.2::g.54::m.54, not unique enough -skipping training candidate: Gene.2478::NM_021783::g.2478::m.2478, not unique enough -skipping training candidate: Gene.1183::NM_152692::g.1183::m.1183, not unique enough -skipping training candidate: Gene.1847::NR_033181::g.1847::m.1847, not unique enough -skipping training candidate: Gene.2515::NM_001166401::g.2515::m.2515, not unique enough -skipping training candidate: Gene.4067::MSTRG.108.3::g.4067::m.4067, not unique enough -skipping training candidate: Gene.4226::NM_005364::g.4226::m.4226, not unique enough -skipping training candidate: Gene.3843::NM_001011548::g.3843::m.3843, not unique enough -skipping training candidate: Gene.3594::NM_001171133::g.3594::m.3594, not unique enough -skipping training candidate: Gene.1731::NM_001080790_dup1::g.1731::m.1731, not unique enough -skipping training candidate: Gene.2297::NM_005365::g.2297::m.2297, not unique enough -skipping training candidate: Gene.2298::NM_005365_dup1::g.2298::m.2298, not unique enough -skipping training candidate: Gene.454::NM_005367::g.454::m.454, not unique enough -skipping training candidate: Gene.940::NM_005362::g.940::m.940, not unique enough -skipping training candidate: Gene.968::NM_175743::g.968::m.968, not unique enough -skipping training candidate: Gene.969::NM_175743_dup1::g.969::m.969, not unique enough -skipping training candidate: Gene.1359::NM_001282502_dup1::g.1359::m.1359, not unique enough -skipping training candidate: Gene.1360::NM_001282502::g.1360::m.1360, not unique enough -skipping training candidate: Gene.1687::NM_005361_dup1::g.1687::m.1687, not unique enough -skipping training candidate: Gene.1688::NM_005361::g.1688::m.1688, not unique enough -skipping training candidate: Gene.2212::NM_001282504_dup1::g.2212::m.2212, not unique enough -skipping training candidate: Gene.2213::NM_001282504::g.2213::m.2213, not unique enough -skipping training candidate: Gene.2330::NM_005363::g.2330::m.2330, not unique enough -skipping training candidate: Gene.3671::NM_001282505_dup1::g.3671::m.3671, not unique enough -skipping training candidate: Gene.3672::NM_001282505::g.3672::m.3672, not unique enough -skipping training candidate: Gene.3700::NM_001282501_dup1::g.3700::m.3700, not unique enough -skipping training candidate: Gene.3701::NM_001282501::g.3701::m.3701, not unique enough -skipping training candidate: Gene.3879::NM_175742_dup1::g.3879::m.3879, not unique enough -skipping training candidate: Gene.3880::NM_175742::g.3880::m.3880, not unique enough -skipping training candidate: Gene.3925::NM_001166386::g.3925::m.3925, not unique enough -skipping training candidate: Gene.2689::NM_001139457::g.2689::m.2689, not unique enough -skipping training candidate: Gene.3287::NM_001258423::g.3287::m.3287, not unique enough -skipping training candidate: Gene.1097::NR_104128::g.1097::m.1097, not unique enough -skipping training candidate: Gene.1107::MSTRG.961.4::g.1107::m.1107, not unique enough -skipping training candidate: Gene.1594::NM_032335::g.1594::m.1594, not unique enough -skipping training candidate: Gene.3997::NR_110022::g.3997::m.3997, not unique enough -skipping training candidate: Gene.4004::NR_110021::g.4004::m.4004, not unique enough -skipping training candidate: Gene.2859::NM_001146151::g.2859::m.2859, not unique enough -skipping training candidate: Gene.3471::NM_177557::g.3471::m.3471, not unique enough -skipping training candidate: Gene.1662::MSTRG.1023.4::g.1662::m.1662, not unique enough -skipping training candidate: Gene.1478::NM_012151::g.1478::m.1478, not unique enough -skipping training candidate: Gene.1647::MSTRG.705.3::g.1647::m.1647, not unique enough -skipping training candidate: Gene.1649::NM_001012755::g.1649::m.1649, not unique enough -skipping training candidate: Gene.2321::NM_012151_dup1::g.2321::m.2321, not unique enough -skipping training candidate: Gene.1060::MSTRG.1042.2::g.1060::m.1060, not unique enough -skipping training candidate: Gene.3623::NM_001282401::g.3623::m.3623, not unique enough -skipping training candidate: Gene.3823::NM_001201583::g.3823::m.3823, not unique enough -skipping training candidate: Gene.2460::NM_001001996::g.2460::m.2460, not unique enough -skipping training candidate: Gene.3486::NM_001100431::g.3486::m.3486, not unique enough -skipping training candidate: Gene.3979::MSTRG.734.5::g.3979::m.3979, not unique enough -skipping training candidate: Gene.170::NM_001170701::g.170::m.170, not unique enough -skipping training candidate: Gene.996::MSTRG.51.3::g.996::m.996, not unique enough -skipping training candidate: Gene.154::NM_001170703::g.154::m.154, not unique enough -skipping training candidate: Gene.1334::MSTRG.912.5::g.1334::m.1334, not unique enough -skipping training candidate: Gene.271::NM_006746::g.271::m.271, not unique enough -skipping training candidate: Gene.343::NM_001007524_dup2::g.343::m.343, not unique enough -skipping training candidate: Gene.1191::NM_001012428::g.1191::m.1191, not unique enough -skipping training candidate: Gene.1480::NM_001007523::g.1480::m.1480, not unique enough -skipping training candidate: Gene.2323::NM_001007523_dup1::g.2323::m.2323, not unique enough -skipping training candidate: Gene.3128::NM_001009934::g.3128::m.3128, not unique enough -skipping training candidate: Gene.3129::NM_001303620::g.3129::m.3129, not unique enough -skipping training candidate: Gene.3130::NM_006730::g.3130::m.3130, not unique enough -skipping training candidate: Gene.3131::NM_001009932::g.3131::m.3131, not unique enough -skipping training candidate: Gene.3132::MSTRG.1028.1::g.3132::m.3132, not unique enough -skipping training candidate: Gene.2324::NM_025159::g.2324::m.2324, not unique enough -skipping training candidate: Gene.2325::MSTRG.205.1::g.2325::m.2325, not unique enough -skipping training candidate: Gene.3423::NM_001184771::g.3423::m.3423, not unique enough -skipping training candidate: Gene.1715::NM_001267713::g.1715::m.1715, not unique enough -skipping training candidate: Gene.3875::NM_019007::g.3875::m.3875, not unique enough -skipping training candidate: Gene.3876::NM_001009584::g.3876::m.3876, not unique enough -skipping training candidate: Gene.4163::MSTRG.651.3::g.4163::m.4163, not unique enough -skipping training candidate: Gene.2551::MSTRG.128.5::g.2551::m.2551, not unique enough -skipping training candidate: Gene.2570::NM_004683::g.2570::m.2570, not unique enough -skipping training candidate: Gene.4281::NM_001171039::g.4281::m.4281, not unique enough -skipping training candidate: Gene.2260::NM_172249::g.2260::m.2260, not unique enough -skipping training candidate: Gene.2470::NM_001199687::g.2470::m.2470, not unique enough -skipping training candidate: Gene.3981::MSTRG.734.3::g.3981::m.3981, not unique enough -skipping training candidate: Gene.4043::MSTRG.1005.2::g.4043::m.4043, not unique enough -skipping training candidate: Gene.2827::NM_001159699::g.2827::m.2827, not unique enough -skipping training candidate: Gene.3705::NM_001025580::g.3705::m.3705, not unique enough -skipping training candidate: Gene.3720::MSTRG.933.1::g.3720::m.3720, not unique enough -skipping training candidate: Gene.1834::NM_001166419::g.1834::m.1834, not unique enough -skipping training candidate: Gene.1959::NM_001256761::g.1959::m.1959, not unique enough -skipping training candidate: Gene.3247::MSTRG.794.3::g.3247::m.3247, not unique enough -skipping training candidate: Gene.173::NM_001170702::g.173::m.173, not unique enough -skipping training candidate: Gene.3363::NM_000116::g.3363::m.3363, not unique enough -skipping training candidate: Gene.2251::NM_001167990::g.2251::m.2251, not unique enough -skipping training candidate: Gene.2371::NM_001174092::g.2371::m.2371, not unique enough -skipping training candidate: Gene.3405::NM_033670::g.3405::m.3405, not unique enough -skipping training candidate: Gene.944::NR_103708::g.944::m.944, not unique enough -skipping training candidate: Gene.3931::NM_003662::g.3931::m.3931, not unique enough -skipping training candidate: Gene.231::MSTRG.909.4::g.231::m.231, not unique enough -skipping training candidate: Gene.317::NM_001080146_dup3::g.317::m.317, not unique enough -skipping training candidate: Gene.318::NM_001080146::g.318::m.318, not unique enough -skipping training candidate: Gene.319::NM_001080146_dup6::g.319::m.319, not unique enough -skipping training candidate: Gene.320::NM_001080146_dup1::g.320::m.320, not unique enough -skipping training candidate: Gene.321::NM_001080146_dup2::g.321::m.321, not unique enough -skipping training candidate: Gene.322::NM_001080146_dup5::g.322::m.322, not unique enough -skipping training candidate: Gene.323::NM_001080146_dup9::g.323::m.323, not unique enough -skipping training candidate: Gene.324::NM_001080146_dup4::g.324::m.324, not unique enough -skipping training candidate: Gene.325::NM_001080146_dup8::g.325::m.325, not unique enough -skipping training candidate: Gene.410::NM_001304990::g.410::m.410, not unique enough -skipping training candidate: Gene.882::NM_032498::g.882::m.882, not unique enough -skipping training candidate: Gene.945::NM_001080137_dup6::g.945::m.945, not unique enough -skipping training candidate: Gene.946::NM_001080137_dup1::g.946::m.946, not unique enough -skipping training candidate: Gene.947::NM_001080137_dup7::g.947::m.947, not unique enough -skipping training candidate: Gene.948::NM_001080137_dup5::g.948::m.948, not unique enough -skipping training candidate: Gene.949::NM_001080137_dup2::g.949::m.949, not unique enough -skipping training candidate: Gene.950::NM_001080137_dup4::g.950::m.950, not unique enough -skipping training candidate: Gene.951::NM_001080137_dup8::g.951::m.951, not unique enough -skipping training candidate: Gene.952::NM_001080137_dup3::g.952::m.952, not unique enough -skipping training candidate: Gene.953::NM_001080137_dup9::g.953::m.953, not unique enough -skipping training candidate: Gene.954::NM_001080137::g.954::m.954, not unique enough -skipping training candidate: Gene.1267::NM_173571_dup7::g.1267::m.1267, not unique enough -skipping training candidate: Gene.1268::NM_173571_dup4::g.1268::m.1268, not unique enough -skipping training candidate: Gene.1269::NM_173571_dup8::g.1269::m.1269, not unique enough -skipping training candidate: Gene.1270::NM_173571_dup3::g.1270::m.1270, not unique enough -skipping training candidate: Gene.1271::NM_173571_dup1::g.1271::m.1271, not unique enough -skipping training candidate: Gene.1272::NM_173571_dup6::g.1272::m.1272, not unique enough -skipping training candidate: Gene.1273::NM_173571_dup9::g.1273::m.1273, not unique enough -skipping training candidate: Gene.1274::NM_173571_dup2::g.1274::m.1274, not unique enough -skipping training candidate: Gene.1275::NM_173571_dup5::g.1275::m.1275, not unique enough -skipping training candidate: Gene.1276::NM_173571::g.1276::m.1276, not unique enough -skipping training candidate: Gene.1564::NM_001080141_dup3::g.1564::m.1564, not unique enough -skipping training candidate: Gene.1565::NM_001080141_dup8::g.1565::m.1565, not unique enough -skipping training candidate: Gene.1566::NM_001080141_dup7::g.1566::m.1566, not unique enough -skipping training candidate: Gene.1567::NM_001080141_dup4::g.1567::m.1567, not unique enough -skipping training candidate: Gene.1568::NM_001080141_dup6::g.1568::m.1568, not unique enough -skipping training candidate: Gene.1569::NM_001080141_dup5::g.1569::m.1569, not unique enough -skipping training candidate: Gene.1570::NM_001080141_dup2::g.1570::m.1570, not unique enough -skipping training candidate: Gene.1571::NM_001080141::g.1571::m.1571, not unique enough -skipping training candidate: Gene.1572::NM_001080141_dup9::g.1572::m.1572, not unique enough -skipping training candidate: Gene.1573::NM_001080141_dup1::g.1573::m.1573, not unique enough -skipping training candidate: Gene.1816::NM_001080138_dup5::g.1816::m.1816, not unique enough -skipping training candidate: Gene.1817::NM_001080138_dup9::g.1817::m.1817, not unique enough -skipping training candidate: Gene.1818::NM_001080138::g.1818::m.1818, not unique enough -skipping training candidate: Gene.1819::NM_001080138_dup6::g.1819::m.1819, not unique enough -skipping training candidate: Gene.1820::NM_001080138_dup8::g.1820::m.1820, not unique enough -skipping training candidate: Gene.1821::NM_001080138_dup1::g.1821::m.1821, not unique enough -skipping training candidate: Gene.1822::NM_001080138_dup2::g.1822::m.1822, not unique enough -skipping training candidate: Gene.1823::NM_001080138_dup4::g.1823::m.1823, not unique enough -skipping training candidate: Gene.1824::NM_001080138_dup7::g.1824::m.1824, not unique enough -skipping training candidate: Gene.1825::NM_001080138_dup3::g.1825::m.1825, not unique enough -skipping training candidate: Gene.2300::NM_001080145_dup1::g.2300::m.2300, not unique enough -skipping training candidate: Gene.2301::NM_001080145_dup2::g.2301::m.2301, not unique enough -skipping training candidate: Gene.2302::NM_001080145_dup5::g.2302::m.2302, not unique enough -skipping training candidate: Gene.2303::NM_001080145::g.2303::m.2303, not unique enough -skipping training candidate: Gene.2304::NM_001080145_dup8::g.2304::m.2304, not unique enough -skipping training candidate: Gene.2305::NM_001080145_dup3::g.2305::m.2305, not unique enough -skipping training candidate: Gene.2306::NM_001080145_dup7::g.2306::m.2306, not unique enough -skipping training candidate: Gene.2307::NM_001080145_dup9::g.2307::m.2307, not unique enough -skipping training candidate: Gene.2308::NM_001080145_dup6::g.2308::m.2308, not unique enough -skipping training candidate: Gene.2309::NM_001080145_dup4::g.2309::m.2309, not unique enough -skipping training candidate: Gene.2349::NM_001080143_dup4::g.2349::m.2349, not unique enough -skipping training candidate: Gene.2350::NM_001080143_dup8::g.2350::m.2350, not unique enough -skipping training candidate: Gene.2351::NM_001080143::g.2351::m.2351, not unique enough -skipping training candidate: Gene.2352::NM_001080143_dup1::g.2352::m.2352, not unique enough -skipping training candidate: Gene.2353::NM_001080143_dup7::g.2353::m.2353, not unique enough -skipping training candidate: Gene.2354::NM_001080143_dup5::g.2354::m.2354, not unique enough -skipping training candidate: Gene.2355::NM_001080143_dup6::g.2355::m.2355, not unique enough -skipping training candidate: Gene.2356::NM_001080143_dup3::g.2356::m.2356, not unique enough -skipping training candidate: Gene.2357::NM_001080143_dup9::g.2357::m.2357, not unique enough -skipping training candidate: Gene.2358::NM_001080143_dup2::g.2358::m.2358, not unique enough -skipping training candidate: Gene.2920::NM_001099685::g.2920::m.2920, not unique enough -skipping training candidate: Gene.2922::NM_001099685_dup1::g.2922::m.2922, not unique enough -skipping training candidate: Gene.2983::NM_001142421::g.2983::m.2983, not unique enough -skipping training candidate: Gene.2984::NM_001142430::g.2984::m.2984, not unique enough -skipping training candidate: Gene.2985::NM_012286::g.2985::m.2985, not unique enough -skipping training candidate: Gene.2986::NM_001142426::g.2986::m.2986, not unique enough -skipping training candidate: Gene.2987::NM_001142418::g.2987::m.2987, not unique enough -skipping training candidate: Gene.2988::NM_001142427::g.2988::m.2988, not unique enough -skipping training candidate: Gene.2989::NM_001142419::g.2989::m.2989, not unique enough -skipping training candidate: Gene.2990::NM_001142420::g.2990::m.2990, not unique enough -skipping training candidate: Gene.2991::NM_001142432::g.2991::m.2991, not unique enough -skipping training candidate: Gene.2992::NM_001142429::g.2992::m.2992, not unique enough -skipping training candidate: Gene.2993::NM_001142428::g.2993::m.2993, not unique enough -skipping training candidate: Gene.2994::NM_001142431::g.2994::m.2994, not unique enough -skipping training candidate: Gene.2995::NM_001142425::g.2995::m.2995, not unique enough -skipping training candidate: Gene.2996::NM_001142423::g.2996::m.2996, not unique enough -skipping training candidate: Gene.2997::MSTRG.695.1::g.2997::m.2997, not unique enough -skipping training candidate: Gene.2998::NM_001142422::g.2998::m.2998, not unique enough -skipping training candidate: Gene.3458::NM_001080140::g.3458::m.3458, not unique enough -skipping training candidate: Gene.3459::NM_001242922::g.3459::m.3459, not unique enough -skipping training candidate: Gene.3460::NM_001242922_dup2::g.3460::m.3460, not unique enough -skipping training candidate: Gene.3461::NM_001242922_dup3::g.3461::m.3461, not unique enough -skipping training candidate: Gene.3462::NM_001242922_dup6::g.3462::m.3462, not unique enough -skipping training candidate: Gene.3463::NM_001242922_dup9::g.3463::m.3463, not unique enough -skipping training candidate: Gene.3464::NM_001242922_dup4::g.3464::m.3464, not unique enough -skipping training candidate: Gene.3465::NM_001242922_dup5::g.3465::m.3465, not unique enough -skipping training candidate: Gene.3466::NM_001242922_dup1::g.3466::m.3466, not unique enough -skipping training candidate: Gene.3467::NM_001242922_dup8::g.3467::m.3467, not unique enough -skipping training candidate: Gene.3468::NM_001242922_dup7::g.3468::m.3468, not unique enough -skipping training candidate: Gene.3774::MSTRG.992.1::g.3774::m.3774, not unique enough -skipping training candidate: Gene.3886::NM_001080144_dup9::g.3886::m.3886, not unique enough -skipping training candidate: Gene.3887::NM_001080144::g.3887::m.3887, not unique enough -skipping training candidate: Gene.3888::NM_001080144_dup6::g.3888::m.3888, not unique enough -skipping training candidate: Gene.3889::NM_001080144_dup4::g.3889::m.3889, not unique enough -skipping training candidate: Gene.3890::NM_001080144_dup3::g.3890::m.3890, not unique enough -skipping training candidate: Gene.3891::NM_001080144_dup1::g.3891::m.3891, not unique enough -skipping training candidate: Gene.3892::NM_001080144_dup7::g.3892::m.3892, not unique enough -skipping training candidate: Gene.3893::NM_001080144_dup2::g.3893::m.3893, not unique enough -skipping training candidate: Gene.3894::NM_001080144_dup8::g.3894::m.3894, not unique enough -skipping training candidate: Gene.3895::NM_001080144_dup5::g.3895::m.3895, not unique enough -skipping training candidate: Gene.4052::NM_001080142_dup9::g.4052::m.4052, not unique enough -skipping training candidate: Gene.4053::NM_001080142_dup8::g.4053::m.4053, not unique enough -skipping training candidate: Gene.4054::NM_001080142_dup6::g.4054::m.4054, not unique enough -skipping training candidate: Gene.4055::NM_001080142_dup1::g.4055::m.4055, not unique enough -skipping training candidate: Gene.4056::NM_001080142_dup2::g.4056::m.4056, not unique enough -skipping training candidate: Gene.4057::NM_001080142_dup5::g.4057::m.4057, not unique enough -skipping training candidate: Gene.4058::NM_001080142_dup7::g.4058::m.4058, not unique enough -skipping training candidate: Gene.4059::NM_001080142_dup4::g.4059::m.4059, not unique enough -skipping training candidate: Gene.4060::NM_001080142::g.4060::m.4060, not unique enough -skipping training candidate: Gene.4061::NM_001080142_dup3::g.4061::m.4061, not unique enough -skipping training candidate: Gene.4102::NM_001080139::g.4102::m.4102, not unique enough -skipping training candidate: Gene.4103::NM_001080139_dup6::g.4103::m.4103, not unique enough -skipping training candidate: Gene.4104::NM_001080139_dup1::g.4104::m.4104, not unique enough -skipping training candidate: Gene.4105::NM_001080139_dup5::g.4105::m.4105, not unique enough -skipping training candidate: Gene.4106::NM_001080139_dup4::g.4106::m.4106, not unique enough -skipping training candidate: Gene.4107::NM_001080139_dup2::g.4107::m.4107, not unique enough -skipping training candidate: Gene.4108::NM_001080139_dup7::g.4108::m.4108, not unique enough -skipping training candidate: Gene.4109::NM_001080139_dup8::g.4109::m.4109, not unique enough -skipping training candidate: Gene.4110::NM_001080139_dup3::g.4110::m.4110, not unique enough -skipping training candidate: Gene.4111::NM_001080139_dup9::g.4111::m.4111, not unique enough -skipping training candidate: Gene.3472::NR_073149::g.3472::m.3472, not unique enough -skipping training candidate: Gene.3832::NM_000166::g.3832::m.3832, not unique enough -skipping training candidate: Gene.700::MSTRG.994.1::g.700::m.700, not unique enough -skipping training candidate: Gene.1951::NM_030763::g.1951::m.1951, not unique enough -skipping training candidate: Gene.3106::NM_001307944::g.3106::m.3106, not unique enough -skipping training candidate: Gene.3147::MSTRG.1041.8::g.3147::m.3147, not unique enough -skipping training candidate: Gene.2828::NR_027621::g.2828::m.2828, not unique enough -skipping training candidate: Gene.2830::NM_001449::g.2830::m.2830, not unique enough -skipping training candidate: Gene.2833::NM_001159704::g.2833::m.2833, not unique enough -skipping training candidate: Gene.2834::NM_001167819::g.2834::m.2834, not unique enough -skipping training candidate: Gene.2838::NM_001159700::g.2838::m.2838, not unique enough -skipping training candidate: Gene.2788::MSTRG.1074.12::g.2788::m.2788, not unique enough -skipping training candidate: Gene.3365::NM_181311::g.3365::m.3365, not unique enough -skipping training candidate: Gene.3390::NM_181312::g.3390::m.3390, not unique enough -skipping training candidate: Gene.861::NM_001170963::g.861::m.861, not unique enough -skipping training candidate: Gene.3337::NM_001128834::g.3337::m.3337, not unique enough -skipping training candidate: Gene.3585::NM_080879::g.3585::m.3585, not unique enough -skipping training candidate: Gene.1660::MSTRG.1023.2::g.1660::m.1660, not unique enough -skipping training candidate: Gene.1247::NM_001130847::g.1247::m.1247, not unique enough -skipping training candidate: Gene.1249::NR_132647::g.1249::m.1249, not unique enough -skipping training candidate: Gene.1252::NM_001130846::g.1252::m.1252, not unique enough -skipping training candidate: Gene.153::MSTRG.889.14::g.153::m.153, not unique enough -skipping training candidate: Gene.156::MSTRG.889.4::g.156::m.156, not unique enough -skipping training candidate: Gene.167::MSTRG.889.12::g.167::m.167, not unique enough -skipping training candidate: Gene.1392::MSTRG.68.8::g.1392::m.1392, not unique enough -skipping training candidate: Gene.1402::MSTRG.68.3::g.1402::m.1402, not unique enough -skipping training candidate: Gene.1406::MSTRG.68.6::g.1406::m.1406, not unique enough -skipping training candidate: Gene.1409::MSTRG.68.16::g.1409::m.1409, not unique enough -skipping training candidate: Gene.1416::NR_034031::g.1416::m.1416, not unique enough -skipping training candidate: Gene.1421::MSTRG.68.14::g.1421::m.1421, not unique enough -skipping training candidate: Gene.1430::MSTRG.68.17::g.1430::m.1430, not unique enough -skipping training candidate: Gene.1955::MSTRG.597.3::g.1955::m.1955, not unique enough -skipping training candidate: Gene.3163::MSTRG.1041.7::g.3163::m.3163, not unique enough -skipping training candidate: Gene.3780::MSTRG.992.2::g.3780::m.3780, not unique enough -skipping training candidate: Gene.220::MSTRG.909.9::g.220::m.220, not unique enough -skipping training candidate: Gene.1387::MSTRG.68.10::g.1387::m.1387, not unique enough -skipping training candidate: Gene.1396::MSTRG.68.5::g.1396::m.1396, not unique enough -skipping training candidate: Gene.2724::MSTRG.159.6::g.2724::m.2724, not unique enough -skipping training candidate: Gene.217::MSTRG.909.8::g.217::m.217, not unique enough -skipping training candidate: Gene.2586::MSTRG.841.2::g.2586::m.2586, not unique enough -skipping training candidate: Gene.1446::NM_001114377::g.1446::m.1446, not unique enough -skipping training candidate: Gene.312::NM_001171991::g.312::m.312, not unique enough -skipping training candidate: Gene.313::NM_001122608::g.313::m.313, not unique enough -skipping training candidate: Gene.1350::NM_001278701::g.1350::m.1350, not unique enough -skipping training candidate: Gene.4312::NM_003147::g.4312::m.4312, not unique enough -skipping training candidate: Gene.4313::NM_003147_dup1::g.4313::m.4313, not unique enough -skipping training candidate: Gene.226::MSTRG.909.1::g.226::m.226, not unique enough -skipping training candidate: Gene.1675::MSTRG.978.1::g.1675::m.1675, not unique enough -skipping training candidate: Gene.2073::NM_001161532::g.2073::m.2073, not unique enough -skipping training candidate: Gene.230::NM_001170756::g.230::m.230, not unique enough -skipping training candidate: Gene.18::NM_017776::g.18::m.18, not unique enough -skipping training candidate: Gene.1256::NM_198456::g.1256::m.1256, not unique enough -skipping training candidate: Gene.1263::NM_001300788::g.1263::m.1263, not unique enough -skipping training candidate: Gene.2249::NM_005710::g.2249::m.2249, not unique enough -skipping training candidate: Gene.2254::NM_001032382::g.2254::m.2254, not unique enough -skipping training candidate: Gene.2255::NM_001032383::g.2255::m.2255, not unique enough -skipping training candidate: Gene.2256::NM_001032381::g.2256::m.2256, not unique enough -skipping training candidate: Gene.2464::NM_005278::g.2464::m.2464, not unique enough -skipping training candidate: Gene.3242::MSTRG.794.4::g.3242::m.3242, not unique enough -skipping training candidate: Gene.3382::NM_181313::g.3382::m.3382, not unique enough -skipping training candidate: Gene.2259::NM_001167989::g.2259::m.2259, not unique enough -skipping training candidate: Gene.2767::MSTRG.1074.10::g.2767::m.2767, not unique enough -skipping training candidate: Gene.2776::MSTRG.1074.2::g.2776::m.2776, not unique enough -skipping training candidate: Gene.2782::MSTRG.1074.3::g.2782::m.2782, not unique enough -skipping training candidate: Gene.2785::MSTRG.1074.8::g.2785::m.2785, not unique enough -skipping training candidate: Gene.119::MSTRG.589.1::g.119::m.119, not unique enough -skipping training candidate: Gene.444::NM_001007::g.444::m.444, not unique enough -skipping training candidate: Gene.924::NM_020473::g.924::m.924, not unique enough -skipping training candidate: Gene.3787::MSTRG.602.2::g.3787::m.3787, not unique enough -skipping training candidate: Gene.416::NM_001037811::g.416::m.416, not unique enough -skipping training candidate: Gene.698::NM_001130997::g.698::m.698, not unique enough -skipping training candidate: Gene.1663::NM_031462::g.1663::m.1663, not unique enough -skipping training candidate: Gene.2158::NM_001168531::g.2158::m.2158, not unique enough -skipping training candidate: Gene.2161::NM_024087::g.2161::m.2161, not unique enough -skipping training candidate: Gene.3366::NM_181311::g.3366::m.3366, not unique enough -skipping training candidate: Gene.3772::MSTRG.992.6::g.3772::m.3772, not unique enough -skipping training candidate: Gene.2537::NM_003492::g.2537::m.2537, not unique enough -skipping training candidate: Gene.428::MSTRG.110.2::g.428::m.428, not unique enough -skipping training candidate: Gene.2960::NM_001012288::g.2960::m.2960, not unique enough -skipping training candidate: Gene.3655::NM_001278702_dup1::g.3655::m.3655, not unique enough -skipping training candidate: Gene.3656::NM_001278702::g.3656::m.3656, not unique enough -skipping training candidate: Gene.3830::NM_001278697::g.3830::m.3830, not unique enough -skipping training candidate: Gene.3831::NM_001278697_dup1::g.3831::m.3831, not unique enough -skipping training candidate: Gene.151::NM_001170704::g.151::m.151, not unique enough -skipping training candidate: Gene.162::MSTRG.889.15::g.162::m.162, not unique enough -skipping training candidate: Gene.172::MSTRG.889.11::g.172::m.172, not unique enough -skipping training candidate: Gene.175::MSTRG.889.18::g.175::m.175, not unique enough -skipping training candidate: Gene.178::MSTRG.889.17::g.178::m.178, not unique enough -skipping training candidate: Gene.180::MSTRG.889.16::g.180::m.180, not unique enough -skipping training candidate: Gene.489::NM_001010862::g.489::m.489, not unique enough -skipping training candidate: Gene.2801::MSTRG.541.3::g.2801::m.2801, not unique enough -skipping training candidate: Gene.3785::NM_001099681::g.3785::m.3785, not unique enough -skipping training candidate: Gene.4302::NM_001006681::g.4302::m.4302, not unique enough -skipping training candidate: Gene.4303::MSTRG.426.1::g.4303::m.4303, not unique enough -skipping training candidate: Gene.4305::NM_001006683::g.4305::m.4305, not unique enough -skipping training candidate: Gene.4307::NM_001006682::g.4307::m.4307, not unique enough -skipping training candidate: Gene.1259::NM_017848::g.1259::m.1259, not unique enough -skipping training candidate: Gene.1630::NM_000425::g.1630::m.1630, not unique enough -skipping training candidate: Gene.1636::NM_024003::g.1636::m.1636, not unique enough -skipping training candidate: Gene.1642::NM_001143963::g.1642::m.1642, not unique enough -skipping training candidate: Gene.2220::MSTRG.222.1::g.2220::m.2220, not unique enough -skipping training candidate: Gene.2290::MSTRG.693.4::g.2290::m.2290, not unique enough -skipping training candidate: Gene.2491::NM_001159296::g.2491::m.2491, not unique enough -skipping training candidate: Gene.682::MSTRG.763.3::g.682::m.682, not unique enough -skipping training candidate: Gene.943::NM_001162491::g.943::m.943, not unique enough -skipping training candidate: Gene.3714::NR_028476::g.3714::m.3714, not unique enough -skipping training candidate: Gene.4003::NR_110023::g.4003::m.4003, not unique enough -skipping training candidate: Gene.1581::NM_001099682::g.1581::m.1581, not unique enough -skipping training candidate: Gene.2558::NM_012080::g.2558::m.2558, not unique enough -skipping training candidate: Gene.2949::NM_001142389::g.2949::m.2949, not unique enough -skipping training candidate: Gene.4165::MSTRG.651.4::g.4165::m.4165, not unique enough -skipping training candidate: Gene.1488::MSTRG.921.7::g.1488::m.1488, not unique enough -skipping training candidate: Gene.1493::MSTRG.921.5::g.1493::m.1493, not unique enough -skipping training candidate: Gene.1498::MSTRG.921.6::g.1498::m.1498, not unique enough -skipping training candidate: Gene.2163::NM_001168530::g.2163::m.2163, not unique enough -skipping training candidate: Gene.4030::MSTRG.8.2::g.4030::m.4030, not unique enough -skipping training candidate: Gene.223::MSTRG.909.17::g.223::m.223, not unique enough -skipping training candidate: Gene.3620::MSTRG.320.1::g.3620::m.3620, not unique enough -skipping training candidate: Gene.307::MSTRG.91.6::g.307::m.307, not unique enough -skipping training candidate: Gene.308::MSTRG.91.9::g.308::m.308, not unique enough -skipping training candidate: Gene.2377::NM_001300884::g.2377::m.2377, not unique enough -skipping training candidate: Gene.227::NM_145284::g.227::m.227, not unique enough -skipping training candidate: Gene.1751::NM_173698::g.1751::m.1751, not unique enough -skipping training candidate: Gene.1843::NM_001171109::g.1843::m.1843, not unique enough -skipping training candidate: Gene.3383::NM_181313::g.3383::m.3383, not unique enough -skipping training candidate: Gene.3435::NM_001171111::g.3435::m.3435, not unique enough -skipping training candidate: Gene.3717::NM_002139::g.3717::m.3717, not unique enough -skipping training candidate: Gene.3719::NR_028477::g.3719::m.3719, not unique enough -skipping training candidate: Gene.215::NM_001166599::g.215::m.215, not unique enough -skipping training candidate: Gene.222::MSTRG.909.16::g.222::m.222, not unique enough -skipping training candidate: Gene.1830::MSTRG.265.4::g.1830::m.1830, not unique enough -skipping training candidate: Gene.3268::MSTRG.664.1::g.3268::m.3268, not unique enough -skipping training candidate: Gene.4319::NR_037916::g.4319::m.4319, not unique enough -skipping training candidate: Gene.2685::NM_005745::g.2685::m.2685, not unique enough -skipping training candidate: Gene.2688::NM_001139441::g.2688::m.2688, not unique enough -skipping training candidate: Gene.3747::NM_001282848::g.3747::m.3747, not unique enough -skipping training candidate: Gene.1884::MSTRG.654.6::g.1884::m.1884, not unique enough -skipping training candidate: Gene.2367::NR_073450::g.2367::m.2367, not unique enough -skipping training candidate: Gene.2759::MSTRG.1074.14::g.2759::m.2759, not unique enough -skipping training candidate: Gene.4250::MSTRG.17.7::g.4250::m.4250, not unique enough -skipping training candidate: Gene.224::MSTRG.909.2::g.224::m.224, not unique enough -skipping training candidate: Gene.1281::MSTRG.45.1::g.1281::m.1281, not unique enough -skipping training candidate: Gene.1782::NM_001012977::g.1782::m.1782, not unique enough -skipping training candidate: Gene.2337::NM_017863::g.2337::m.2337, not unique enough -skipping training candidate: Gene.3935::NR_037859::g.3935::m.3935, not unique enough -skipping training candidate: Gene.4069::NM_001042480::g.4069::m.4069, not unique enough -skipping training candidate: Gene.4078::NM_017856::g.4078::m.4078, not unique enough -skipping training candidate: Gene.4323::NM_199478::g.4323::m.4323, not unique enough -skipping training candidate: Gene.229::NM_001166600::g.229::m.229, not unique enough -skipping training candidate: Gene.329::MSTRG.980.5::g.329::m.329, not unique enough -skipping training candidate: Gene.904::NM_001104545::g.904::m.904, not unique enough -skipping training candidate: Gene.2480::MSTRG.459.5::g.2480::m.2480, not unique enough -skipping training candidate: Gene.3320::NM_006950::g.3320::m.3320, not unique enough -skipping training candidate: Gene.430::MSTRG.110.9::g.430::m.430, not unique enough -skipping training candidate: Gene.3360::MSTRG.1029.2::g.3360::m.3360, not unique enough -skipping training candidate: Gene.3364::NM_000116::g.3364::m.3364, not unique enough -skipping training candidate: Gene.3376::MSTRG.1029.4::g.3376::m.3376, not unique enough -skipping training candidate: Gene.3391::NM_181312::g.3391::m.3391, not unique enough -skipping training candidate: Gene.1383::MSTRG.68.9::g.1383::m.1383, not unique enough -skipping training candidate: Gene.2231::MSTRG.222.2::g.2231::m.2231, not unique enough -skipping training candidate: Gene.3507::MSTRG.268.7::g.3507::m.3507, not unique enough -skipping training candidate: Gene.3517::MSTRG.268.3::g.3517::m.3517, not unique enough -skipping training candidate: Gene.3846::NM_001267053::g.3846::m.3846, not unique enough -skipping training candidate: Gene.1250::NR_132647::g.1250::m.1250, not unique enough -skipping training candidate: Gene.3184::NM_001163321::g.3184::m.3184, not unique enough -skipping training candidate: Gene.3592::MSTRG.1037.1::g.3592::m.3592, not unique enough -skipping training candidate: Gene.840::NM_001169125::g.840::m.840, not unique enough -skipping training candidate: Gene.843::NM_001169122::g.843::m.843, not unique enough -skipping training candidate: Gene.332::NM_005342::g.332::m.332, not unique enough -skipping training candidate: Gene.2887::MSTRG.858.1::g.2887::m.2887, not unique enough -skipping training candidate: Gene.3173::NM_001271835::g.3173::m.3173, not unique enough -skipping training candidate: Gene.3177::NM_033626::g.3177::m.3177, not unique enough -skipping training candidate: Gene.3180::NM_001271836::g.3180::m.3180, not unique enough -skipping training candidate: Gene.3182::NM_001163323::g.3182::m.3182, not unique enough -skipping training candidate: Gene.4160::MSTRG.651.12::g.4160::m.4160, not unique enough -skipping training candidate: Gene.4161::MSTRG.651.15::g.4161::m.4161, not unique enough -skipping training candidate: Gene.4170::MSTRG.651.13::g.4170::m.4170, not unique enough -skipping training candidate: Gene.327::NM_001301229::g.327::m.327, not unique enough -skipping training candidate: Gene.2972::MSTRG.209.9::g.2972::m.2972, not unique enough -skipping training candidate: Gene.4344::NM_001170570::g.4344::m.4344, not unique enough -skipping training candidate: Gene.2559::NM_001178135::g.2559::m.2559, not unique enough -skipping training candidate: Gene.3215::NM_001164417_dup1::g.3215::m.3215, not unique enough -skipping training candidate: Gene.3216::NM_001164417::g.3216::m.3216, not unique enough -skipping training candidate: Gene.3821::NM_175698_dup1::g.3821::m.3821, not unique enough -skipping training candidate: Gene.3822::NM_175698::g.3822::m.3822, not unique enough -skipping training candidate: Gene.3998::NR_110022::g.3998::m.3998, not unique enough -skipping training candidate: Gene.2903::NM_024082::g.2903::m.2903, not unique enough -skipping training candidate: Gene.1114::MSTRG.961.1::g.1114::m.1114, not unique enough -skipping training candidate: Gene.1180::NM_001171095::g.1180::m.1180, not unique enough -skipping training candidate: Gene.2563::NM_001171092::g.2563::m.2563, not unique enough -skipping training candidate: Gene.3580::MSTRG.303.1::g.3580::m.3580, not unique enough -skipping training candidate: Gene.3586::NM_021806::g.3586::m.3586, not unique enough -skipping training candidate: Gene.3597::NM_001282312::g.3597::m.3597, not unique enough -skipping training candidate: Gene.1772::NM_001256120::g.1772::m.1772, not unique enough -skipping training candidate: Gene.3782::MSTRG.992.7::g.3782::m.3782, not unique enough -skipping training candidate: Gene.1574::NM_001193281::g.1574::m.1574, not unique enough -skipping training candidate: Gene.2411::NR_104391::g.2411::m.2411, not unique enough -skipping training candidate: Gene.4336::MSTRG.345.4::g.4336::m.4336, not unique enough -skipping training candidate: Gene.216::MSTRG.909.15::g.216::m.216, not unique enough -skipping training candidate: Gene.1287::NM_001122898::g.1287::m.1287, not unique enough -skipping training candidate: Gene.1482::NM_001282849::g.1482::m.1482, not unique enough -skipping training candidate: Gene.2383::MSTRG.405.3::g.2383::m.2383, not unique enough -skipping training candidate: Gene.2385::MSTRG.405.6::g.2385::m.2385, not unique enough -skipping training candidate: Gene.2738::NM_001184831::g.2738::m.2738, not unique enough -skipping training candidate: Gene.3377::MSTRG.1029.4::g.3377::m.3377, not unique enough -skipping training candidate: Gene.4290::MSTRG.32.4::g.4290::m.4290, not unique enough -skipping training candidate: Gene.225::MSTRG.909.5::g.225::m.225, not unique enough -skipping training candidate: Gene.1300::NM_001139501::g.1300::m.1300, not unique enough -skipping training candidate: Gene.2239::MSTRG.113.1::g.2239::m.2239, not unique enough -skipping training candidate: Gene.2404::NR_104392::g.2404::m.2404, not unique enough -skipping training candidate: Gene.2415::NR_104394::g.2415::m.2415, not unique enough -skipping training candidate: Gene.3107::NM_001139502::g.3107::m.3107, not unique enough -skipping training candidate: Gene.261::MSTRG.26.2::g.261::m.261, not unique enough -skipping training candidate: Gene.2632::NM_006883::g.2632::m.2632, not unique enough -skipping training candidate: Gene.1868::MSTRG.578.1::g.1868::m.1868, not unique enough -skipping training candidate: Gene.1878::NM_001303277::g.1878::m.1878, not unique enough -skipping training candidate: Gene.2610::NM_001282647::g.2610::m.2610, not unique enough -skipping training candidate: Gene.4220::NM_001291530::g.4220::m.4220, not unique enough -skipping training candidate: Gene.4267::MSTRG.1024.2::g.4267::m.4267, not unique enough -skipping training candidate: Gene.221::MSTRG.909.3::g.221::m.221, not unique enough -skipping training candidate: Gene.404::NM_001080851::g.404::m.404, not unique enough -skipping training candidate: Gene.1462::NM_033053::g.1462::m.1462, not unique enough -skipping training candidate: Gene.1464::NM_033053_dup1::g.1464::m.1464, not unique enough -skipping training candidate: Gene.219::MSTRG.909.7::g.219::m.219, not unique enough -skipping training candidate: Gene.2519::NM_001305004::g.2519::m.2519, not unique enough -skipping training candidate: Gene.2203::NM_005834::g.2203::m.2203, not unique enough -skipping training candidate: Gene.3270::MSTRG.664.2::g.3270::m.3270, not unique enough -skipping training candidate: Gene.330::NM_001301231::g.330::m.330, not unique enough -skipping training candidate: Gene.464::NM_178175::g.464::m.464, not unique enough -skipping training candidate: Gene.1770::NM_001256119::g.1770::m.1770, not unique enough -skipping training candidate: Gene.117::NM_001171581::g.117::m.117, not unique enough -skipping training candidate: Gene.3610::NM_001144885::g.3610::m.3610, not unique enough -skipping training candidate: Gene.4219::NM_001291529::g.4219::m.4219, not unique enough -skipping training candidate: Gene.1067::NM_000950::g.1067::m.1067, not unique enough -skipping training candidate: Gene.1285::NM_001277710::g.1285::m.1285, not unique enough -skipping training candidate: Gene.2612::NM_001282648::g.2612::m.2612, not unique enough -skipping training candidate: Gene.3193::NM_001173489::g.3193::m.3193, not unique enough -skipping training candidate: Gene.3341::NM_001142395::g.3341::m.3341, not unique enough -skipping training candidate: Gene.85::MSTRG.759.24::g.85::m.85, not unique enough -skipping training candidate: Gene.299::NM_003372::g.299::m.299, not unique enough -skipping training candidate: Gene.837::NM_002025::g.837::m.837, not unique enough -skipping training candidate: Gene.846::NM_001169124::g.846::m.846, not unique enough -skipping training candidate: Gene.1020::MSTRG.913.2::g.1020::m.1020, not unique enough -skipping training candidate: Gene.1801::MSTRG.4.6::g.1801::m.1801, not unique enough -skipping training candidate: Gene.2587::MSTRG.841.2::g.2587::m.2587, not unique enough -skipping training candidate: Gene.3154::MSTRG.1041.6::g.3154::m.3154, not unique enough -skipping training candidate: Gene.4279::MSTRG.32.1::g.4279::m.4279, not unique enough -skipping training candidate: Gene.4285::NM_005088::g.4285::m.4285, not unique enough -skipping training candidate: Gene.4291::MSTRG.32.4::g.4291::m.4291, not unique enough -skipping training candidate: Gene.3252::NM_001305841::g.3252::m.3252, not unique enough -skipping training candidate: Gene.3253::NM_001305842::g.3253::m.3253, not unique enough -skipping training candidate: Gene.3254::NM_001006937::g.3254::m.3254, not unique enough -skipping training candidate: Gene.3256::NM_001305840::g.3256::m.3256, not unique enough -skipping training candidate: Gene.3257::NM_001006935::g.3257::m.3257, not unique enough -skipping training candidate: Gene.3259::NM_024863::g.3259::m.3259, not unique enough -skipping training candidate: Gene.359::NM_173494::g.359::m.359, not unique enough -skipping training candidate: Gene.548::NM_006013::g.548::m.548, not unique enough -skipping training candidate: Gene.552::MSTRG.1025.4::g.552::m.552, not unique enough -skipping training candidate: Gene.563::NM_001303625::g.563::m.563, not unique enough -skipping training candidate: Gene.566::NM_001303624::g.566::m.566, not unique enough -skipping training candidate: Gene.573::MSTRG.1025.1::g.573::m.573, not unique enough -skipping training candidate: Gene.2847::NM_006280::g.2847::m.2847, not unique enough -skipping training candidate: Gene.3388::MSTRG.1029.11::g.3388::m.3388, not unique enough -skipping training candidate: Gene.1164::MSTRG.364.1::g.1164::m.1164, not unique enough -skipping training candidate: Gene.1167::MSTRG.364.2::g.1167::m.1167, not unique enough -skipping training candidate: Gene.1169::NM_001242491_dup1::g.1169::m.1169, not unique enough -skipping training candidate: Gene.1170::MSTRG.364.3::g.1170::m.1170, not unique enough -skipping training candidate: Gene.1172::MSTRG.364.5::g.1172::m.1172, not unique enough -skipping training candidate: Gene.1228::NM_001242490::g.1228::m.1228, not unique enough -skipping training candidate: Gene.1229::MSTRG.369.13::g.1229::m.1229, not unique enough -skipping training candidate: Gene.1230::NM_001242494::g.1230::m.1230, not unique enough -skipping training candidate: Gene.1231::NM_014138::g.1231::m.1231, not unique enough -skipping training candidate: Gene.1232::NM_001242493::g.1232::m.1232, not unique enough -skipping training candidate: Gene.1233::MSTRG.369.2::g.1233::m.1233, not unique enough -skipping training candidate: Gene.1235::NM_001242497::g.1235::m.1235, not unique enough -skipping training candidate: Gene.1236::NM_001242491::g.1236::m.1236, not unique enough -skipping training candidate: Gene.1237::NM_001242496::g.1237::m.1237, not unique enough -skipping training candidate: Gene.1238::NM_001242489::g.1238::m.1238, not unique enough -skipping training candidate: Gene.1239::NM_001099684::g.1239::m.1239, not unique enough -skipping training candidate: Gene.1240::NM_001242492::g.1240::m.1240, not unique enough -skipping training candidate: Gene.1241::NM_001242495::g.1241::m.1241, not unique enough -skipping training candidate: Gene.1669::NM_134446::g.1669::m.1669, not unique enough -skipping training candidate: Gene.3299::NM_000054::g.3299::m.3299, not unique enough -skipping training candidate: Gene.3595::NM_001171134::g.3595::m.3595, not unique enough -skipping training candidate: Gene.3262::NM_001316889::g.3262::m.3262, not unique enough -skipping training candidate: Gene.3411::NM_021796::g.3411::m.3411, not unique enough -skipping training candidate: Gene.3539::NM_001316888::g.3539::m.3539, not unique enough -skipping training candidate: Gene.235::MSTRG.279.8::g.235::m.235, not unique enough -skipping training candidate: Gene.237::MSTRG.279.7::g.237::m.237, not unique enough -skipping training candidate: Gene.239::MSTRG.279.11::g.239::m.239, not unique enough -skipping training candidate: Gene.241::MSTRG.279.6::g.241::m.241, not unique enough -skipping training candidate: Gene.243::MSTRG.279.2::g.243::m.243, not unique enough -skipping training candidate: Gene.245::MSTRG.279.3::g.245::m.245, not unique enough -skipping training candidate: Gene.247::NM_007130::g.247::m.247, not unique enough -skipping training candidate: Gene.249::MSTRG.279.1::g.249::m.249, not unique enough -skipping training candidate: Gene.251::MSTRG.279.5::g.251::m.251, not unique enough -skipping training candidate: Gene.253::MSTRG.279.10::g.253::m.253, not unique enough -skipping training candidate: Gene.255::MSTRG.279.4::g.255::m.255, not unique enough -skipping training candidate: Gene.2556::NM_001178136::g.2556::m.2556, not unique enough -skipping training candidate: Gene.3707::NM_001171689::g.3707::m.3707, not unique enough -skipping training candidate: Gene.9::NM_013346::g.9::m.9, not unique enough -skipping training candidate: Gene.212::NM_001291543_dup2::g.212::m.212, not unique enough -skipping training candidate: Gene.213::NM_001291543::g.213::m.213, not unique enough -skipping training candidate: Gene.214::NM_001291543_dup1::g.214::m.214, not unique enough -skipping training candidate: Gene.558::MSTRG.1025.2::g.558::m.558, not unique enough -skipping training candidate: Gene.2526::NM_004840::g.2526::m.2526, not unique enough -skipping training candidate: Gene.2528::MSTRG.929.1::g.2528::m.2528, not unique enough -skipping training candidate: Gene.263::MSTRG.142.5::g.263::m.263, not unique enough -skipping training candidate: Gene.265::NM_001037536::g.265::m.265, not unique enough -skipping training candidate: Gene.269::NM_001037535::g.269::m.269, not unique enough -skipping training candidate: Gene.551::MSTRG.1025.3::g.551::m.551, not unique enough -skipping training candidate: Gene.562::MSTRG.1025.6::g.562::m.562, not unique enough -skipping training candidate: Gene.1335::MSTRG.912.5::g.1335::m.1335, not unique enough -skipping training candidate: Gene.326::MSTRG.980.6::g.326::m.326, not unique enough -skipping training candidate: Gene.3346::NM_024689::g.3346::m.3346, not unique enough -skipping training candidate: Gene.2381::MSTRG.405.7::g.2381::m.2381, not unique enough -skipping training candidate: Gene.2382::MSTRG.405.5::g.2382::m.2382, not unique enough -skipping training candidate: Gene.2388::MSTRG.405.4::g.2388::m.2388, not unique enough -skipping training candidate: Gene.2691::NM_013452::g.2691::m.2691, not unique enough -skipping training candidate: Gene.3052::NR_104114::g.3052::m.3052, not unique enough -skipping training candidate: Gene.3520::MSTRG.268.6::g.3520::m.3520, not unique enough -skipping training candidate: Gene.4::NM_001256188::g.4::m.4, not unique enough -skipping training candidate: Gene.694::MSTRG.994.4::g.694::m.694, not unique enough -skipping training candidate: Gene.1776::MSTRG.718.5::g.1776::m.1776, not unique enough -skipping training candidate: Gene.2761::MSTRG.1074.11::g.2761::m.2761, not unique enough -skipping training candidate: Gene.2774::MSTRG.1074.4::g.2774::m.2774, not unique enough -skipping training candidate: Gene.4039::MSTRG.1005.3::g.4039::m.4039, not unique enough -skipping training candidate: Gene.469::NM_181762::g.469::m.469, not unique enough -skipping training candidate: Gene.1814::NM_004651::g.1814::m.1814, not unique enough -skipping training candidate: Gene.2513::MSTRG.714.3::g.2513::m.2513, not unique enough -skipping training candidate: Gene.1548::MSTRG.697.2::g.1548::m.1548, not unique enough -skipping training candidate: Gene.2106::NM_001291277::g.2106::m.2106, not unique enough -skipping training candidate: Gene.3336::NM_004251::g.3336::m.3336, not unique enough -skipping training candidate: Gene.4184::NM_001178032::g.4184::m.4184, not unique enough -skipping training candidate: Gene.4185::NR_045044::g.4185::m.4185, not unique enough -skipping training candidate: Gene.4188::NM_001243804::g.4188::m.4188, not unique enough -skipping training candidate: Gene.2287::NM_032926::g.2287::m.2287, not unique enough -skipping training candidate: Gene.2292::NM_001006933::g.2292::m.2292, not unique enough -skipping training candidate: Gene.3797::MSTRG.232.1::g.3797::m.3797, not unique enough -skipping training candidate: Gene.3801::MSTRG.232.2::g.3801::m.3801, not unique enough -skipping training candidate: Gene.527::MSTRG.337.1::g.527::m.527, not unique enough -skipping training candidate: Gene.1030::MSTRG.305.1::g.1030::m.1030, not unique enough -skipping training candidate: Gene.1245::NM_003916::g.1245::m.1245, not unique enough -skipping training candidate: Gene.3020::NM_001139498::g.3020::m.3020, not unique enough -skipping training candidate: Gene.4037::NM_001666::g.4037::m.4037, not unique enough -skipping training candidate: Gene.4047::MSTRG.1005.1::g.4047::m.4047, not unique enough -skipping training candidate: Gene.4268::MSTRG.1024.2::g.4268::m.4268, not unique enough -skipping training candidate: Gene.19::NM_001129899::g.19::m.19, not unique enough -skipping training candidate: Gene.1840::NM_001166422::g.1840::m.1840, not unique enough -skipping training candidate: Gene.2484::MSTRG.459.1::g.2484::m.2484, not unique enough -skipping training candidate: Gene.3409::NM_176786::g.3409::m.3409, not unique enough -skipping training candidate: Gene.3953::MSTRG.124.2::g.3953::m.3953, not unique enough -skipping training candidate: Gene.3954::MSTRG.124.3::g.3954::m.3954, not unique enough -skipping training candidate: Gene.2835::NM_001159703::g.2835::m.2835, not unique enough -skipping training candidate: Gene.3636::NM_001168361::g.3636::m.3636, not unique enough -skipping training candidate: Gene.205::NM_001195214::g.205::m.205, not unique enough -skipping training candidate: Gene.2766::MSTRG.1074.6::g.2766::m.2766, not unique enough -skipping training candidate: Gene.2867::NM_004143::g.2867::m.2867, not unique enough -skipping training candidate: Gene.3126::NM_001144886::g.3126::m.3126, not unique enough -skipping training candidate: Gene.17::NM_001129900::g.17::m.17, not unique enough -skipping training candidate: Gene.533::NM_001282157::g.533::m.533, not unique enough -skipping training candidate: Gene.1000::MSTRG.51.1::g.1000::m.1000, not unique enough -skipping training candidate: Gene.1472::NM_033642::g.1472::m.1472, not unique enough -skipping training candidate: Gene.1795::MSTRG.4.3::g.1795::m.1795, not unique enough -skipping training candidate: Gene.1803::NM_018390::g.1803::m.1803, not unique enough -skipping training candidate: Gene.3845::NM_144968::g.3845::m.3845, not unique enough -skipping training candidate: Gene.2344::NM_001142::g.2344::m.2344, not unique enough -skipping training candidate: Gene.3367::MSTRG.1029.12::g.3367::m.3367, not unique enough -skipping training candidate: Gene.1666::NM_134445::g.1666::m.1666, not unique enough -skipping training candidate: Gene.218::NM_001170757::g.218::m.218, not unique enough -skipping training candidate: Gene.931::NM_001007551_dup2::g.931::m.931, not unique enough -skipping training candidate: Gene.932::NM_001007551_dup1::g.932::m.932, not unique enough -skipping training candidate: Gene.933::NM_001007551::g.933::m.933, not unique enough -skipping training candidate: Gene.1676::NM_001184808::g.1676::m.1676, not unique enough -skipping training candidate: Gene.2046::NM_001291540_dup2::g.2046::m.2046, not unique enough -skipping training candidate: Gene.2165::NM_001291540::g.2165::m.2165, not unique enough -skipping training candidate: Gene.2166::NM_001291540_dup1::g.2166::m.2166, not unique enough -skipping training candidate: Gene.2756::NM_001017436::g.2756::m.2756, not unique enough -skipping training candidate: Gene.3101::NM_001291535::g.3101::m.3101, not unique enough -skipping training candidate: Gene.3102::NM_001291535_dup1::g.3102::m.3102, not unique enough -skipping training candidate: Gene.3525::NM_152582_dup1::g.3525::m.3525, not unique enough -skipping training candidate: Gene.3526::NM_152582_dup2::g.3526::m.3526, not unique enough -skipping training candidate: Gene.3912::NM_001172288_dup2::g.3912::m.3912, not unique enough -skipping training candidate: Gene.3913::NM_001172288_dup1::g.3913::m.3913, not unique enough -skipping training candidate: Gene.3914::NM_001172288::g.3914::m.3914, not unique enough -skipping training candidate: Gene.4025::NM_001017438_dup1::g.4025::m.4025, not unique enough -skipping training candidate: Gene.4026::NM_001017438_dup2::g.4026::m.4026, not unique enough -skipping training candidate: Gene.4027::NM_001017438::g.4027::m.4027, not unique enough -skipping training candidate: Gene.4217::NM_001291528::g.4217::m.4217, not unique enough -skipping training candidate: Gene.1213::NM_175723::g.1213::m.1213, not unique enough -skipping training candidate: Gene.1517::MSTRG.327.3::g.1517::m.1517, not unique enough -skipping training candidate: Gene.1521::NM_003173::g.1521::m.1521, not unique enough -skipping training candidate: Gene.1842::MSTRG.520.6::g.1842::m.1842, not unique enough -skipping training candidate: Gene.2740::NM_005635::g.2740::m.2740, not unique enough -skipping training candidate: Gene.3829::NM_005636::g.3829::m.3829, not unique enough -skipping training candidate: Gene.3965::MSTRG.82.6::g.3965::m.3965, not unique enough -skipping training candidate: Gene.3968::NR_109776::g.3968::m.3968, not unique enough -skipping training candidate: Gene.3971::NM_013427::g.3971::m.3971, not unique enough -skipping training candidate: Gene.4351::NM_001034832::g.4351::m.4351, not unique enough -skipping training candidate: Gene.4352::NM_001034832_dup1::g.4352::m.4352, not unique enough -skipping training candidate: Gene.2866::NM_020766::g.2866::m.2866, not unique enough -skipping training candidate: Gene.3354::NM_001105243::g.3354::m.3354, not unique enough -skipping training candidate: Gene.2174::NM_001256197::g.2174::m.2174, not unique enough -skipping training candidate: Gene.2758::NM_016379::g.2758::m.2758, not unique enough -skipping training candidate: Gene.2783::MSTRG.1074.3::g.2783::m.2783, not unique enough -skipping training candidate: Gene.586::NM_001184875::g.586::m.586, not unique enough -skipping training candidate: Gene.592::NM_138437::g.592::m.592, not unique enough -skipping training candidate: Gene.596::NM_001199818::g.596::m.596, not unique enough -skipping training candidate: Gene.603::NM_001004051::g.603::m.603, not unique enough -skipping training candidate: Gene.607::NM_001184874::g.607::m.607, not unique enough -skipping training candidate: Gene.2750::MSTRG.143.2::g.2750::m.2750, not unique enough -skipping training candidate: Gene.2777::MSTRG.1074.2::g.2777::m.2777, not unique enough -skipping training candidate: Gene.1836::NM_001166420::g.1836::m.1836, not unique enough -skipping training candidate: Gene.2696::NM_001007088::g.2696::m.2696, not unique enough -skipping training candidate: Gene.2699::NM_006962::g.2699::m.2699, not unique enough -skipping training candidate: Gene.2702::MSTRG.294.4::g.2702::m.2702, not unique enough -skipping training candidate: Gene.3361::MSTRG.1029.2::g.3361::m.3361, not unique enough -skipping training candidate: Gene.1376::MSTRG.68.18::g.1376::m.1376, not unique enough -skipping training candidate: Gene.1447::NM_001114377::g.1447::m.1447, not unique enough -skipping training candidate: Gene.1697::NM_001271186::g.1697::m.1697, not unique enough -skipping training candidate: Gene.1700::NM_021183::g.1700::m.1700, not unique enough -skipping training candidate: Gene.4141::MSTRG.216.5::g.4141::m.4141, not unique enough -skipping training candidate: Gene.4145::NM_001098791::g.4145::m.4145, not unique enough -skipping training candidate: Gene.4149::NM_021242::g.4149::m.4149, not unique enough -skipping training candidate: Gene.4153::NM_001098790::g.4153::m.4153, not unique enough -skipping training candidate: Gene.1838::NR_051952::g.1838::m.1838, not unique enough -skipping training candidate: Gene.1920::NM_001025242::g.1920::m.1920, not unique enough -skipping training candidate: Gene.1923::NM_001025243::g.1923::m.1923, not unique enough -skipping training candidate: Gene.1537::NM_014060::g.1537::m.1537, not unique enough -skipping training candidate: Gene.2924::NM_001141920::g.2924::m.2924, not unique enough -skipping training candidate: Gene.3092::NM_198511::g.3092::m.3092, not unique enough -skipping training candidate: Gene.1003::NM_001327::g.1003::m.1003, not unique enough -skipping training candidate: Gene.2285::NM_139250_dup1::g.2285::m.2285, not unique enough -skipping training candidate: Gene.2286::NM_139250::g.2286::m.2286, not unique enough -skipping training candidate: Gene.2651::MSTRG.508.1::g.2651::m.2651, not unique enough -skipping training candidate: Gene.2653::MSTRG.508.2::g.2653::m.2653, not unique enough -skipping training candidate: Gene.3293::NM_175569::g.3293::m.3293, not unique enough -skipping training candidate: Gene.1703::NM_001145149::g.1703::m.1703, not unique enough -skipping training candidate: Gene.1796::MSTRG.4.3::g.1796::m.1796, not unique enough -skipping training candidate: Gene.1804::NM_018390::g.1804::m.1804, not unique enough -skipping training candidate: Gene.570::NM_001256580::g.570::m.570, not unique enough -skipping training candidate: Gene.1144::NM_017711::g.1144::m.1144, not unique enough -skipping training candidate: Gene.2362::NM_001171193::g.2362::m.2362, not unique enough -skipping training candidate: Gene.3491::NM_001171192::g.3491::m.3491, not unique enough -skipping training candidate: Gene.528::MSTRG.337.1::g.528::m.528, not unique enough -skipping training candidate: Gene.838::NM_002025::g.838::m.838, not unique enough -skipping training candidate: Gene.841::NM_001169125::g.841::m.841, not unique enough -skipping training candidate: Gene.844::NM_001169122::g.844::m.844, not unique enough -skipping training candidate: Gene.847::NM_001169124::g.847::m.847, not unique enough -skipping training candidate: Gene.1837::NM_001166448::g.1837::m.1837, not unique enough -skipping training candidate: Gene.3053::NR_104114::g.3053::m.3053, not unique enough -skipping training candidate: Gene.3269::MSTRG.664.1::g.3269::m.3269, not unique enough -skipping training candidate: Gene.3271::MSTRG.664.2::g.3271::m.3271, not unique enough -skipping training candidate: Gene.2670::NM_001171907::g.2670::m.2670, not unique enough -skipping training candidate: Gene.2347::NM_182681::g.2347::m.2347, not unique enough -skipping training candidate: Gene.3123::NR_026710::g.3123::m.3123, not unique enough -skipping training candidate: Gene.937::NR_033772_dup1::g.937::m.937, not unique enough -skipping training candidate: Gene.2368::NM_001282302::g.2368::m.2368, not unique enough -skipping training candidate: Gene.2487::MSTRG.459.2::g.2487::m.2487, not unique enough -skipping training candidate: Gene.3141::NR_033773_dup1::g.3141::m.3141, not unique enough -skipping training candidate: Gene.3144::NR_033773::g.3144::m.3144, not unique enough -skipping training candidate: Gene.3155::MSTRG.1041.6::g.3155::m.3155, not unique enough -skipping training candidate: Gene.3164::MSTRG.1041.7::g.3164::m.3164, not unique enough -skipping training candidate: Gene.3735::MSTRG.387.3::g.3735::m.3735, not unique enough -skipping training candidate: Gene.3738::NM_001184896::g.3738::m.3738, not unique enough -skipping training candidate: Gene.4342::NM_001170569::g.4342::m.4342, not unique enough -skipping training candidate: Gene.2370::NR_104121::g.2370::m.2370, not unique enough -skipping training candidate: Gene.3249::MSTRG.967.1::g.3249::m.3249, not unique enough -skipping training candidate: Gene.1425::MSTRG.68.7::g.1425::m.1425, not unique enough -skipping training candidate: Gene.1680::NM_001256789::g.1680::m.1680, not unique enough -skipping training candidate: Gene.2257::NM_001167992::g.2257::m.2257, not unique enough -skipping training candidate: Gene.2771::MSTRG.1074.1::g.2771::m.2771, not unique enough -skipping training candidate: Gene.2791::MSTRG.1074.7::g.2791::m.2791, not unique enough -skipping training candidate: Gene.3415::NM_005183::g.3415::m.3415, not unique enough -skipping training candidate: Gene.2253::NM_144495::g.2253::m.2253, not unique enough -skipping training candidate: Gene.2474::MSTRG.459.4::g.2474::m.2474, not unique enough -skipping training candidate: Gene.4264::MSTRG.17.6::g.4264::m.4264, not unique enough -skipping training candidate: Gene.927::NR_033835::g.927::m.927, not unique enough -skipping training candidate: Gene.929::NR_033836::g.929::m.929, not unique enough -skipping training candidate: Gene.966::NM_153477::g.966::m.966, not unique enough -skipping training candidate: Gene.1128::NM_001079900_dup1::g.1128::m.1128, not unique enough -skipping training candidate: Gene.2172::NM_001654::g.2172::m.2172, not unique enough -skipping training candidate: Gene.2177::NM_001256196::g.2177::m.2177, not unique enough -skipping training candidate: Gene.3211::MSTRG.76.2::g.3211::m.3211, not unique enough -skipping training candidate: Gene.3395::NM_001281463::g.3395::m.3395, not unique enough -skipping training candidate: Gene.3709::MSTRG.739.4::g.3709::m.3709, not unique enough -skipping training candidate: Gene.1631::NM_000425::g.1631::m.1631, not unique enough -skipping training candidate: Gene.1637::NM_024003::g.1637::m.1637, not unique enough -skipping training candidate: Gene.1643::NM_001143963::g.1643::m.1643, not unique enough -skipping training candidate: Gene.2327::MSTRG.205.2::g.2327::m.2327, not unique enough -skipping training candidate: Gene.3035::MSTRG.338.6::g.3035::m.3035, not unique enough -skipping training candidate: Gene.3037::NM_001136157::g.3037::m.3037, not unique enough -skipping training candidate: Gene.3040::NM_001136159::g.3040::m.3040, not unique enough -skipping training candidate: Gene.701::MSTRG.994.1::g.701::m.701, not unique enough -skipping training candidate: Gene.938::NR_033772_dup1::g.938::m.938, not unique enough -skipping training candidate: Gene.1797::MSTRG.4.3::g.1797::m.1797, not unique enough -skipping training candidate: Gene.1805::NM_018390::g.1805::m.1805, not unique enough -skipping training candidate: Gene.2947::NM_001172672::g.2947::m.2947, not unique enough -skipping training candidate: Gene.3142::NR_033773_dup1::g.3142::m.3142, not unique enough -skipping training candidate: Gene.3145::NR_033773::g.3145::m.3145, not unique enough -skipping training candidate: Gene.4254::MSTRG.17.2::g.4254::m.4254, not unique enough -skipping training candidate: Gene.55::MSTRG.668.2::g.55::m.55, not unique enough -skipping training candidate: Gene.73::MSTRG.759.9::g.73::m.73, not unique enough -skipping training candidate: Gene.74::NM_018466::g.74::m.74, not unique enough -skipping training candidate: Gene.926::MSTRG.116.5::g.926::m.926, not unique enough -skipping training candidate: Gene.1098::MSTRG.961.7::g.1098::m.1098, not unique enough -skipping training candidate: Gene.4142::MSTRG.216.5::g.4142::m.4142, not unique enough -skipping training candidate: Gene.4146::NM_001098791::g.4146::m.4146, not unique enough -skipping training candidate: Gene.4150::NM_021242::g.4150::m.4150, not unique enough -skipping training candidate: Gene.4154::NM_001098790::g.4154::m.4154, not unique enough -skipping training candidate: Gene.1304::NM_153183::g.1304::m.1304, not unique enough -skipping training candidate: Gene.1529::NM_001282201::g.1529::m.1529, not unique enough -skipping training candidate: Gene.1531::NM_001190255::g.1531::m.1531, not unique enough -skipping training candidate: Gene.1533::NM_001282202::g.1533::m.1533, not unique enough -skipping training candidate: Gene.1853::MSTRG.925.2::g.1853::m.1853, not unique enough -skipping training candidate: Gene.1856::NM_001163280::g.1856::m.1856, not unique enough -skipping training candidate: Gene.3676::NM_005393::g.3676::m.3676, not unique enough -skipping training candidate: Gene.679::MSTRG.763.1::g.679::m.679, not unique enough -skipping training candidate: Gene.3950::MSTRG.124.9::g.3950::m.3950, not unique enough -skipping training candidate: Gene.3952::MSTRG.124.1::g.3952::m.3952, not unique enough -skipping training candidate: Gene.3956::MSTRG.124.8::g.3956::m.3956, not unique enough -skipping training candidate: Gene.7::NM_001256185::g.7::m.7, not unique enough -skipping training candidate: Gene.303::NM_001282174::g.303::m.303, not unique enough -skipping training candidate: Gene.4237::NM_020717::g.4237::m.4237, not unique enough -skipping training candidate: Gene.297::NM_001303545::g.297::m.297, not unique enough -skipping training candidate: Gene.1319::MSTRG.311.2::g.1319::m.1319, not unique enough -skipping training candidate: Gene.1844::NR_027419::g.1844::m.1844, not unique enough -skipping training candidate: Gene.3413::NR_033254_dup1::g.3413::m.3413, not unique enough -skipping training candidate: Gene.4234::NR_033257_dup1::g.4234::m.4234, not unique enough -skipping training candidate: Gene.4235::NR_033257::g.4235::m.4235, not unique enough -skipping training candidate: Gene.513::MSTRG.549.7::g.513::m.513, not unique enough -skipping training candidate: Gene.706::NM_205856_dup1::g.706::m.706, not unique enough -skipping training candidate: Gene.707::NM_205856::g.707::m.707, not unique enough -skipping training candidate: Gene.2445::NM_001306188::g.2445::m.2445, not unique enough -skipping training candidate: Gene.3901::NM_004780::g.3901::m.3901, not unique enough -skipping training candidate: Gene.3902::MSTRG.694.2::g.3902::m.3902, not unique enough -skipping training candidate: Gene.3904::NM_001006639::g.3904::m.3904, not unique enough -skipping training candidate: Gene.3905::NM_001168400::g.3905::m.3905, not unique enough -skipping training candidate: Gene.1604::NM_005647::g.1604::m.1604, not unique enough -skipping training candidate: Gene.2276::MSTRG.973.4::g.2276::m.2276, not unique enough -skipping training candidate: Gene.2277::MSTRG.973.3::g.2277::m.2277, not unique enough -skipping training candidate: Gene.2278::NM_001013845::g.2278::m.2278, not unique enough -skipping training candidate: Gene.2452::MSTRG.109.10::g.2452::m.2452, not unique enough -skipping training candidate: Gene.2545::NM_005089::g.2545::m.2545, not unique enough -skipping training candidate: Gene.2550::MSTRG.128.1::g.2550::m.2550, not unique enough -skipping training candidate: Gene.2658::NM_001171908::g.2658::m.2658, not unique enough -skipping training candidate: Gene.2666::NM_178124::g.2666::m.2666, not unique enough -skipping training candidate: Gene.2671::NM_001171907::g.2671::m.2671, not unique enough -skipping training candidate: Gene.4125::NM_001039891::g.4125::m.4125, not unique enough -skipping training candidate: Gene.4127::NM_001190417::g.4127::m.4127, not unique enough -skipping training candidate: Gene.4129::NM_001146291::g.4129::m.4129, not unique enough -skipping training candidate: Gene.4131::MSTRG.266.4::g.4131::m.4131, not unique enough -skipping training candidate: Gene.649::NM_001278740::g.649::m.649, not unique enough -skipping training candidate: Gene.650::NM_001278741::g.650::m.650, not unique enough -skipping training candidate: Gene.958::MSTRG.324.2::g.958::m.958, not unique enough -skipping training candidate: Gene.2017::NR_104107::g.2017::m.2017, not unique enough -skipping training candidate: Gene.3730::NM_001184897::g.3730::m.3730, not unique enough -skipping training candidate: Gene.3733::NM_015107::g.3733::m.3733, not unique enough -skipping training candidate: Gene.3736::MSTRG.387.3::g.3736::m.3736, not unique enough -skipping training candidate: Gene.3739::NM_001184896::g.3739::m.3739, not unique enough -skipping training candidate: Gene.3741::MSTRG.387.1::g.3741::m.3741, not unique enough -skipping training candidate: Gene.4306::NM_001282462::g.4306::m.4306, not unique enough -skipping training candidate: Gene.4308::NM_001282461::g.4308::m.4308, not unique enough -skipping training candidate: Gene.1650::NM_001012755::g.1650::m.1650, not unique enough -skipping training candidate: Gene.1652::MSTRG.705.2::g.1652::m.1652, not unique enough -skipping training candidate: Gene.1654::MSTRG.705.4::g.1654::m.1654, not unique enough -skipping training candidate: Gene.1779::MSTRG.718.6::g.1779::m.1779, not unique enough -skipping training candidate: Gene.2697::NM_001007088::g.2697::m.2697, not unique enough -skipping training candidate: Gene.2700::NM_006962::g.2700::m.2700, not unique enough -skipping training candidate: Gene.2703::MSTRG.294.4::g.2703::m.2703, not unique enough -skipping training candidate: Gene.3300::NM_000054::g.3300::m.3300, not unique enough -skipping training candidate: Gene.1544::MSTRG.53.1::g.1544::m.1544, not unique enough -skipping training candidate: Gene.2187::NM_177537::g.2187::m.2187, not unique enough -skipping training candidate: Gene.3374::MSTRG.1029.1::g.3374::m.3374, not unique enough -skipping training candidate: Gene.3649::NM_019045::g.3649::m.3649, not unique enough -skipping training candidate: Gene.3651::NM_001184966::g.3651::m.3651, not unique enough -skipping training candidate: Gene.3814::NM_177535_dup1::g.3814::m.3814, not unique enough -skipping training candidate: Gene.3818::NM_177537_dup1::g.3818::m.3818, not unique enough -skipping training candidate: Gene.4224::NR_033380::g.4224::m.4224, not unique enough -skipping training candidate: Gene.4225::MSTRG.38.1::g.4225::m.4225, not unique enough -skipping training candidate: Gene.350::NM_001163265::g.350::m.350, not unique enough -skipping training candidate: Gene.362::NM_001163264::g.362::m.362, not unique enough -skipping training candidate: Gene.829::NM_001135998::g.829::m.829, not unique enough -skipping training candidate: Gene.1095::MSTRG.961.2::g.1095::m.1095, not unique enough -skipping training candidate: Gene.1099::MSTRG.961.7::g.1099::m.1099, not unique enough -skipping training candidate: Gene.1108::MSTRG.961.4::g.1108::m.1108, not unique enough -skipping training candidate: Gene.1420::MSTRG.68.20::g.1420::m.1420, not unique enough -skipping training candidate: Gene.1765::NM_001040612::g.1765::m.1765, not unique enough -skipping training candidate: Gene.1854::MSTRG.925.2::g.1854::m.1854, not unique enough -skipping training candidate: Gene.1857::NM_001163280::g.1857::m.1857, not unique enough -skipping training candidate: Gene.3018::NM_175729::g.3018::m.3018, not unique enough -skipping training candidate: Gene.3019::NM_175729_dup1::g.3019::m.3019, not unique enough -skipping training candidate: Gene.3602::NR_126093::g.3602::m.3602, not unique enough -skipping training candidate: Gene.3605::NM_001193417::g.3605::m.3605, not unique enough -skipping training candidate: Gene.3607::NM_001356::g.3607::m.3607, not unique enough -skipping training candidate: Gene.3677::NM_005393::g.3677::m.3677, not unique enough -skipping training candidate: Gene.471::MSTRG.799.2::g.471::m.471, not unique enough -skipping training candidate: Gene.803::MSTRG.275.3::g.803::m.803, not unique enough -skipping training candidate: Gene.814::MSTRG.275.4::g.814::m.814, not unique enough -skipping training candidate: Gene.1632::NM_000425::g.1632::m.1632, not unique enough -skipping training candidate: Gene.1638::NM_024003::g.1638::m.1638, not unique enough -skipping training candidate: Gene.1644::NM_001143963::g.1644::m.1644, not unique enough -skipping training candidate: Gene.2876::NM_170750::g.2876::m.2876, not unique enough -skipping training candidate: Gene.3685::NM_001291421::g.3685::m.3685, not unique enough -skipping training candidate: Gene.1011::NM_022117::g.1011::m.1011, not unique enough -skipping training candidate: Gene.2485::MSTRG.459.1::g.2485::m.2485, not unique enough -skipping training candidate: Gene.2488::MSTRG.459.2::g.2488::m.2488, not unique enough -skipping training candidate: Gene.2861::NM_001146151::g.2861::m.2861, not unique enough -skipping training candidate: Gene.4333::MSTRG.345.2::g.4333::m.4333, not unique enough -skipping training candidate: Gene.4337::MSTRG.345.4::g.4337::m.4337, not unique enough -skipping training candidate: Gene.395::MSTRG.1012.4::g.395::m.395, not unique enough -skipping training candidate: Gene.397::NM_005334::g.397::m.397, not unique enough -skipping training candidate: Gene.399::MSTRG.1012.3::g.399::m.399, not unique enough -skipping training candidate: Gene.1388::MSTRG.68.10::g.1388::m.1388, not unique enough -skipping training candidate: Gene.2677::NM_015075::g.2677::m.2677, not unique enough -skipping training candidate: Gene.3105::NR_030774::g.3105::m.3105, not unique enough -skipping training candidate: Gene.661::MSTRG.34.8::g.661::m.661, not unique enough -skipping training candidate: Gene.662::MSTRG.34.3::g.662::m.662, not unique enough -skipping training candidate: Gene.2098::NM_001164619::g.2098::m.2098, not unique enough -skipping training candidate: Gene.2100::NM_001164618::g.2100::m.2100, not unique enough -skipping training candidate: Gene.2102::NM_001164617::g.2102::m.2102, not unique enough -skipping training candidate: Gene.3331::MSTRG.663.1::g.3331::m.3331, not unique enough -skipping training candidate: Gene.3975::MSTRG.734.6::g.3975::m.3975, not unique enough -skipping training candidate: Gene.3977::NM_017698::g.3977::m.3977, not unique enough -skipping training candidate: Gene.4196::NM_001005613::g.4196::m.4196, not unique enough -skipping training candidate: Gene.3368::MSTRG.1029.12::g.3368::m.3368, not unique enough -skipping training candidate: Gene.4143::MSTRG.216.5::g.4143::m.4143, not unique enough -skipping training candidate: Gene.4151::NM_021242::g.4151::m.4151, not unique enough -skipping training candidate: Gene.695::MSTRG.994.4::g.695::m.695, not unique enough -skipping training candidate: Gene.699::NM_001130997::g.699::m.699, not unique enough -skipping training candidate: Gene.713::NM_016120::g.713::m.713, not unique enough -skipping training candidate: Gene.715::MSTRG.537.1::g.715::m.715, not unique enough -skipping training candidate: Gene.717::NM_183353::g.717::m.717, not unique enough -skipping training candidate: Gene.2020::MSTRG.867.6::g.2020::m.2020, not unique enough -skipping training candidate: Gene.2183::NM_001272062::g.2183::m.2183, not unique enough -skipping training candidate: Gene.2185::NM_001272063::g.2185::m.2185, not unique enough -skipping training candidate: Gene.2188::NM_177537::g.2188::m.2188, not unique enough -skipping training candidate: Gene.2270::MSTRG.973.2::g.2270::m.2270, not unique enough -skipping training candidate: Gene.2272::MSTRG.973.1::g.2272::m.2272, not unique enough -skipping training candidate: Gene.2656::NM_001171909::g.2656::m.2656, not unique enough -skipping training candidate: Gene.2659::MSTRG.963.2::g.2659::m.2659, not unique enough -skipping training candidate: Gene.2664::MSTRG.963.3::g.2664::m.2664, not unique enough -skipping training candidate: Gene.2668::MSTRG.963.1::g.2668::m.2668, not unique enough -skipping training candidate: Gene.3003::NM_001097604_dup1::g.3003::m.3003, not unique enough -skipping training candidate: Gene.3518::MSTRG.268.3::g.3518::m.3518, not unique enough -skipping training candidate: Gene.3809::NM_001272061_dup1::g.3809::m.3809, not unique enough -skipping training candidate: Gene.3812::NM_030801_dup1::g.3812::m.3812, not unique enough -skipping training candidate: Gene.3815::NM_177535_dup1::g.3815::m.3815, not unique enough -skipping training candidate: Gene.3819::NM_177537_dup1::g.3819::m.3819, not unique enough -skipping training candidate: Gene.3836::NM_001097594_dup1::g.3836::m.3836, not unique enough -skipping training candidate: Gene.3837::NM_001097594::g.3837::m.3837, not unique enough -skipping training candidate: Gene.4238::NM_020717::g.4238::m.4238, not unique enough -skipping training candidate: Gene.530::MSTRG.302.6::g.530::m.530, not unique enough -skipping training candidate: Gene.554::MSTRG.1025.5::g.554::m.554, not unique enough -skipping training candidate: Gene.612::NM_001287760::g.612::m.612, not unique enough -skipping training candidate: Gene.629::NM_033641::g.629::m.629, not unique enough -skipping training candidate: Gene.993::NM_001847::g.993::m.993, not unique enough -skipping training candidate: Gene.1203::MSTRG.131.6::g.1203::m.1203, not unique enough -skipping training candidate: Gene.1206::MSTRG.131.5::g.1206::m.1206, not unique enough -skipping training candidate: Gene.3371::NM_001303465::g.3371::m.3371, not unique enough -skipping training candidate: Gene.3385::MSTRG.1029.3::g.3385::m.3385, not unique enough -skipping training candidate: Gene.283::NM_206917::g.283::m.283, not unique enough -skipping training candidate: Gene.730::NM_031407::g.730::m.730, not unique enough -skipping training candidate: Gene.733::MSTRG.397.21::g.733::m.733, not unique enough -skipping training candidate: Gene.735::MSTRG.397.6::g.735::m.735, not unique enough -skipping training candidate: Gene.738::MSTRG.397.7::g.738::m.738, not unique enough -skipping training candidate: Gene.741::MSTRG.397.5::g.741::m.741, not unique enough -skipping training candidate: Gene.744::MSTRG.397.18::g.744::m.744, not unique enough -skipping training candidate: Gene.746::MSTRG.397.26::g.746::m.746, not unique enough -skipping training candidate: Gene.748::MSTRG.397.17::g.748::m.748, not unique enough -skipping training candidate: Gene.750::MSTRG.397.24::g.750::m.750, not unique enough -skipping training candidate: Gene.752::MSTRG.397.2::g.752::m.752, not unique enough -skipping training candidate: Gene.755::MSTRG.397.27::g.755::m.755, not unique enough -skipping training candidate: Gene.757::MSTRG.397.8::g.757::m.757, not unique enough -skipping training candidate: Gene.760::MSTRG.397.23::g.760::m.760, not unique enough -skipping training candidate: Gene.762::MSTRG.397.12::g.762::m.762, not unique enough -skipping training candidate: Gene.764::MSTRG.397.19::g.764::m.764, not unique enough -skipping training candidate: Gene.766::MSTRG.397.22::g.766::m.766, not unique enough -skipping training candidate: Gene.768::MSTRG.397.9::g.768::m.768, not unique enough -skipping training candidate: Gene.770::MSTRG.397.14::g.770::m.770, not unique enough -skipping training candidate: Gene.772::MSTRG.397.25::g.772::m.772, not unique enough -skipping training candidate: Gene.774::MSTRG.397.10::g.774::m.774, not unique enough -skipping training candidate: Gene.776::MSTRG.397.11::g.776::m.776, not unique enough -skipping training candidate: Gene.779::MSTRG.397.15::g.779::m.779, not unique enough -skipping training candidate: Gene.782::MSTRG.397.4::g.782::m.782, not unique enough -skipping training candidate: Gene.785::MSTRG.397.28::g.785::m.785, not unique enough -skipping training candidate: Gene.787::MSTRG.397.3::g.787::m.787, not unique enough -skipping training candidate: Gene.790::MSTRG.397.20::g.790::m.790, not unique enough -skipping training candidate: Gene.792::MSTRG.397.16::g.792::m.792, not unique enough -skipping training candidate: Gene.964::NR_045560::g.964::m.964, not unique enough -skipping training candidate: Gene.3508::MSTRG.268.7::g.3508::m.3508, not unique enough -skipping training candidate: Gene.3686::NM_001291421::g.3686::m.3686, not unique enough -skipping training candidate: Gene.3688::NM_001291417::g.3688::m.3688, not unique enough -skipping training candidate: Gene.3690::NM_021140::g.3690::m.3690, not unique enough -skipping training candidate: Gene.3695::NM_001291418::g.3695::m.3695, not unique enough -skipping training candidate: Gene.3697::NM_001291416::g.3697::m.3697, not unique enough -skipping training candidate: Gene.3699::NM_001291415::g.3699::m.3699, not unique enough -skipping training candidate: Gene.8::NM_001256187::g.8::m.8, not unique enough -skipping training candidate: Gene.1031::MSTRG.305.1::g.1031::m.1031, not unique enough -skipping training candidate: Gene.2477::MSTRG.459.3::g.2477::m.2477, not unique enough -skipping training candidate: Gene.2479::NM_021783::g.2479::m.2479, not unique enough -skipping training candidate: Gene.2486::MSTRG.459.1::g.2486::m.2486, not unique enough -skipping training candidate: Gene.3665::NM_020994::g.3665::m.3665, not unique enough -skipping training candidate: Gene.4034::NM_001282621::g.4034::m.4034, not unique enough -skipping training candidate: Gene.4093::NM_001146257::g.4093::m.4093, not unique enough -skipping training candidate: Gene.2448::MSTRG.109.1::g.2448::m.2448, not unique enough -skipping training candidate: Gene.2910::NM_001168649::g.2910::m.2910, not unique enough -skipping training candidate: Gene.2914::NM_014927::g.2914::m.2914, not unique enough -skipping training candidate: Gene.2917::NM_001168647::g.2917::m.2917, not unique enough -skipping training candidate: Gene.3273::NM_001242617::g.3273::m.3273, not unique enough -skipping training candidate: Gene.3327::NM_021029::g.3327::m.3327, not unique enough -skipping training candidate: Gene.1389::MSTRG.68.10::g.1389::m.1389, not unique enough -skipping training candidate: Gene.1393::MSTRG.68.8::g.1393::m.1393, not unique enough -skipping training candidate: Gene.1400::MSTRG.68.2::g.1400::m.1400, not unique enough -skipping training candidate: Gene.1410::MSTRG.68.16::g.1410::m.1410, not unique enough -skipping training candidate: Gene.3682::MSTRG.258.8::g.3682::m.3682, not unique enough -skipping training candidate: Gene.1579::MSTRG.250.5::g.1579::m.1579, not unique enough -skipping training candidate: Gene.2449::NM_001011658::g.2449::m.2449, not unique enough -skipping training candidate: Gene.3692::MSTRG.258.9::g.3692::m.3692, not unique enough -skipping training candidate: Gene.3743::NM_001184898::g.3743::m.3743, not unique enough -skipping training candidate: Gene.3783::MSTRG.992.7::g.3783::m.3783, not unique enough -skipping training candidate: Gene.3867::MSTRG.476.2::g.3867::m.3867, not unique enough -skipping training candidate: Gene.4239::NM_020717::g.4239::m.4239, not unique enough -skipping training candidate: Gene.3::NM_001256186::g.3::m.3, not unique enough -skipping training candidate: Gene.1145::NM_017711::g.1145::m.1145, not unique enough -skipping training candidate: Gene.2091::NM_017883::g.2091::m.2091, not unique enough -skipping training candidate: Gene.3492::NM_001171192::g.3492::m.3492, not unique enough -skipping training candidate: Gene.4035::NM_001282621::g.4035::m.4035, not unique enough -skipping training candidate: Gene.1486::MSTRG.921.1::g.1486::m.1486, not unique enough -skipping training candidate: Gene.1490::MSTRG.921.3::g.1490::m.1490, not unique enough -skipping training candidate: Gene.1502::MSTRG.921.2::g.1502::m.1502, not unique enough -skipping training candidate: Gene.1778::MSTRG.718.1::g.1778::m.1778, not unique enough -skipping training candidate: Gene.2469::NM_001184819::g.2469::m.2469, not unique enough -skipping training candidate: Gene.3083::MSTRG.641.8::g.3083::m.3083, not unique enough -skipping training candidate: Gene.3161::NM_001099857::g.3161::m.3161, not unique enough -skipping training candidate: Gene.189::NM_001008534::g.189::m.189, not unique enough -skipping training candidate: Gene.651::NM_001278742::g.651::m.651, not unique enough -skipping training candidate: Gene.1041::MSTRG.305.6::g.1041::m.1041, not unique enough -skipping training candidate: Gene.1762::MSTRG.306.1::g.1762::m.1762, not unique enough -skipping training candidate: Gene.2582::NM_014725::g.2582::m.2582, not unique enough -skipping training candidate: Gene.2879::NM_001142504::g.2879::m.2879, not unique enough -skipping training candidate: Gene.3477::NM_001271183::g.3477::m.3477, not unique enough -skipping training candidate: Gene.3479::MSTRG.404.8::g.3479::m.3479, not unique enough -skipping training candidate: Gene.3482::NM_001271184::g.3482::m.3482, not unique enough -skipping training candidate: Gene.3835::NM_001172739::g.3835::m.3835, not unique enough -skipping training candidate: Gene.3976::MSTRG.734.6::g.3976::m.3976, not unique enough -skipping training candidate: Gene.3978::NM_017698::g.3978::m.3978, not unique enough -skipping training candidate: Gene.3980::MSTRG.734.5::g.3980::m.3980, not unique enough -skipping training candidate: Gene.3982::MSTRG.734.3::g.3982::m.3982, not unique enough -skipping training candidate: Gene.3984::MSTRG.734.2::g.3984::m.3984, not unique enough -skipping training candidate: Gene.4193::NM_001005609::g.4193::m.4193, not unique enough -skipping training candidate: Gene.30::MSTRG.438.2::g.30::m.30, not unique enough -skipping training candidate: Gene.195::NR_001564::g.195::m.195, not unique enough -skipping training candidate: Gene.198::MSTRG.531.1::g.198::m.198, not unique enough -skipping training candidate: Gene.201::MSTRG.531.3::g.201::m.201, not unique enough -skipping training candidate: Gene.804::MSTRG.275.3::g.804::m.804, not unique enough -skipping training candidate: Gene.808::NM_001170460::g.808::m.808, not unique enough -skipping training candidate: Gene.811::MSTRG.275.2::g.811::m.811, not unique enough -skipping training candidate: Gene.815::MSTRG.275.4::g.815::m.815, not unique enough -skipping training candidate: Gene.819::MSTRG.275.7::g.819::m.819, not unique enough -skipping training candidate: Gene.822::MSTRG.275.6::g.822::m.822, not unique enough -skipping training candidate: Gene.826::NM_006201::g.826::m.826, not unique enough -skipping training candidate: Gene.2636::MSTRG.615.2::g.2636::m.2636, not unique enough -skipping training candidate: Gene.2637::MSTRG.615.1::g.2637::m.2637, not unique enough -skipping training candidate: Gene.3119::MSTRG.16.1::g.3119::m.3119, not unique enough -skipping training candidate: Gene.3560::NM_000495::g.3560::m.3560, not unique enough -skipping training candidate: Gene.3769::MSTRG.992.3::g.3769::m.3769, not unique enough -skipping training candidate: Gene.3778::NR_073156::g.3778::m.3778, not unique enough -skipping training candidate: Gene.1973::MSTRG.62.2::g.1973::m.1973, not unique enough -skipping training candidate: Gene.1975::MSTRG.62.1::g.1975::m.1975, not unique enough -skipping training candidate: Gene.2042::NM_006521::g.2042::m.2042, not unique enough -skipping training candidate: Gene.2614::MSTRG.488.1::g.2614::m.2614, not unique enough -skipping training candidate: Gene.2615::NR_033212::g.2615::m.2615, not unique enough -skipping training candidate: Gene.3246::NM_145305::g.3246::m.3246, not unique enough -skipping training candidate: Gene.4195::NM_001005610::g.4195::m.4195, not unique enough -skipping training candidate: Gene.196::NR_001564::g.196::m.196, not unique enough -skipping training candidate: Gene.199::MSTRG.531.1::g.199::m.199, not unique enough -skipping training candidate: Gene.202::MSTRG.531.3::g.202::m.202, not unique enough -skipping training candidate: Gene.816::MSTRG.275.4::g.816::m.816, not unique enough -skipping training candidate: Gene.827::NM_006201::g.827::m.827, not unique enough -skipping training candidate: Gene.1264::NM_001300788::g.1264::m.1264, not unique enough -skipping training candidate: Gene.1535::NM_001144003::g.1535::m.1535, not unique enough -skipping training candidate: Gene.2169::MSTRG.284.1::g.2169::m.2169, not unique enough -skipping training candidate: Gene.2660::MSTRG.963.2::g.2660::m.2660, not unique enough -skipping training candidate: Gene.2793::NM_001039582::g.2793::m.2793, not unique enough -skipping training candidate: Gene.3232::NM_001144005::g.3232::m.3232, not unique enough -skipping training candidate: Gene.3721::MSTRG.933.1::g.3721::m.3721, not unique enough -skipping training candidate: Gene.4194::NM_001005609::g.4194::m.4194, not unique enough -skipping training candidate: Gene.4198::NM_001005612::g.4198::m.4198, not unique enough -skipping training candidate: Gene.4199::NM_001005612::g.4199::m.4199, not unique enough -skipping training candidate: Gene.62::MSTRG.759.10::g.62::m.62, not unique enough -skipping training candidate: Gene.71::MSTRG.759.2::g.71::m.71, not unique enough -skipping training candidate: Gene.76::MSTRG.759.21::g.76::m.76, not unique enough -skipping training candidate: Gene.78::MSTRG.759.11::g.78::m.78, not unique enough -skipping training candidate: Gene.82::NM_001168385::g.82::m.82, not unique enough -skipping training candidate: Gene.1005::NM_001143982::g.1005::m.1005, not unique enough -skipping training candidate: Gene.1038::MSTRG.305.8::g.1038::m.1038, not unique enough -skipping training candidate: Gene.2365::NM_145234::g.2365::m.2365, not unique enough -skipping training candidate: Gene.3087::MSTRG.641.7::g.3087::m.3087, not unique enough -skipping training candidate: Gene.3827::NM_001145252::g.3827::m.3827, not unique enough -skipping training candidate: Gene.3870::NM_001143981::g.3870::m.3870, not unique enough -skipping training candidate: Gene.2737::NM_174951::g.2737::m.2737, not unique enough -skipping training candidate: Gene.4276::NR_027383::g.4276::m.4276, not unique enough -skipping training candidate: Gene.4292::MSTRG.32.4::g.4292::m.4292, not unique enough -skipping training candidate: Gene.1519::MSTRG.327.3::g.1519::m.1519, not unique enough -skipping training candidate: Gene.1522::NM_003173::g.1522::m.1522, not unique enough -skipping training candidate: Gene.3380::NR_024048::g.3380::m.3380, not unique enough -skipping training candidate: Gene.3454::NM_001123385::g.3454::m.3454, not unique enough -skipping training candidate: Gene.1184::NM_130467::g.1184::m.1184, not unique enough -skipping training candidate: Gene.2001::NM_005676::g.2001::m.2001, not unique enough -skipping training candidate: Gene.2008::NM_001204468::g.2008::m.2008, not unique enough -skipping training candidate: Gene.2081::NR_029427::g.2081::m.2081, not unique enough -skipping training candidate: Gene.2084::MSTRG.325.4::g.2084::m.2084, not unique enough -skipping training candidate: Gene.2087::NM_001166426::g.2087::m.2087, not unique enough -skipping training candidate: Gene.2092::NM_017883::g.2092::m.2092, not unique enough -skipping training candidate: Gene.405::NM_001080851::g.405::m.405, not unique enough -skipping training candidate: Gene.652::NM_001278743::g.652::m.652, not unique enough -skipping training candidate: Gene.902::MSTRG.822.4::g.902::m.902, not unique enough -skipping training candidate: Gene.1463::NM_033053::g.1463::m.1463, not unique enough -skipping training candidate: Gene.1465::NM_033053_dup1::g.1465::m.1465, not unique enough -skipping training candidate: Gene.1605::NM_005647::g.1605::m.1605, not unique enough -skipping training candidate: Gene.1659::MSTRG.1023.3::g.1659::m.1659, not unique enough -skipping training candidate: Gene.1661::MSTRG.1023.2::g.1661::m.1661, not unique enough -skipping training candidate: Gene.1756::NM_001166700::g.1756::m.1756, not unique enough -skipping training candidate: Gene.2786::MSTRG.1074.8::g.2786::m.2786, not unique enough -skipping training candidate: Gene.3577::NR_026594::g.3577::m.3577, not unique enough -skipping training candidate: Gene.4210::NR_110830::g.4210::m.4210, not unique enough -skipping training candidate: Gene.520::NM_001080485::g.520::m.520, not unique enough -skipping training candidate: Gene.555::MSTRG.1025.5::g.555::m.555, not unique enough -skipping training candidate: Gene.1752::NM_001166701::g.1752::m.1752, not unique enough -skipping training candidate: Gene.1755::NM_138362::g.1755::m.1755, not unique enough -skipping training candidate: Gene.1771::NM_001256119::g.1771::m.1771, not unique enough -skipping training candidate: Gene.1773::NM_001256120::g.1773::m.1773, not unique enough -skipping training candidate: Gene.2002::NM_005676::g.2002::m.2002, not unique enough -skipping training candidate: Gene.2005::NM_001204466::g.2005::m.2005, not unique enough -skipping training candidate: Gene.2009::NM_001204468::g.2009::m.2009, not unique enough -skipping training candidate: Gene.2012::NM_152856::g.2012::m.2012, not unique enough -skipping training candidate: Gene.2070::NM_021949::g.2070::m.2070, not unique enough -skipping training candidate: Gene.2455::MSTRG.109.7::g.2455::m.2455, not unique enough -skipping training candidate: Gene.3909::NM_001168401::g.3909::m.3909, not unique enough -skipping training candidate: Gene.3910::NM_032621::g.3910::m.3910, not unique enough -skipping training candidate: Gene.4311::NM_003918::g.4311::m.4311, not unique enough -skipping training candidate: Gene.1019::MSTRG.913.3::g.1019::m.1019, not unique enough -skipping training candidate: Gene.1298::NM_001129826_dup1::g.1298::m.1298, not unique enough -skipping training candidate: Gene.1554::MSTRG.502.3::g.1554::m.1554, not unique enough -skipping training candidate: Gene.1557::NM_001171162::g.1557::m.1557, not unique enough -skipping training candidate: Gene.1559::NM_005096::g.1559::m.1559, not unique enough -skipping training candidate: Gene.1561::MSTRG.502.2::g.1561::m.1561, not unique enough -skipping training candidate: Gene.1563::MSTRG.502.1::g.1563::m.1563, not unique enough -skipping training candidate: Gene.1718::MSTRG.9.3::g.1718::m.1718, not unique enough -skipping training candidate: Gene.1882::MSTRG.654.2::g.1882::m.1882, not unique enough -skipping training candidate: Gene.1886::MSTRG.654.1::g.1886::m.1886, not unique enough -skipping training candidate: Gene.1888::MSTRG.654.3::g.1888::m.1888, not unique enough -skipping training candidate: Gene.3244::MSTRG.794.2::g.3244::m.3244, not unique enough -skipping training candidate: Gene.3282::NM_001109879::g.3282::m.3282, not unique enough -skipping training candidate: Gene.3446::MSTRG.230.7::g.3446::m.3446, not unique enough -skipping training candidate: Gene.2576::NM_001145140_dup1::g.2576::m.2576, not unique enough -skipping training candidate: Gene.4295::NM_001145139_dup1::g.4295::m.4295, not unique enough -skipping training candidate: Gene.4299::NM_001145139::g.4299::m.4299, not unique enough -skipping training candidate: Gene.567::NM_001303624::g.567::m.567, not unique enough -skipping training candidate: Gene.1058::NM_001114937::g.1058::m.1058, not unique enough -skipping training candidate: Gene.1866::NM_001291868::g.1866::m.1866, not unique enough -skipping training candidate: Gene.2384::MSTRG.405.3::g.2384::m.2384, not unique enough -skipping training candidate: Gene.2389::MSTRG.405.4::g.2389::m.2389, not unique enough -skipping training candidate: Gene.3553::NM_001291867::g.3553::m.3553, not unique enough -skipping training candidate: Gene.3631::NM_001136024::g.3631::m.3631, not unique enough -skipping training candidate: Gene.3833::NM_000166::g.3833::m.3833, not unique enough -skipping training candidate: Gene.959::MSTRG.324.2::g.959::m.959, not unique enough -skipping training candidate: Gene.982::NM_001168302::g.982::m.982, not unique enough -skipping training candidate: Gene.1320::MSTRG.311.2::g.1320::m.1320, not unique enough -skipping training candidate: Gene.1494::MSTRG.921.5::g.1494::m.1494, not unique enough -skipping training candidate: Gene.1499::MSTRG.921.6::g.1499::m.1499, not unique enough -skipping training candidate: Gene.1633::NM_000425::g.1633::m.1633, not unique enough -skipping training candidate: Gene.1639::NM_024003::g.1639::m.1639, not unique enough -skipping training candidate: Gene.1645::NM_001143963::g.1645::m.1645, not unique enough -skipping training candidate: Gene.2376::NM_019863::g.2376::m.2376, not unique enough -skipping training candidate: Gene.2483::NM_001242310::g.2483::m.2483, not unique enough -skipping training candidate: Gene.2713::MSTRG.363.1::g.2713::m.2713, not unique enough -skipping training candidate: Gene.2754::NM_001037343::g.2754::m.2754, not unique enough -skipping training candidate: Gene.3212::MSTRG.76.2::g.3212::m.3212, not unique enough -skipping training candidate: Gene.3678::NM_001204811::g.3678::m.3678, not unique enough -skipping training candidate: Gene.3763::MSTRG.992.5::g.3763::m.3763, not unique enough -skipping training candidate: Gene.3770::MSTRG.992.3::g.3770::m.3770, not unique enough -skipping training candidate: Gene.3791::MSTRG.602.3::g.3791::m.3791, not unique enough -skipping training candidate: Gene.4092::NM_001146256::g.4092::m.4092, not unique enough -skipping training candidate: Gene.4094::NM_001146257::g.4094::m.4094, not unique enough -skipping training candidate: Gene.4176::MSTRG.208.3::g.4176::m.4176, not unique enough -skipping training candidate: Gene.4178::NM_152787::g.4178::m.4178, not unique enough -skipping training candidate: Gene.4181::MSTRG.208.2::g.4181::m.4181, not unique enough -skipping training candidate: Gene.1090::NM_021048::g.1090::m.1090, not unique enough -skipping training candidate: Gene.1178::NM_001011543::g.1178::m.1178, not unique enough -skipping training candidate: Gene.1725::MSTRG.147.4::g.1725::m.1725, not unique enough -skipping training candidate: Gene.2735::NM_001170931::g.2735::m.2735, not unique enough -skipping training candidate: Gene.3166::MSTRG.1041.5::g.3166::m.3166, not unique enough -skipping training candidate: Gene.3248::MSTRG.794.3::g.3248::m.3248, not unique enough -skipping training candidate: Gene.3608::NM_001356::g.3608::m.3608, not unique enough -skipping training candidate: Gene.1374::MSTRG.68.1::g.1374::m.1374, not unique enough -skipping training candidate: Gene.1378::MSTRG.68.18::g.1378::m.1378, not unique enough -skipping training candidate: Gene.1390::MSTRG.68.10::g.1390::m.1390, not unique enough -skipping training candidate: Gene.1394::MSTRG.68.8::g.1394::m.1394, not unique enough -skipping training candidate: Gene.1397::MSTRG.68.5::g.1397::m.1397, not unique enough -skipping training candidate: Gene.1403::MSTRG.68.3::g.1403::m.1403, not unique enough -skipping training candidate: Gene.1407::MSTRG.68.6::g.1407::m.1407, not unique enough -skipping training candidate: Gene.1411::MSTRG.68.16::g.1411::m.1411, not unique enough -skipping training candidate: Gene.1417::NR_034031::g.1417::m.1417, not unique enough -skipping training candidate: Gene.1423::MSTRG.68.14::g.1423::m.1423, not unique enough -skipping training candidate: Gene.1431::MSTRG.68.17::g.1431::m.1431, not unique enough -skipping training candidate: Gene.2509::NR_027401::g.2509::m.2509, not unique enough -skipping training candidate: Gene.3228::NM_001303513::g.3228::m.3228, not unique enough -skipping training candidate: Gene.3693::MSTRG.258.9::g.3693::m.3693, not unique enough -skipping training candidate: Gene.266::NM_001037536::g.266::m.266, not unique enough -skipping training candidate: Gene.268::NM_001037540::g.268::m.268, not unique enough -skipping training candidate: Gene.270::NM_001037535::g.270::m.270, not unique enough -skipping training candidate: Gene.272::NM_006746::g.272::m.272, not unique enough -skipping training candidate: Gene.2802::MSTRG.541.3::g.2802::m.2802, not unique enough -skipping training candidate: Gene.4286::NM_005088::g.4286::m.4286, not unique enough -skipping training candidate: Gene.521::NM_001080485::g.521::m.521, not unique enough -skipping training candidate: Gene.719::NM_020922::g.719::m.719, not unique enough -skipping training candidate: Gene.1081::MSTRG.604.2::g.1081::m.1081, not unique enough -skipping training candidate: Gene.1322::MSTRG.311.3::g.1322::m.1322, not unique enough -skipping training candidate: Gene.1352::NM_001080425::g.1352::m.1352, not unique enough -skipping training candidate: Gene.1432::MSTRG.68.17::g.1432::m.1432, not unique enough -skipping training candidate: Gene.3124::NR_130733::g.3124::m.3124, not unique enough -skipping training candidate: Gene.3584::NM_001282535::g.3584::m.3584, not unique enough -skipping training candidate: Gene.3711::NM_001282607::g.3711::m.3711, not unique enough -skipping training candidate: Gene.3949::NR_026551::g.3949::m.3949, not unique enough -skipping training candidate: Gene.3958::NM_013423::g.3958::m.3958, not unique enough -skipping training candidate: Gene.3963::NM_001287242::g.3963::m.3963, not unique enough -skipping training candidate: Gene.3972::NM_013427::g.3972::m.3972, not unique enough -skipping training candidate: Gene.29::NR_015353::g.29::m.29, not unique enough -skipping training candidate: Gene.31::MSTRG.438.2::g.31::m.31, not unique enough -skipping training candidate: Gene.474::NM_001282161::g.474::m.474, not unique enough -skipping training candidate: Gene.777::MSTRG.397.11::g.777::m.777, not unique enough -skipping training candidate: Gene.1415::MSTRG.68.4::g.1415::m.1415, not unique enough -skipping training candidate: Gene.1495::MSTRG.921.5::g.1495::m.1495, not unique enough -skipping training candidate: Gene.1612::NM_001139466::g.1612::m.1612, not unique enough -skipping training candidate: Gene.1706::NR_033714::g.1706::m.1706, not unique enough -skipping training candidate: Gene.1798::MSTRG.4.3::g.1798::m.1798, not unique enough -skipping training candidate: Gene.1806::NM_018390::g.1806::m.1806, not unique enough -skipping training candidate: Gene.1809::NR_028057::g.1809::m.1809, not unique enough -skipping training candidate: Gene.2453::MSTRG.109.9::g.2453::m.2453, not unique enough -skipping training candidate: Gene.3511::NM_001257291::g.3511::m.3511, not unique enough -skipping training candidate: Gene.155::NM_001170703::g.155::m.155, not unique enough -skipping training candidate: Gene.158::MSTRG.889.4::g.158::m.158, not unique enough -skipping training candidate: Gene.160::MSTRG.889.3::g.160::m.160, not unique enough -skipping training candidate: Gene.164::MSTRG.889.2::g.164::m.164, not unique enough -skipping training candidate: Gene.166::NM_133486::g.166::m.166, not unique enough -skipping training candidate: Gene.169::NM_018388::g.169::m.169, not unique enough -skipping training candidate: Gene.171::NM_001170701::g.171::m.171, not unique enough -skipping training candidate: Gene.174::NM_001170702::g.174::m.174, not unique enough -skipping training candidate: Gene.177::MSTRG.889.1::g.177::m.177, not unique enough -skipping training candidate: Gene.928::NR_033835::g.928::m.928, not unique enough -skipping training candidate: Gene.1615::NM_178151::g.1615::m.1615, not unique enough -skipping training candidate: Gene.1799::MSTRG.4.3::g.1799::m.1799, not unique enough -skipping training candidate: Gene.1807::NM_018390::g.1807::m.1807, not unique enough -skipping training candidate: Gene.2318::NM_001171706::g.2318::m.2318, not unique enough -skipping training candidate: Gene.2391::NR_104390::g.2391::m.2391, not unique enough -skipping training candidate: Gene.2396::NR_104395::g.2396::m.2396, not unique enough -skipping training candidate: Gene.2398::NR_104393::g.2398::m.2398, not unique enough -skipping training candidate: Gene.2400::NR_104389::g.2400::m.2400, not unique enough -skipping training candidate: Gene.2405::NR_104392::g.2405::m.2405, not unique enough -skipping training candidate: Gene.2409::NR_104387::g.2409::m.2409, not unique enough -skipping training candidate: Gene.2412::NR_104391::g.2412::m.2412, not unique enough -skipping training candidate: Gene.2416::NR_104394::g.2416::m.2416, not unique enough -skipping training candidate: Gene.2418::NR_104388::g.2418::m.2418, not unique enough -skipping training candidate: Gene.2508::NM_178153::g.2508::m.2508, not unique enough -skipping training candidate: Gene.3213::MSTRG.76.2::g.3213::m.3213, not unique enough -skipping training candidate: Gene.3226::NM_000555::g.3226::m.3226, not unique enough -skipping training candidate: Gene.3402::NM_001195553::g.3402::m.3402, not unique enough -skipping training candidate: Gene.3781::MSTRG.992.2::g.3781::m.3781, not unique enough -skipping training candidate: Gene.3908::NM_001168399::g.3908::m.3908, not unique enough -skipping training candidate: Gene.4144::MSTRG.216.5::g.4144::m.4144, not unique enough -skipping training candidate: Gene.4147::NM_001098791::g.4147::m.4147, not unique enough -skipping training candidate: Gene.4152::NM_021242::g.4152::m.4152, not unique enough -skipping training candidate: Gene.4155::NM_001098790::g.4155::m.4155, not unique enough -skipping training candidate: Gene.371::NM_001127199_dup3::g.371::m.371, not unique enough -skipping training candidate: Gene.372::NM_001127199_dup6::g.372::m.372, not unique enough -skipping training candidate: Gene.373::NM_001127199::g.373::m.373, not unique enough -skipping training candidate: Gene.374::NM_001127199_dup5::g.374::m.374, not unique enough -skipping training candidate: Gene.375::NM_001127199_dup2::g.375::m.375, not unique enough -skipping training candidate: Gene.376::NM_001127199_dup4::g.376::m.376, not unique enough -skipping training candidate: Gene.377::NM_001127199_dup1::g.377::m.377, not unique enough -skipping training candidate: Gene.637::NM_001098407::g.637::m.637, not unique enough -skipping training candidate: Gene.1055::NM_001476::g.1055::m.1055, not unique enough -skipping training candidate: Gene.1056::NM_001476_dup1::g.1056::m.1056, not unique enough -skipping training candidate: Gene.1057::NM_001476_dup2::g.1057::m.1057, not unique enough -skipping training candidate: Gene.1116::NM_001098418_dup2::g.1116::m.1116, not unique enough -skipping training candidate: Gene.1117::NM_001098418_dup3::g.1117::m.1117, not unique enough -skipping training candidate: Gene.1118::NM_001098418_dup5::g.1118::m.1118, not unique enough -skipping training candidate: Gene.1119::NM_001098418::g.1119::m.1119, not unique enough -skipping training candidate: Gene.1120::NM_001098418_dup4::g.1120::m.1120, not unique enough -skipping training candidate: Gene.1121::NM_001098418_dup1::g.1121::m.1121, not unique enough -skipping training candidate: Gene.1305::NM_001098409_dup3::g.1305::m.1305, not unique enough -skipping training candidate: Gene.1306::NM_001098409_dup2::g.1306::m.1306, not unique enough -skipping training candidate: Gene.1307::NM_001098409::g.1307::m.1307, not unique enough -skipping training candidate: Gene.1308::NM_001098409_dup1::g.1308::m.1308, not unique enough -skipping training candidate: Gene.1309::NM_001098409_dup4::g.1309::m.1309, not unique enough -skipping training candidate: Gene.1310::NM_001098409_dup5::g.1310::m.1310, not unique enough -skipping training candidate: Gene.1401::MSTRG.68.2::g.1401::m.1401, not unique enough -skipping training candidate: Gene.1426::MSTRG.68.7::g.1426::m.1426, not unique enough -skipping training candidate: Gene.1428::MSTRG.68.19::g.1428::m.1428, not unique enough -skipping training candidate: Gene.1453::NM_001306144::g.1453::m.1453, not unique enough -skipping training candidate: Gene.1455::NM_003828::g.1455::m.1455, not unique enough -skipping training candidate: Gene.1500::MSTRG.921.6::g.1500::m.1500, not unique enough -skipping training candidate: Gene.1505::NM_012196::g.1505::m.1505, not unique enough -skipping training candidate: Gene.1690::NM_001474_dup1::g.1690::m.1690, not unique enough -skipping training candidate: Gene.1691::NM_001474_dup2::g.1691::m.1691, not unique enough -skipping training candidate: Gene.1692::NM_001474::g.1692::m.1692, not unique enough -skipping training candidate: Gene.1694::NM_001271187::g.1694::m.1694, not unique enough -skipping training candidate: Gene.1695::MSTRG.887.3::g.1695::m.1695, not unique enough -skipping training candidate: Gene.1699::MSTRG.887.8::g.1699::m.1699, not unique enough -skipping training candidate: Gene.1786::NM_001098406::g.1786::m.1786, not unique enough -skipping training candidate: Gene.1890::NM_013453::g.1890::m.1890, not unique enough -skipping training candidate: Gene.2058::NM_001006684::g.2058::m.2058, not unique enough -skipping training candidate: Gene.2071::NM_021949::g.2071::m.2071, not unique enough -skipping training candidate: Gene.2312::NM_001127345::g.2312::m.2312, not unique enough -skipping training candidate: Gene.2313::NM_001127345_dup1::g.2313::m.2313, not unique enough -skipping training candidate: Gene.2314::NM_001127345_dup2::g.2314::m.2314, not unique enough -skipping training candidate: Gene.2530::NM_001477::g.2530::m.2530, not unique enough -skipping training candidate: Gene.2531::NM_001477_dup1::g.2531::m.2531, not unique enough -skipping training candidate: Gene.2532::NM_001477_dup2::g.2532::m.2532, not unique enough -skipping training candidate: Gene.2868::NM_001098408::g.2868::m.2868, not unique enough -skipping training candidate: Gene.2869::NM_001098408_dup2::g.2869::m.2869, not unique enough -skipping training candidate: Gene.2870::NM_001098408_dup5::g.2870::m.2870, not unique enough -skipping training candidate: Gene.2871::NM_001098408_dup1::g.2871::m.2871, not unique enough -skipping training candidate: Gene.2872::NM_001098408_dup3::g.2872::m.2872, not unique enough -skipping training candidate: Gene.2873::NM_001098408_dup4::g.2873::m.2873, not unique enough -skipping training candidate: Gene.2937::NM_001475_dup1::g.2937::m.2937, not unique enough -skipping training candidate: Gene.2938::NM_001475_dup2::g.2938::m.2938, not unique enough -skipping training candidate: Gene.2939::NM_001475::g.2939::m.2939, not unique enough -skipping training candidate: Gene.2975::NM_021123_dup2::g.2975::m.2975, not unique enough -skipping training candidate: Gene.2976::NM_021123_dup1::g.2976::m.2976, not unique enough -skipping training candidate: Gene.2977::NM_021123::g.2977::m.2977, not unique enough -skipping training candidate: Gene.3079::NM_001456::g.3079::m.3079, not unique enough -skipping training candidate: Gene.3233::NM_001098410_dup2::g.3233::m.3233, not unique enough -skipping training candidate: Gene.3234::NM_001098410_dup1::g.3234::m.3234, not unique enough -skipping training candidate: Gene.3235::NM_001098410_dup3::g.3235::m.3235, not unique enough -skipping training candidate: Gene.3236::NM_001098410::g.3236::m.3236, not unique enough -skipping training candidate: Gene.3303::NM_001040663::g.3303::m.3303, not unique enough -skipping training candidate: Gene.3305::NM_001127200::g.3305::m.3305, not unique enough -skipping training candidate: Gene.3316::NM_145662_dup1::g.3316::m.3316, not unique enough -skipping training candidate: Gene.3317::NM_145662::g.3317::m.3317, not unique enough -skipping training candidate: Gene.3443::NM_080720_dup1::g.3443::m.3443, not unique enough -skipping training candidate: Gene.3564::NM_001098412::g.3564::m.3564, not unique enough -skipping training candidate: Gene.3938::NM_001017990::g.3938::m.3938, not unique enough -skipping training candidate: Gene.4017::NM_001098405_dup2::g.4017::m.4017, not unique enough -skipping training candidate: Gene.4018::NM_001098405::g.4018::m.4018, not unique enough -skipping training candidate: Gene.4019::NM_001098405_dup5::g.4019::m.4019, not unique enough -skipping training candidate: Gene.4020::NM_001098405_dup3::g.4020::m.4020, not unique enough -skipping training candidate: Gene.4021::NM_001098405_dup4::g.4021::m.4021, not unique enough -skipping training candidate: Gene.4022::NM_001098405_dup1::g.4022::m.4022, not unique enough -skipping training candidate: Gene.365::MSTRG.1055.2::g.365::m.365, not unique enough -skipping training candidate: Gene.806::MSTRG.275.3::g.806::m.806, not unique enough -skipping training candidate: Gene.809::NM_001170460::g.809::m.809, not unique enough -skipping training candidate: Gene.812::MSTRG.275.2::g.812::m.812, not unique enough -skipping training candidate: Gene.817::MSTRG.275.4::g.817::m.817, not unique enough -skipping training candidate: Gene.820::MSTRG.275.7::g.820::m.820, not unique enough -skipping training candidate: Gene.823::MSTRG.275.6::g.823::m.823, not unique enough -skipping training candidate: Gene.828::NM_006201::g.828::m.828, not unique enough -skipping training candidate: Gene.1899::MSTRG.443.1::g.1899::m.1899, not unique enough -skipping training candidate: Gene.1901::NM_001173480::g.1901::m.1901, not unique enough -skipping training candidate: Gene.1903::MSTRG.443.3::g.1903::m.1903, not unique enough -skipping training candidate: Gene.1905::MSTRG.443.2::g.1905::m.1905, not unique enough -skipping training candidate: Gene.1907::NM_001173479::g.1907::m.1907, not unique enough -skipping training candidate: Gene.1909::MSTRG.443.9::g.1909::m.1909, not unique enough -skipping training candidate: Gene.1911::NM_015185::g.1911::m.1911, not unique enough -skipping training candidate: Gene.1914::MSTRG.443.5::g.1914::m.1914, not unique enough -skipping training candidate: Gene.2316::NM_001472::g.2316::m.2316, not unique enough -skipping training candidate: Gene.2471::NM_001199687::g.2471::m.2471, not unique enough -skipping training candidate: Gene.2475::MSTRG.459.4::g.2475::m.2475, not unique enough -skipping training candidate: Gene.2489::MSTRG.459.2::g.2489::m.2489, not unique enough -skipping training candidate: Gene.2678::NM_015075::g.2678::m.2678, not unique enough -skipping training candidate: Gene.2706::NM_016542::g.2706::m.2706, not unique enough -skipping training candidate: Gene.3565::NM_001127212::g.3565::m.3565, not unique enough -skipping training candidate: Gene.3936::NR_037859::g.3936::m.3936, not unique enough -skipping training candidate: Gene.3989::NM_145799::g.3989::m.3989, not unique enough -skipping training candidate: Gene.4045::MSTRG.1005.2::g.4045::m.4045, not unique enough -skipping training candidate: Gene.462::NM_001128166::g.462::m.462, not unique enough -skipping training candidate: Gene.691::NM_001129896::g.691::m.691, not unique enough -skipping training candidate: Gene.1398::MSTRG.68.5::g.1398::m.1398, not unique enough -skipping training candidate: Gene.1404::MSTRG.68.3::g.1404::m.1404, not unique enough -skipping training candidate: Gene.1427::MSTRG.68.7::g.1427::m.1427, not unique enough -skipping training candidate: Gene.1433::MSTRG.68.17::g.1433::m.1433, not unique enough -skipping training candidate: Gene.1780::MSTRG.718.3::g.1780::m.1780, not unique enough -skipping training candidate: Gene.1862::NM_001170780::g.1862::m.1862, not unique enough -skipping training candidate: Gene.2035::NM_001178106::g.2035::m.2035, not unique enough -skipping training candidate: Gene.2707::NM_016542::g.2707::m.2707, not unique enough -skipping training candidate: Gene.2864::NM_001174068::g.2864::m.2864, not unique enough -skipping training candidate: Gene.3192::NM_001017991_dup2::g.3192::m.3192, not unique enough -skipping training candidate: Gene.3442::NM_001017991_dup1::g.3442::m.3442, not unique enough -skipping training candidate: Gene.3937::NM_001017991::g.3937::m.3937, not unique enough -skipping training candidate: Gene.51::NM_001097605::g.51::m.51, not unique enough -skipping training candidate: Gene.412::NM_001304990::g.412::m.412, not unique enough -skipping training candidate: Gene.470::NM_181762::g.470::m.470, not unique enough -skipping training candidate: Gene.477::NM_003336::g.477::m.477, not unique enough -skipping training candidate: Gene.522::NM_001080485::g.522::m.522, not unique enough -skipping training candidate: Gene.587::NM_001184875::g.587::m.587, not unique enough -skipping training candidate: Gene.593::NM_138437::g.593::m.593, not unique enough -skipping training candidate: Gene.597::NM_001199818::g.597::m.597, not unique enough -skipping training candidate: Gene.604::NM_001004051::g.604::m.604, not unique enough -skipping training candidate: Gene.608::NM_001184874::g.608::m.608, not unique enough -skipping training candidate: Gene.909::NM_004135::g.909::m.909, not unique enough -skipping training candidate: Gene.1076::NM_001830::g.1076::m.1076, not unique enough -skipping training candidate: Gene.1186::NM_001103151::g.1186::m.1186, not unique enough -skipping training candidate: Gene.1370::NM_001282875::g.1370::m.1370, not unique enough -skipping training candidate: Gene.1372::NM_001282874::g.1372::m.1372, not unique enough -skipping training candidate: Gene.1754::NM_001166703::g.1754::m.1754, not unique enough -skipping training candidate: Gene.2044::NM_001204402::g.2044::m.2044, not unique enough -skipping training candidate: Gene.2118::NM_001081550::g.2118::m.2118, not unique enough -skipping training candidate: Gene.2120::MSTRG.839.4::g.2120::m.2120, not unique enough -skipping training candidate: Gene.2122::MSTRG.839.5::g.2122::m.2122, not unique enough -skipping training candidate: Gene.2125::MSTRG.839.3::g.2125::m.2125, not unique enough -skipping training candidate: Gene.2684::NM_001142386::g.2684::m.2684, not unique enough -skipping training candidate: Gene.2811::MSTRG.456.6::g.2811::m.2811, not unique enough -skipping training candidate: Gene.2813::NM_014799::g.2813::m.2813, not unique enough -skipping training candidate: Gene.2816::NM_001282141::g.2816::m.2816, not unique enough -skipping training candidate: Gene.2818::NM_138737::g.2818::m.2818, not unique enough -skipping training candidate: Gene.2821::MSTRG.456.2::g.2821::m.2821, not unique enough -skipping training candidate: Gene.2831::NM_001449::g.2831::m.2831, not unique enough -skipping training candidate: Gene.2836::NM_001159703::g.2836::m.2836, not unique enough -skipping training candidate: Gene.2841::NM_001103150::g.2841::m.2841, not unique enough -skipping training candidate: Gene.2958::NM_001097596_dup1::g.2958::m.2958, not unique enough -skipping training candidate: Gene.2959::NM_001097596::g.2959::m.2959, not unique enough -skipping training candidate: Gene.3148::MSTRG.1041.8::g.3148::m.3148, not unique enough -skipping training candidate: Gene.3422::MSTRG.906.2::g.3422::m.3422, not unique enough -skipping training candidate: Gene.3722::MSTRG.933.1::g.3722::m.3722, not unique enough -skipping training candidate: Gene.3776::MSTRG.992.1::g.3776::m.3776, not unique enough -skipping training candidate: Gene.4216::NM_052926::g.4216::m.4216, not unique enough -skipping training candidate: Gene.211::NM_013364::g.211::m.211, not unique enough -skipping training candidate: Gene.501::NM_031892::g.501::m.501, not unique enough -skipping training candidate: Gene.504::MSTRG.151.5::g.504::m.504, not unique enough -skipping training candidate: Gene.2043::NM_006521::g.2043::m.2043, not unique enough -skipping training candidate: Gene.2343::NM_182680::g.2343::m.2343, not unique enough -skipping training candidate: Gene.2345::NM_001142::g.2345::m.2345, not unique enough -skipping training candidate: Gene.2420::NM_001017931::g.2420::m.2420, not unique enough -skipping training candidate: Gene.3329::NM_001199974::g.3329::m.3329, not unique enough -skipping training candidate: Gene.3541::NR_033349::g.3541::m.3541, not unique enough -skipping training candidate: Gene.3644::NM_001171252::g.3644::m.3644, not unique enough -skipping training candidate: Gene.3939::NM_001078173::g.3939::m.3939, not unique enough -skipping training candidate: Gene.26::MSTRG.438.4::g.26::m.26, not unique enough -skipping training candidate: Gene.413::NM_001304990::g.413::m.413, not unique enough -skipping training candidate: Gene.633::NR_034116_dup1::g.633::m.633, not unique enough -skipping training candidate: Gene.1284::NM_002414::g.1284::m.1284, not unique enough -skipping training candidate: Gene.1286::NM_001277710::g.1286::m.1286, not unique enough -skipping training candidate: Gene.2173::NM_001654::g.2173::m.2173, not unique enough -skipping training candidate: Gene.2178::NM_001256196::g.2178::m.2178, not unique enough -skipping training candidate: Gene.2763::MSTRG.1074.9::g.2763::m.2763, not unique enough -skipping training candidate: Gene.2925::NM_001141920::g.2925::m.2925, not unique enough -skipping training candidate: Gene.3093::NM_198511::g.3093::m.3093, not unique enough -skipping training candidate: Gene.3587::NM_021806::g.3587::m.3587, not unique enough -skipping training candidate: Gene.3589::NM_001282311::g.3589::m.3589, not unique enough -skipping training candidate: Gene.3593::MSTRG.1037.1::g.3593::m.3593, not unique enough -skipping training candidate: Gene.3596::NM_001171134::g.3596::m.3596, not unique enough -skipping training candidate: Gene.3864::NR_120493::g.3864::m.3864, not unique enough -skipping training candidate: Gene.3865::NR_120493_dup1::g.3865::m.3865, not unique enough -skipping training candidate: Gene.44::NM_002893::g.44::m.44, not unique enough -skipping training candidate: Gene.132::MSTRG.376.9::g.132::m.132, not unique enough -skipping training candidate: Gene.135::MSTRG.376.4::g.135::m.135, not unique enough -skipping training candidate: Gene.137::NM_004187::g.137::m.137, not unique enough -skipping training candidate: Gene.139::NM_001282622::g.139::m.139, not unique enough -skipping training candidate: Gene.142::MSTRG.376.2::g.142::m.142, not unique enough -skipping training candidate: Gene.145::MSTRG.376.8::g.145::m.145, not unique enough -skipping training candidate: Gene.147::MSTRG.376.1::g.147::m.147, not unique enough -skipping training candidate: Gene.149::NM_001146702::g.149::m.149, not unique enough -skipping training candidate: Gene.279::NM_014380::g.279::m.279, not unique enough -skipping training candidate: Gene.472::MSTRG.799.2::g.472::m.472, not unique enough -skipping training candidate: Gene.475::NM_001282161::g.475::m.475, not unique enough -skipping training candidate: Gene.1012::NM_022117::g.1012::m.1012, not unique enough -skipping training candidate: Gene.1667::NM_134445::g.1667::m.1667, not unique enough -skipping training candidate: Gene.1670::NM_134446::g.1670::m.1670, not unique enough -skipping training candidate: Gene.1673::NM_001242614::g.1673::m.1673, not unique enough -skipping training candidate: Gene.1677::NM_001184808::g.1677::m.1677, not unique enough -skipping training candidate: Gene.1867::NM_001291868::g.1867::m.1867, not unique enough -skipping training candidate: Gene.1921::NM_001025242::g.1921::m.1921, not unique enough -skipping training candidate: Gene.1924::NM_001025243::g.1924::m.1924, not unique enough -skipping training candidate: Gene.1942::NR_033348::g.1942::m.1942, not unique enough -skipping training candidate: Gene.2162::NM_024087::g.2162::m.2162, not unique enough -skipping training candidate: Gene.2164::NM_001168530::g.2164::m.2164, not unique enough -skipping training candidate: Gene.2311::NM_001159560::g.2311::m.2311, not unique enough -skipping training candidate: Gene.2428::MSTRG.702.2::g.2428::m.2428, not unique enough -skipping training candidate: Gene.2592::NM_001195578::g.2592::m.2592, not unique enough -skipping training candidate: Gene.3263::NM_001195576::g.3263::m.3263, not unique enough -skipping training candidate: Gene.3294::NM_175569::g.3294::m.3294, not unique enough -skipping training candidate: Gene.3494::NM_000044::g.3494::m.3494, not unique enough -skipping training candidate: Gene.3554::NM_001291867::g.3554::m.3554, not unique enough -skipping training candidate: Gene.3632::NM_001136024::g.3632::m.3632, not unique enough -skipping training candidate: Gene.3860::NM_130776::g.3860::m.3860, not unique enough -skipping training candidate: Gene.4029::NM_207339::g.4029::m.4029, not unique enough -skipping training candidate: Gene.4080::MSTRG.719.3::g.4080::m.4080, not unique enough -skipping training candidate: Gene.4248::MSTRG.17.1::g.4248::m.4248, not unique enough -skipping training candidate: Gene.4255::MSTRG.17.2::g.4255::m.4255, not unique enough -skipping training candidate: Gene.4257::NM_004192::g.4257::m.4257, not unique enough -skipping training candidate: Gene.4259::NM_001173473::g.4259::m.4259, not unique enough -skipping training candidate: Gene.4262::NM_001173474::g.4262::m.4262, not unique enough -skipping training candidate: Gene.4265::MSTRG.17.6::g.4265::m.4265, not unique enough -skipping training candidate: Gene.197::NR_001564::g.197::m.197, not unique enough -skipping training candidate: Gene.200::MSTRG.531.1::g.200::m.200, not unique enough -skipping training candidate: Gene.203::MSTRG.531.3::g.203::m.203, not unique enough -skipping training candidate: Gene.262::MSTRG.26.2::g.262::m.262, not unique enough -skipping training candidate: Gene.683::MSTRG.763.3::g.683::m.683, not unique enough -skipping training candidate: Gene.736::MSTRG.397.6::g.736::m.736, not unique enough -skipping training candidate: Gene.739::MSTRG.397.7::g.739::m.739, not unique enough -skipping training candidate: Gene.742::MSTRG.397.5::g.742::m.742, not unique enough -skipping training candidate: Gene.753::MSTRG.397.2::g.753::m.753, not unique enough -skipping training candidate: Gene.758::MSTRG.397.8::g.758::m.758, not unique enough -skipping training candidate: Gene.783::MSTRG.397.4::g.783::m.783, not unique enough -skipping training candidate: Gene.788::MSTRG.397.3::g.788::m.788, not unique enough -skipping training candidate: Gene.1092::NM_001129828::g.1092::m.1092, not unique enough -skipping training candidate: Gene.1297::NM_001129828_dup1::g.1297::m.1297, not unique enough -skipping training candidate: Gene.1429::MSTRG.68.19::g.1429::m.1429, not unique enough -skipping training candidate: Gene.1634::NM_000425::g.1634::m.1634, not unique enough -skipping training candidate: Gene.1640::NM_024003::g.1640::m.1640, not unique enough -skipping training candidate: Gene.1646::NM_001143963::g.1646::m.1646, not unique enough -skipping training candidate: Gene.1775::NM_001244892_dup1::g.1775::m.1775, not unique enough -skipping training candidate: Gene.2846::NR_037927::g.2846::m.2846, not unique enough -skipping training candidate: Gene.2874::NM_001144064_dup1::g.2874::m.2874, not unique enough -skipping training candidate: Gene.2875::NM_001144064::g.2875::m.2875, not unique enough -skipping training candidate: Gene.2893::NM_001145414::g.2893::m.2893, not unique enough -skipping training candidate: Gene.3096::MSTRG.36.2::g.3096::m.3096, not unique enough -skipping training candidate: Gene.3097::MSTRG.36.1::g.3097::m.3097, not unique enough -skipping training candidate: Gene.3167::MSTRG.1041.5::g.3167::m.3167, not unique enough -skipping training candidate: Gene.3194::NM_001134321::g.3194::m.3194, not unique enough -skipping training candidate: Gene.3558::NM_033380::g.3558::m.3558, not unique enough -skipping training candidate: Gene.3766::MSTRG.992.4::g.3766::m.3766, not unique enough -skipping training candidate: Gene.588::NM_001184875::g.588::m.588, not unique enough -skipping training candidate: Gene.594::NM_138437::g.594::m.594, not unique enough -skipping training candidate: Gene.605::NM_001004051::g.605::m.605, not unique enough -skipping training candidate: Gene.609::NM_001184874::g.609::m.609, not unique enough -skipping training candidate: Gene.1984::NM_001145409::g.1984::m.1984, not unique enough -skipping training candidate: Gene.1986::NM_001145410::g.1986::m.1986, not unique enough -skipping training candidate: Gene.1988::NM_007363::g.1988::m.1988, not unique enough -skipping training candidate: Gene.2291::MSTRG.693.4::g.2291::m.2291, not unique enough -skipping training candidate: Gene.2293::NM_001006933::g.2293::m.2293, not unique enough -skipping training candidate: Gene.2296::MSTRG.693.3::g.2296::m.2296, not unique enough -skipping training candidate: Gene.2577::NM_001145140_dup1::g.2577::m.2577, not unique enough -skipping training candidate: Gene.2583::NM_014725::g.2583::m.2583, not unique enough -skipping training candidate: Gene.2880::NM_001142504::g.2880::m.2880, not unique enough -skipping training candidate: Gene.3771::MSTRG.992.3::g.3771::m.3771, not unique enough -skipping training candidate: Gene.3773::MSTRG.992.6::g.3773::m.3773, not unique enough -skipping training candidate: Gene.3784::MSTRG.992.7::g.3784::m.3784, not unique enough -skipping training candidate: Gene.3793::NM_001184704::g.3793::m.3793, not unique enough -skipping training candidate: Gene.4068::MSTRG.108.3::g.4068::m.4068, not unique enough -skipping training candidate: Gene.4071::NM_001042480::g.4071::m.4071, not unique enough -skipping training candidate: Gene.4073::NM_001042479::g.4073::m.4073, not unique enough -skipping training candidate: Gene.4075::MSTRG.108.1::g.4075::m.4075, not unique enough -skipping training candidate: Gene.4079::NM_017856::g.4079::m.4079, not unique enough -skipping training candidate: Gene.4207::NM_001448::g.4207::m.4207, not unique enough -skipping training candidate: Gene.4296::NM_001145139_dup1::g.4296::m.4296, not unique enough -skipping training candidate: Gene.4300::NM_001145139::g.4300::m.4300, not unique enough -skipping training candidate: Gene.369::NM_001018024::g.369::m.369, not unique enough -skipping training candidate: Gene.939::NR_033772_dup1::g.939::m.939, not unique enough -skipping training candidate: Gene.994::NR_120499::g.994::m.994, not unique enough -skipping training candidate: Gene.995::NR_120499_dup1::g.995::m.995, not unique enough -skipping training candidate: Gene.1168::MSTRG.364.2::g.1168::m.1168, not unique enough -skipping training candidate: Gene.1171::MSTRG.364.3::g.1171::m.1171, not unique enough -skipping training candidate: Gene.1181::NM_001171095::g.1181::m.1181, not unique enough -skipping training candidate: Gene.1234::MSTRG.369.2::g.1234::m.1234, not unique enough -skipping training candidate: Gene.1365::NR_120494_dup1::g.1365::m.1365, not unique enough -skipping training candidate: Gene.1366::NR_120494::g.1366::m.1366, not unique enough -skipping training candidate: Gene.2423::MSTRG.702.3::g.2423::m.2423, not unique enough -skipping training candidate: Gene.2564::NM_001171092::g.2564::m.2564, not unique enough -skipping training candidate: Gene.3026::NM_001114123::g.3026::m.3026, not unique enough -skipping training candidate: Gene.3143::NR_033773_dup1::g.3143::m.3143, not unique enough -skipping training candidate: Gene.3146::NR_033773::g.3146::m.3146, not unique enough -skipping training candidate: Gene.3324::NM_133499::g.3324::m.3324, not unique enough -skipping training candidate: Gene.3362::MSTRG.1029.2::g.3362::m.3362, not unique enough -skipping training candidate: Gene.3369::MSTRG.1029.12::g.3369::m.3369, not unique enough -skipping training candidate: Gene.3375::MSTRG.1029.1::g.3375::m.3375, not unique enough -skipping training candidate: Gene.3378::MSTRG.1029.4::g.3378::m.3378, not unique enough -skipping training candidate: Gene.3386::MSTRG.1029.3::g.3386::m.3386, not unique enough -skipping training candidate: Gene.3389::MSTRG.1029.11::g.3389::m.3389, not unique enough -skipping training candidate: Gene.3764::MSTRG.992.5::g.3764::m.3764, not unique enough -skipping training candidate: Gene.891::MSTRG.331.3::g.891::m.891, not unique enough -skipping training candidate: Gene.893::MSTRG.331.1::g.893::m.893, not unique enough -skipping training candidate: Gene.895::MSTRG.331.2::g.895::m.895, not unique enough -skipping training candidate: Gene.897::MSTRG.331.4::g.897::m.897, not unique enough -skipping training candidate: Gene.901::NM_001104544::g.901::m.901, not unique enough -skipping training candidate: Gene.903::MSTRG.822.4::g.903::m.903, not unique enough -skipping training candidate: Gene.905::NM_001104545::g.905::m.905, not unique enough -skipping training candidate: Gene.1848::NR_033181::g.1848::m.1848, not unique enough -skipping training candidate: Gene.2674::NM_001128167::g.2674::m.2674, not unique enough -skipping training candidate: Gene.3122::MSTRG.16.1::g.3122::m.3122, not unique enough -skipping training candidate: Gene.3654::NM_001184830::g.3654::m.3654, not unique enough -skipping training candidate: Gene.388::MSTRG.945.1::g.388::m.388, not unique enough -skipping training candidate: Gene.1693::MSTRG.887.7::g.1693::m.1693, not unique enough -skipping training candidate: Gene.2003::NM_005676::g.2003::m.2003, not unique enough -skipping training candidate: Gene.2006::NM_001204466::g.2006::m.2006, not unique enough -skipping training candidate: Gene.2010::NM_001204468::g.2010::m.2010, not unique enough -skipping training candidate: Gene.2013::NM_152856::g.2013::m.2013, not unique enough -skipping training candidate: Gene.2274::MSTRG.973.1::g.2274::m.2274, not unique enough -skipping training candidate: Gene.2657::NM_001171909::g.2657::m.2657, not unique enough -skipping training candidate: Gene.2661::MSTRG.963.2::g.2661::m.2661, not unique enough -skipping training candidate: Gene.2662::MSTRG.963.2::g.2662::m.2662, not unique enough -skipping training candidate: Gene.2665::MSTRG.963.3::g.2665::m.2665, not unique enough -skipping training candidate: Gene.2669::MSTRG.963.1::g.2669::m.2669, not unique enough -skipping training candidate: Gene.2768::MSTRG.1074.10::g.2768::m.2768, not unique enough -skipping training candidate: Gene.2772::MSTRG.1074.1::g.2772::m.2772, not unique enough -skipping training candidate: Gene.2778::MSTRG.1074.2::g.2778::m.2778, not unique enough -skipping training candidate: Gene.2780::MSTRG.1074.5::g.2780::m.2780, not unique enough -skipping training candidate: Gene.2784::MSTRG.1074.3::g.2784::m.2784, not unique enough -skipping training candidate: Gene.2787::MSTRG.1074.8::g.2787::m.2787, not unique enough -skipping training candidate: Gene.3094::NM_198511::g.3094::m.3094, not unique enough -skipping training candidate: Gene.3290::NM_004595::g.3290::m.3290, not unique enough -skipping training candidate: Gene.3330::NM_001199972::g.3330::m.3330, not unique enough -skipping training candidate: Gene.3428::NR_024499::g.3428::m.3428, not unique enough -skipping training candidate: Gene.3849::MSTRG.74.2::g.3849::m.3849, not unique enough -skipping training candidate: Gene.4076::MSTRG.108.1::g.4076::m.4076, not unique enough -skipping training candidate: Gene.101::MSTRG.862.1::g.101::m.101, not unique enough -skipping training candidate: Gene.104::NM_001127197::g.104::m.104, not unique enough -skipping training candidate: Gene.107::MSTRG.862.3::g.107::m.107, not unique enough -skipping training candidate: Gene.110::NM_001421::g.110::m.110, not unique enough -skipping training candidate: Gene.113::MSTRG.862.4::g.113::m.113, not unique enough -skipping training candidate: Gene.1380::MSTRG.68.12::g.1380::m.1380, not unique enough -skipping training candidate: Gene.1384::MSTRG.68.9::g.1384::m.1384, not unique enough -skipping training candidate: Gene.1386::MSTRG.68.13::g.1386::m.1386, not unique enough -skipping training candidate: Gene.1395::MSTRG.68.8::g.1395::m.1395, not unique enough -skipping training candidate: Gene.1405::MSTRG.68.3::g.1405::m.1405, not unique enough -skipping training candidate: Gene.1408::MSTRG.68.6::g.1408::m.1408, not unique enough -skipping training candidate: Gene.1413::MSTRG.68.16::g.1413::m.1413, not unique enough -skipping training candidate: Gene.1419::NR_034031::g.1419::m.1419, not unique enough -skipping training candidate: Gene.1424::MSTRG.68.14::g.1424::m.1424, not unique enough -skipping training candidate: Gene.1434::MSTRG.68.17::g.1434::m.1434, not unique enough -skipping training candidate: Gene.1681::NM_001256789::g.1681::m.1681, not unique enough -skipping training candidate: Gene.1928::MSTRG.860.1::g.1928::m.1928, not unique enough -skipping training candidate: Gene.1930::NM_001184772::g.1930::m.1930, not unique enough -skipping training candidate: Gene.1932::MSTRG.860.3::g.1932::m.1932, not unique enough -skipping training candidate: Gene.1934::MSTRG.860.6::g.1934::m.1934, not unique enough -skipping training candidate: Gene.1936::MSTRG.860.2::g.1936::m.1936, not unique enough -skipping training candidate: Gene.2072::NM_021949::g.2072::m.2072, not unique enough -skipping training candidate: Gene.2440::NM_001143983::g.2440::m.2440, not unique enough -skipping training candidate: Gene.2502::NM_153280::g.2502::m.2502, not unique enough -skipping training candidate: Gene.3284::NM_001586::g.3284::m.3284, not unique enough -skipping training candidate: Gene.3416::NM_005183::g.3416::m.3416, not unique enough -skipping training candidate: Gene.3505::NM_032591::g.3505::m.3505, not unique enough -skipping training candidate: Gene.3509::MSTRG.268.7::g.3509::m.3509, not unique enough -skipping training candidate: Gene.3512::NM_001257291::g.3512::m.3512, not unique enough -skipping training candidate: Gene.3514::MSTRG.268.2::g.3514::m.3514, not unique enough -skipping training candidate: Gene.3516::MSTRG.268.1::g.3516::m.3516, not unique enough -skipping training candidate: Gene.3519::MSTRG.268.3::g.3519::m.3519, not unique enough -skipping training candidate: Gene.3521::MSTRG.268.6::g.3521::m.3521, not unique enough -skipping training candidate: Gene.3871::NM_001143981::g.3871::m.3871, not unique enough -skipping training candidate: Gene.4203::MSTRG.876.1::g.4203::m.4203, not unique enough -skipping training candidate: Gene.1034::NM_203474::g.1034::m.1034, not unique enough -skipping training candidate: Gene.1036::NM_022825::g.1036::m.1036, not unique enough -skipping training candidate: Gene.1039::MSTRG.305.8::g.1039::m.1039, not unique enough -skipping training candidate: Gene.1042::MSTRG.305.6::g.1042::m.1042, not unique enough -skipping training candidate: Gene.1044::NM_203475::g.1044::m.1044, not unique enough -skipping training candidate: Gene.1046::NM_203473::g.1046::m.1046, not unique enough -skipping training candidate: Gene.1049::MSTRG.305.7::g.1049::m.1049, not unique enough -skipping training candidate: Gene.1052::NM_001282167::g.1052::m.1052, not unique enough -skipping training candidate: Gene.1151::MSTRG.2.1::g.1151::m.1151, not unique enough -skipping training candidate: Gene.1326::NM_007213::g.1326::m.1326, not unique enough -skipping training candidate: Gene.1391::MSTRG.68.10::g.1391::m.1391, not unique enough -skipping training candidate: Gene.1399::MSTRG.68.5::g.1399::m.1399, not unique enough -skipping training candidate: Gene.2283::MSTRG.468.4::g.2283::m.2283, not unique enough -skipping training candidate: Gene.2289::NM_032926::g.2289::m.2289, not unique enough -skipping training candidate: Gene.2339::NM_016303::g.2339::m.2339, not unique enough -skipping training candidate: Gene.2340::NM_001006612::g.2340::m.2340, not unique enough -skipping training candidate: Gene.2341::NM_001006614::g.2341::m.2341, not unique enough -skipping training candidate: Gene.2503::NM_153280::g.2503::m.2503, not unique enough -skipping training candidate: Gene.2555::NM_000533::g.2555::m.2555, not unique enough -skipping training candidate: Gene.2578::NM_001145140_dup1::g.2578::m.2578, not unique enough -skipping training candidate: Gene.2892::NM_001171184::g.2892::m.2892, not unique enough -skipping training candidate: Gene.2915::NM_014927::g.2915::m.2915, not unique enough -skipping training candidate: Gene.2918::NM_001168647::g.2918::m.2918, not unique enough -skipping training candidate: Gene.3549::NM_024597::g.3549::m.3549, not unique enough -skipping training candidate: Gene.4266::MSTRG.17.6::g.4266::m.4266, not unique enough -skipping training candidate: Gene.4297::NM_001145139_dup1::g.4297::m.4297, not unique enough -skipping training candidate: Gene.4301::NM_001145139::g.4301::m.4301, not unique enough -skipping training candidate: Gene.4324::NM_199478::g.4324::m.4324, not unique enough -skipping training candidate: Gene.179::MSTRG.889.17::g.179::m.179, not unique enough -skipping training candidate: Gene.2433::NM_033215::g.2433::m.2433, not unique enough -skipping training candidate: Gene.514::MSTRG.549.7::g.514::m.514, not unique enough -skipping training candidate: Gene.1260::NM_017848::g.1260::m.1260, not unique enough -skipping training candidate: Gene.1265::NM_001300788::g.1265::m.1265, not unique enough -skipping training candidate: Gene.1668::NM_134445::g.1668::m.1668, not unique enough -skipping training candidate: Gene.1671::NM_134446::g.1671::m.1671, not unique enough -skipping training candidate: Gene.1674::NM_001242614::g.1674::m.1674, not unique enough -skipping training candidate: Gene.1678::NM_001184808::g.1678::m.1678, not unique enough -skipping training candidate: Gene.2082::NR_029427::g.2082::m.2082, not unique enough -skipping training candidate: Gene.2085::MSTRG.325.4::g.2085::m.2085, not unique enough -skipping training candidate: Gene.2089::NM_001166426::g.2089::m.2089, not unique enough -skipping training candidate: Gene.2093::NM_017883::g.2093::m.2093, not unique enough -skipping training candidate: Gene.2596::MSTRG.301.3::g.2596::m.2596, not unique enough -skipping training candidate: Gene.2601::MSTRG.301.2::g.2601::m.2601, not unique enough -skipping training candidate: Gene.2762::MSTRG.1074.11::g.2762::m.2762, not unique enough -skipping training candidate: Gene.2764::MSTRG.1074.9::g.2764::m.2764, not unique enough -skipping training candidate: Gene.2769::MSTRG.1074.10::g.2769::m.2769, not unique enough -skipping training candidate: Gene.2814::NM_014799::g.2814::m.2814, not unique enough -skipping training candidate: Gene.2819::NM_138737::g.2819::m.2819, not unique enough -skipping training candidate: Gene.2822::MSTRG.456.2::g.2822::m.2822, not unique enough -skipping training candidate: Gene.3304::NM_001040663::g.3304::m.3304, not unique enough -skipping training candidate: Gene.102::MSTRG.862.1::g.102::m.102, not unique enough -skipping training candidate: Gene.105::NM_001127197::g.105::m.105, not unique enough -skipping training candidate: Gene.108::MSTRG.862.3::g.108::m.108, not unique enough -skipping training candidate: Gene.111::NM_001421::g.111::m.111, not unique enough -skipping training candidate: Gene.114::MSTRG.862.4::g.114::m.114, not unique enough -skipping training candidate: Gene.284::NM_206917::g.284::m.284, not unique enough -skipping training candidate: Gene.534::NM_001282157::g.534::m.534, not unique enough -skipping training candidate: Gene.536::NM_012280::g.536::m.536, not unique enough -skipping training candidate: Gene.549::NM_006013::g.549::m.549, not unique enough -skipping training candidate: Gene.556::MSTRG.1025.5::g.556::m.556, not unique enough -skipping training candidate: Gene.560::NM_001256577::g.560::m.560, not unique enough -skipping training candidate: Gene.564::NM_001303625::g.564::m.564, not unique enough -skipping training candidate: Gene.568::NM_001303624::g.568::m.568, not unique enough -skipping training candidate: Gene.571::NM_001256580::g.571::m.571, not unique enough -skipping training candidate: Gene.574::MSTRG.1025.1::g.574::m.574, not unique enough -skipping training candidate: Gene.1016::NM_152634::g.1016::m.1016, not unique enough -skipping training candidate: Gene.1018::NM_001297563::g.1018::m.1018, not unique enough -skipping training candidate: Gene.1210::NM_000513::g.1210::m.1210, not unique enough -skipping training candidate: Gene.1212::NM_000513_dup2::g.1212::m.1212, not unique enough -skipping training candidate: Gene.1266::NM_001300788::g.1266::m.1266, not unique enough -skipping training candidate: Gene.1815::NM_004651::g.1815::m.1815, not unique enough -skipping training candidate: Gene.1954::MSTRG.597.1::g.1954::m.1954, not unique enough -skipping training candidate: Gene.1956::MSTRG.597.3::g.1956::m.1956, not unique enough -skipping training candidate: Gene.2421::NM_001017931::g.2421::m.2421, not unique enough -skipping training candidate: Gene.2447::NM_001128835::g.2447::m.2447, not unique enough -skipping training candidate: Gene.2906::NM_000451::g.2906::m.2906, not unique enough -skipping training candidate: Gene.3027::NM_001114123::g.3027::m.3027, not unique enough -skipping training candidate: Gene.3195::MSTRG.907.2::g.3195::m.3195, not unique enough -skipping training candidate: Gene.3221::NM_000402::g.3221::m.3221, not unique enough -skipping training candidate: Gene.3223::NM_001042351::g.3223::m.3223, not unique enough -skipping training candidate: Gene.3668::NM_032539::g.3668::m.3668, not unique enough -skipping training candidate: Gene.550::NM_006013::g.550::m.550, not unique enough -skipping training candidate: Gene.557::MSTRG.1025.5::g.557::m.557, not unique enough -skipping training candidate: Gene.561::NM_001256577::g.561::m.561, not unique enough -skipping training candidate: Gene.565::NM_001303625::g.565::m.565, not unique enough -skipping training candidate: Gene.569::NM_001303624::g.569::m.569, not unique enough -skipping training candidate: Gene.572::NM_001256580::g.572::m.572, not unique enough -skipping training candidate: Gene.575::MSTRG.1025.1::g.575::m.575, not unique enough -skipping training candidate: Gene.721::NM_033290::g.721::m.721, not unique enough -skipping training candidate: Gene.1063::MSTRG.1042.3::g.1063::m.1063, not unique enough -skipping training candidate: Gene.1066::MSTRG.1042.1::g.1066::m.1066, not unique enough -skipping training candidate: Gene.1314::NM_002637::g.1314::m.1314, not unique enough -skipping training candidate: Gene.1316::NM_001172436::g.1316::m.1316, not unique enough -skipping training candidate: Gene.1760::MSTRG.306.3::g.1760::m.1760, not unique enough -skipping training candidate: Gene.2265::NM_001098624::g.2265::m.2265, not unique enough -skipping training candidate: Gene.2543::MSTRG.128.4::g.2543::m.2543, not unique enough -skipping training candidate: Gene.2781::MSTRG.1074.5::g.2781::m.2781, not unique enough -skipping training candidate: Gene.2955::NM_033289::g.2955::m.2955, not unique enough -skipping training candidate: Gene.3153::NM_001145255::g.3153::m.3153, not unique enough -skipping training candidate: Gene.3157::MSTRG.1041.6::g.3157::m.3157, not unique enough -skipping training candidate: Gene.3159::NM_003639::g.3159::m.3159, not unique enough -skipping training candidate: Gene.3162::NM_001099857::g.3162::m.3162, not unique enough -skipping training candidate: Gene.3165::MSTRG.1041.7::g.3165::m.3165, not unique enough -skipping training candidate: Gene.3169::MSTRG.1041.9::g.3169::m.3169, not unique enough -skipping training candidate: Gene.3171::NM_001099856::g.3171::m.3171, not unique enough -skipping training candidate: Gene.3372::NM_001303465::g.3372::m.3372, not unique enough -skipping training candidate: Gene.3387::MSTRG.1029.3::g.3387::m.3387, not unique enough -skipping training candidate: Gene.3432::NM_001193277::g.3432::m.3432, not unique enough -skipping training candidate: Gene.3670::NM_147175::g.3670::m.3670, not unique enough -skipping training candidate: Gene.3790::NM_198450::g.3790::m.3790, not unique enough -skipping training candidate: Gene.4077::MSTRG.108.1::g.4077::m.4077, not unique enough -skipping training candidate: Gene.675::NM_001184835::g.675::m.675, not unique enough -skipping training candidate: Gene.677::NM_001079859::g.677::m.677, not unique enough -skipping training candidate: Gene.883::NM_032498::g.883::m.883, not unique enough -skipping training candidate: Gene.1077::NM_001830::g.1077::m.1077, not unique enough -skipping training candidate: Gene.1101::MSTRG.961.7::g.1101::m.1101, not unique enough -skipping training candidate: Gene.1103::NM_000202::g.1103::m.1103, not unique enough -skipping training candidate: Gene.1106::MSTRG.961.3::g.1106::m.1106, not unique enough -skipping training candidate: Gene.1110::MSTRG.961.4::g.1110::m.1110, not unique enough -skipping training candidate: Gene.1112::NM_001166550::g.1112::m.1112, not unique enough -skipping training candidate: Gene.1115::MSTRG.961.1::g.1115::m.1115, not unique enough -skipping training candidate: Gene.1219::NM_001163278::g.1219::m.1219, not unique enough -skipping training candidate: Gene.1686::NR_109985::g.1686::m.1686, not unique enough -skipping training candidate: Gene.1994::NM_001079860::g.1994::m.1994, not unique enough -skipping training candidate: Gene.2196::NM_007137::g.2196::m.2196, not unique enough -skipping training candidate: Gene.2198::MSTRG.292.4::g.2198::m.2198, not unique enough -skipping training candidate: Gene.2245::NM_014253::g.2245::m.2245, not unique enough -skipping training candidate: Gene.2454::MSTRG.109.9::g.2454::m.2454, not unique enough -skipping training candidate: Gene.2463::NM_001001994::g.2463::m.2463, not unique enough -skipping training candidate: Gene.2465::NM_005278::g.2465::m.2465, not unique enough -skipping training candidate: Gene.2510::NR_027401::g.2510::m.2510, not unique enough -skipping training candidate: Gene.2591::MSTRG.841.1::g.2591::m.2591, not unique enough -skipping training candidate: Gene.2680::NM_001079858::g.2680::m.2680, not unique enough -skipping training candidate: Gene.2746::NM_001184834::g.2746::m.2746, not unique enough -skipping training candidate: Gene.2832::NM_001449::g.2832::m.2832, not unique enough -skipping training candidate: Gene.2837::NM_001159703::g.2837::m.2837, not unique enough -skipping training candidate: Gene.2902::NM_005756::g.2902::m.2902, not unique enough -skipping training candidate: Gene.2921::NM_001099685::g.2921::m.2921, not unique enough -skipping training candidate: Gene.2923::NM_001099685_dup1::g.2923::m.2923, not unique enough -skipping training candidate: Gene.2926::NM_001141920::g.2926::m.2926, not unique enough -skipping training candidate: Gene.3061::NM_001142529::g.3061::m.3061, not unique enough -skipping training candidate: Gene.3063::NM_030639::g.3063::m.3063, not unique enough -skipping training candidate: Gene.3065::NM_001142528::g.3065::m.3065, not unique enough -skipping training candidate: Gene.3067::NM_001142530::g.3067::m.3067, not unique enough -skipping training candidate: Gene.3069::NM_001142526::g.3069::m.3069, not unique enough -skipping training candidate: Gene.3071::NM_001142527::g.3071::m.3071, not unique enough -skipping training candidate: Gene.3073::NM_001142524::g.3073::m.3073, not unique enough -skipping training candidate: Gene.3190::NM_001184836::g.3190::m.3190, not unique enough -skipping training candidate: Gene.3295::NM_175569::g.3295::m.3295, not unique enough -skipping training candidate: Gene.3578::NR_026594::g.3578::m.3578, not unique enough -skipping training candidate: Gene.3662::NM_001184837::g.3662::m.3662, not unique enough -skipping training candidate: Gene.3820::NM_177537_dup1::g.3820::m.3820, not unique enough -skipping training candidate: Gene.3868::NR_103770::g.3868::m.3868, not unique enough -skipping training candidate: Gene.385::MSTRG.945.3::g.385::m.385, not unique enough -redundancy-minimized set includes 1645 / 4259 = 38.62% * Running CMD: /build/transdecoder-5.0.1/util/get_top_longest_fasta_entries.pl stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr 500 > stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest PCT_GC: 46 * Running CMD: /build/transdecoder-5.0.1/util/seq_n_baseprobs_to_loglikelihood_vals.pl stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest stringtie_merged.transcripts.fasta.transdecoder_dir/base_freqs.dat > stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores * Running CMD: /build/transdecoder-5.0.1/util/score_CDS_likelihood_all_6_frames.pl stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds stringtie_merged.transcripts.fasta.transdecoder_dir/hexamer.scores > stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores * Running CMD: /build/transdecoder-5.0.1/util/select_best_ORFs_per_transcript.pl --gff3_file stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 749 > stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 -indexing [Gene.2979::MSTRG.1.1::g.2979] -indexing [Gene.2978::MSTRG.1.1::g.2978] -indexing [Gene.3929::MSTRG.10.1::g.3929] -indexing [Gene.293::MSTRG.1000.4::g.293] -indexing [Gene.292::MSTRG.1000.4::g.292] -indexing [Gene.910::MSTRG.1001.1::g.910] -indexing [Gene.911::MSTRG.1001.1::g.911] -indexing [Gene.912::MSTRG.1001.1::g.912] -indexing [Gene.913::MSTRG.1001.2::g.913] -indexing [Gene.4047::MSTRG.1005.1::g.4047] -indexing [Gene.4046::MSTRG.1005.1::g.4046] -indexing [Gene.4042::MSTRG.1005.2::g.4042] -indexing [Gene.4043::MSTRG.1005.2::g.4043] -indexing [Gene.4045::MSTRG.1005.2::g.4045] -indexing [Gene.4044::MSTRG.1005.2::g.4044] -indexing [Gene.4041::MSTRG.1005.3::g.4041] -indexing [Gene.4040::MSTRG.1005.3::g.4040] -indexing [Gene.4038::MSTRG.1005.3::g.4038] -indexing [Gene.4039::MSTRG.1005.3::g.4039] -indexing [Gene.2536::MSTRG.1009.2::g.2536] -indexing [Gene.1979::MSTRG.101.1::g.1979] -indexing [Gene.1978::MSTRG.101.1::g.1978] -indexing [Gene.1977::MSTRG.101.1::g.1977] -indexing [Gene.393::MSTRG.1012.1::g.393] -indexing [Gene.392::MSTRG.1012.1::g.392] -indexing [Gene.399::MSTRG.1012.3::g.399] -indexing [Gene.398::MSTRG.1012.3::g.398] -indexing [Gene.394::MSTRG.1012.4::g.394] -indexing [Gene.395::MSTRG.1012.4::g.395] -indexing [Gene.2490::MSTRG.1017.1::g.2490] -indexing [Gene.3075::MSTRG.1021.3::g.3075] -indexing [Gene.1661::MSTRG.1023.2::g.1661] -indexing [Gene.1660::MSTRG.1023.2::g.1660] -indexing [Gene.1658::MSTRG.1023.3::g.1658] -indexing [Gene.1659::MSTRG.1023.3::g.1659] -indexing [Gene.1662::MSTRG.1023.4::g.1662] -indexing [Gene.4267::MSTRG.1024.2::g.4267] -indexing [Gene.4268::MSTRG.1024.2::g.4268] -indexing [Gene.575::MSTRG.1025.1::g.575] -indexing [Gene.574::MSTRG.1025.1::g.574] -indexing [Gene.573::MSTRG.1025.1::g.573] -indexing [Gene.547::MSTRG.1025.12::g.547] -indexing [Gene.558::MSTRG.1025.2::g.558] -indexing [Gene.551::MSTRG.1025.3::g.551] -indexing [Gene.552::MSTRG.1025.4::g.552] -indexing [Gene.553::MSTRG.1025.4::g.553] -indexing [Gene.557::MSTRG.1025.5::g.557] -indexing [Gene.554::MSTRG.1025.5::g.554] -indexing [Gene.556::MSTRG.1025.5::g.556] -indexing [Gene.555::MSTRG.1025.5::g.555] -indexing [Gene.562::MSTRG.1025.6::g.562] -indexing [Gene.3132::MSTRG.1028.1::g.3132] -indexing [Gene.3374::MSTRG.1029.1::g.3374] -indexing [Gene.3373::MSTRG.1029.1::g.3373] -indexing [Gene.3375::MSTRG.1029.1::g.3375] -indexing [Gene.3389::MSTRG.1029.11::g.3389] -indexing [Gene.3388::MSTRG.1029.11::g.3388] -indexing [Gene.3369::MSTRG.1029.12::g.3369] -indexing [Gene.3368::MSTRG.1029.12::g.3368] -indexing [Gene.3367::MSTRG.1029.12::g.3367] -indexing [Gene.3362::MSTRG.1029.2::g.3362] -indexing [Gene.3361::MSTRG.1029.2::g.3361] -indexing [Gene.3360::MSTRG.1029.2::g.3360] -indexing [Gene.3386::MSTRG.1029.3::g.3386] -indexing [Gene.3384::MSTRG.1029.3::g.3384] -indexing [Gene.3385::MSTRG.1029.3::g.3385] -indexing [Gene.3387::MSTRG.1029.3::g.3387] -indexing [Gene.3378::MSTRG.1029.4::g.3378] -indexing [Gene.3376::MSTRG.1029.4::g.3376] -indexing [Gene.3377::MSTRG.1029.4::g.3377] -indexing [Gene.1341::MSTRG.1034.2::g.1341] -indexing [Gene.1340::MSTRG.1034.2::g.1340] -indexing [Gene.1949::MSTRG.1036.1::g.1949] -indexing [Gene.3592::MSTRG.1037.1::g.3592] -indexing [Gene.3593::MSTRG.1037.1::g.3593] -indexing [Gene.3591::MSTRG.1037.8::g.3591] -indexing [Gene.3217::MSTRG.1040.3::g.3217] -indexing 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[Gene.1847::NR_033181::g.1847] -indexing [Gene.1848::NR_033181::g.1848] -indexing [Gene.2615::NR_033212::g.2615] -indexing [Gene.3412::NR_033254::g.3412] -indexing [Gene.3413::NR_033254_dup1::g.3413] -indexing [Gene.4235::NR_033257::g.4235] -indexing [Gene.4234::NR_033257_dup1::g.4234] -indexing [Gene.1347::NR_033262::g.1347] -indexing [Gene.1941::NR_033348::g.1941] -indexing [Gene.1940::NR_033348::g.1940] -indexing [Gene.1942::NR_033348::g.1942] -indexing [Gene.3541::NR_033349::g.3541] -indexing [Gene.3542::NR_033349::g.3542] -indexing [Gene.3540::NR_033349::g.3540] -indexing [Gene.4224::NR_033380::g.4224] -indexing [Gene.4223::NR_033381::g.4223] -indexing [Gene.1736::NR_033699::g.1736] -indexing [Gene.1741::NR_033700::g.1741] -indexing [Gene.1706::NR_033714::g.1706] -indexing [Gene.1705::NR_033715::g.1705] -indexing [Gene.2068::NR_033717::g.2068] -indexing [Gene.1766::NR_033742::g.1766] -indexing [Gene.1767::NR_033742::g.1767] -indexing [Gene.936::NR_033772::g.936] -indexing [Gene.935::NR_033772::g.935] -indexing [Gene.934::NR_033772::g.934] -indexing [Gene.937::NR_033772_dup1::g.937] -indexing [Gene.939::NR_033772_dup1::g.939] -indexing [Gene.938::NR_033772_dup1::g.938] -indexing [Gene.3146::NR_033773::g.3146] -indexing [Gene.3144::NR_033773::g.3144] -indexing [Gene.3145::NR_033773::g.3145] -indexing [Gene.3142::NR_033773_dup1::g.3142] -indexing [Gene.3141::NR_033773_dup1::g.3141] -indexing [Gene.3143::NR_033773_dup1::g.3143] -indexing [Gene.927::NR_033835::g.927] -indexing [Gene.928::NR_033835::g.928] -indexing [Gene.929::NR_033836::g.929] -indexing [Gene.831::NR_033924::g.831] -indexing [Gene.1416::NR_034031::g.1416] -indexing [Gene.1418::NR_034031::g.1418] -indexing [Gene.1417::NR_034031::g.1417] -indexing [Gene.1419::NR_034031::g.1419] -indexing [Gene.632::NR_034116::g.632] -indexing [Gene.633::NR_034116_dup1::g.633] -indexing [Gene.1504::NR_037183::g.1504] -indexing [Gene.1503::NR_037183::g.1503] -indexing [Gene.3935::NR_037859::g.3935] -indexing [Gene.3934::NR_037859::g.3934] -indexing [Gene.3936::NR_037859::g.3936] -indexing [Gene.4319::NR_037916::g.4319] -indexing [Gene.2846::NR_037927::g.2846] -indexing [Gene.2795::NR_039980::g.2795] -indexing [Gene.856::NR_039991_dup1::g.856] -indexing [Gene.4185::NR_045044::g.4185] -indexing [Gene.797::NR_045260::g.797] -indexing [Gene.965::NR_045559::g.965] -indexing [Gene.964::NR_045560::g.964] -indexing [Gene.3048::NR_045861::g.3048] -indexing [Gene.3049::NR_045864::g.3049] -indexing [Gene.2246::NR_046101::g.2246] -indexing [Gene.2931::NR_046750::g.2931] -indexing [Gene.2930::NR_046750::g.2930] -indexing [Gene.1839::NR_051952::g.1839] -indexing [Gene.1838::NR_051952::g.1838] -indexing [Gene.3473::NR_073148::g.3473] -indexing [Gene.3472::NR_073149::g.3472] -indexing [Gene.3779::NR_073156::g.3779] -indexing [Gene.3778::NR_073156::g.3778] -indexing [Gene.3777::NR_073156::g.3777] -indexing [Gene.445::NR_073393::g.445] -indexing [Gene.2367::NR_073450::g.2367] -indexing [Gene.2505::NR_102268::g.2505] -indexing [Gene.2579::NR_102272::g.2579] -indexing [Gene.2580::NR_102272::g.2580] -indexing [Gene.944::NR_103708::g.944] -indexing [Gene.942::NR_103709::g.942] -indexing [Gene.3074::NR_103715::g.3074] -indexing [Gene.3868::NR_103770::g.3868] -indexing [Gene.2016::NR_104107::g.2016] -indexing [Gene.2017::NR_104107::g.2017] -indexing [Gene.2622::NR_104109::g.2622] -indexing [Gene.3052::NR_104114::g.3052] -indexing [Gene.3053::NR_104114::g.3053] -indexing [Gene.2370::NR_104121::g.2370] -indexing [Gene.1097::NR_104128::g.1097] -indexing [Gene.2409::NR_104387::g.2409] -indexing [Gene.2408::NR_104387::g.2408] -indexing [Gene.2417::NR_104388::g.2417] -indexing [Gene.2418::NR_104388::g.2418] -indexing [Gene.2400::NR_104389::g.2400] -indexing [Gene.2399::NR_104389::g.2399] -indexing [Gene.2391::NR_104390::g.2391] -indexing [Gene.2390::NR_104390::g.2390] -indexing [Gene.2410::NR_104391::g.2410] -indexing [Gene.2411::NR_104391::g.2411] -indexing [Gene.2412::NR_104391::g.2412] -indexing [Gene.2405::NR_104392::g.2405] -indexing [Gene.2404::NR_104392::g.2404] -indexing [Gene.2403::NR_104392::g.2403] -indexing [Gene.2397::NR_104393::g.2397] -indexing [Gene.2398::NR_104393::g.2398] -indexing [Gene.2416::NR_104394::g.2416] -indexing [Gene.2415::NR_104394::g.2415] -indexing [Gene.2414::NR_104394::g.2414] -indexing [Gene.2396::NR_104395::g.2396] -indexing [Gene.2394::NR_104395::g.2394] -indexing [Gene.2395::NR_104395::g.2395] -indexing [Gene.2406::NR_104396::g.2406] -indexing [Gene.2407::NR_104396::g.2407] -indexing [Gene.3966::NR_109776::g.3966] -indexing [Gene.3968::NR_109776::g.3968] -indexing [Gene.3969::NR_109776::g.3969] -indexing [Gene.3967::NR_109776::g.3967] -indexing [Gene.1686::NR_109985::g.1686] -indexing [Gene.4005::NR_110021::g.4005] -indexing [Gene.4004::NR_110021::g.4004] -indexing [Gene.3997::NR_110022::g.3997] -indexing [Gene.3998::NR_110022::g.3998] -indexing [Gene.4003::NR_110023::g.4003] -indexing [Gene.4002::NR_110023::g.4002] -indexing [Gene.4346::NR_110311::g.4346] -indexing [Gene.1336::NR_110381::g.1336] -indexing [Gene.4200::NR_110385::g.4200] -indexing [Gene.1995::NR_110386::g.1995] -indexing [Gene.3311::NR_110399::g.3311] -indexing [Gene.3854::NR_110456::g.3854] -indexing [Gene.1915::NR_110506::g.1915] -indexing [Gene.4210::NR_110830::g.4210] -indexing [Gene.4208::NR_110830::g.4208] -indexing [Gene.4209::NR_110830::g.4209] -indexing [Gene.3679::NR_111960::g.3679] -indexing [Gene.3680::NR_111960::g.3680] -indexing [Gene.3864::NR_120493::g.3864] -indexing [Gene.3865::NR_120493_dup1::g.3865] -indexing [Gene.1366::NR_120494::g.1366] -indexing [Gene.1365::NR_120494_dup1::g.1365] -indexing [Gene.994::NR_120499::g.994] -indexing [Gene.995::NR_120499_dup1::g.995] -indexing [Gene.3601::NR_126093::g.3601] -indexing [Gene.3602::NR_126093::g.3602] -indexing [Gene.3603::NR_126093::g.3603] -indexing [Gene.3124::NR_130733::g.3124] -indexing [Gene.3358::NR_130768::g.3358] -indexing [Gene.3658::NR_131982::g.3658] -indexing [Gene.3134::NR_132337::g.3134] -indexing [Gene.1249::NR_132647::g.1249] -indexing [Gene.1250::NR_132647::g.1250] * Running CMD: /build/transdecoder-5.0.1/util/train_start_PWM.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement * Running CMD: /build/transdecoder-5.0.1/util/PWM/build_atgPWM_+-.pl --transcripts stringtie_merged.transcripts.fasta --selected_orfs stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest --out_prefix stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement --pwm_left 20 --pwm_right 10 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --features_minus stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores > stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/deplete_feature_noise.pl --features_plus stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.+.features --pwm_minus stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.pwm --out_prefix stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced num features: 324 num_incorporate: 97 -feature swap of score: 0.529100395515446 instead of -4.05263500498361 -feature swap of score: 3.9143393878225 instead of -2.91075238221323 -feature swap of score: 1.39869220368004 instead of -2.53594716655218 -feature swap of score: -0.380788972176992 instead of -2.6038503083093 -feature swap of score: -0.377898812676178 instead of -2.09737517921886 -feature swap of score: 5.47481993170006 instead of -2.14305851084516 -feature swap of score: 0.538995311482997 instead of -1.70755783804005 -feature swap of score: 2.86701143575849 instead of -1.52928866333055 -feature swap of score: 1.42870941296158 instead of -1.49394873763037 -feature swap of score: 1.20216965603885 instead of -1.3295650844692 -feature swap of score: -0.42991871549387 instead of -1.19625182630726 -feature swap of score: 2.29024235509541 instead of -1.20889884763754 -feature swap of score: 4.7705127292727 instead of -1.14568578423388 -feature swap of score: 2.43465496256688 instead of -2.16485722980534 -feature swap of score: -1.19195942615406 instead of -1.35176962905185 -feature swap of score: 6.51754712131989 instead of -1.25221933525334 -feature swap of score: 1.52882544944146 instead of -1.21112773294167 -feature swap of score: 0.0830239881919773 instead of -0.829931517304013 -feature swap of score: 5.15573082150999 instead of -0.712468217805508 -feature swap of score: 1.62457993147678 instead of -0.563534131069329 -feature swap of score: 2.58558850481236 instead of -0.645616140329767 -feature swap of score: 0.834090672740889 instead of -0.844598308434728 -feature swap of score: 6.07753390345999 instead of -0.480266093156959 -feature swap of score: 3.49300434049089 instead of -0.446657232159395 -feature swap of score: 1.14026417546277 instead of -0.296412718636387 -feature swap of score: 1.13565842259237 instead of -0.383522265758323 -feature swap of score: 0.522631190235407 instead of -0.317571156732523 -feature swap of score: 1.34040164732515 instead of -0.206276114048225 -feature swap of score: 3.22673748173348 instead of 0.0936496731939758 -feature swap of score: 1.0126359153794 instead of 0.218600472036215 -feature swap of score: 0.813869241696647 instead of 0.268464485031227 -feature swap of score: 0.357593470772349 instead of 0.337358738300514 -feature swap of score: 6.4733940101118 instead of 0.171763333389891 -feature swap of score: 0.501467463234322 instead of 0.00475938915540808 -feature swap of score: 0.812487905855119 instead of 0.0477511649573856 -feature swap of score: 0.650653859935431 instead of -0.0245817203012335 -feature swap of score: 3.88372699521488 instead of 0.0952320487308486 -feature swap of score: 5.42980313629669 instead of 0.156401703130819 -feature swap of score: 1.83271184509333 instead of 0.316403632646691 -feature swap of score: 2.47203682885726 instead of 0.258062611202618 -feature swap of score: 4.54123720852914 instead of 0.355481810625811 -feature swap of score: 1.21093371875202 instead of 0.508916224602088 -feature swap of score: 1.20647088969228 instead of 0.243058998151095 -feature swap of score: 3.92230788141277 instead of 0.737949929200865 -feature swap of score: 7.40790565276692 instead of 0.664895088245865 -feature swap of score: 1.74709944522839 instead of 0.221835460854404 -feature swap of score: 5.86542532743029 instead of 0.667075362923049 -feature swap of score: 3.53025768073754 instead of 0.827937810581167 -feature swap of score: 2.52577862941615 instead of 0.534079436107526 -feature swap of score: 6.470476918358 instead of 0.707104993424136 -feature swap of score: 4.35830660678762 instead of -0.137716499116044 -feature swap of score: 7.4692346845916 instead of 0.258351685982711 -feature swap of score: 0.343381469790556 instead of 0.226514451340386 -feature swap of score: 2.22401572390117 instead of 0.373715006274766 -feature swap of score: 3.52637589853404 instead of 0.537242834700416 -feature swap of score: 3.90664498438979 instead of 0.865165810029229 -feature swap of score: 0.916359352738721 instead of 0.536065143724725 -feature swap of score: 6.45116970153842 instead of 0.881669087272405 -feature swap of score: 4.21545975957764 instead of 0.843894614338434 -feature swap of score: 1.65926423492173 instead of 0.839850912776057 -feature swap of score: 6.41373122720588 instead of 0.751918065859049 -feature swap of score: 8.5369803561795 instead of 0.828373171534407 -feature swap of score: 13.5277543267579 instead of 0.870719285303391 -feature swap of score: 0.987567329601704 instead of 0.669245207707554 -feature swap of score: 3.9033868664738 instead of 1.2516717439748 -feature swap of score: 3.70773579563765 instead of 1.23153472333284 -feature swap of score: 4.49505262227725 instead of 1.05448397973177 -feature swap of score: 2.40074488903615 instead of 1.21714628063869 -feature swap of score: 4.18670898244112 instead of 1.18483269114586 -feature swap of score: 6.42533728738614 instead of 1.26400263921462 -feature swap of score: 8.7128465115572 instead of 1.19492739897794 -feature swap of score: 5.92149009365192 instead of 1.08057337682716 -feature swap of score: 3.48935121932328 instead of 0.739809495791444 -feature swap of score: 7.25926911861027 instead of 1.18494939979508 -feature swap of score: 9.78468720389293 instead of 1.58301793019836 -feature swap of score: 2.00221218589297 instead of 1.71312518180255 -feature swap of score: 3.51639206981473 instead of 1.54096625115719 -feature swap of score: 4.46482123485486 instead of 1.53920089641459 -feature swap of score: 5.51228366843219 instead of 1.46256311977846 -feature swap of score: 4.45668299152127 instead of 1.74938013914745 -feature swap of score: 9.87945860958298 instead of 1.65670535292723 -feature swap of score: 3.41893531875537 instead of 1.54632711395831 -feature swap of score: 2.90318459906146 instead of 1.76879678214414 -feature swap of score: 6.49946544012161 instead of 1.9639763767397 -feature swap of score: 5.73191128925215 instead of 2.29491958331059 -feature swap of score: 7.16291828484766 instead of 2.47325777600616 -feature swap of score: 4.25987516611605 instead of 2.36097987020496 -feature swap of score: 6.16476136043549 instead of 2.40084439178123 -feature swap of score: 5.16980940468093 instead of 2.51812578648253 -feature swap of score: 3.59698143853452 instead of 2.60931520361239 -feature swap of score: 6.25180203823686 instead of 2.61476676025972 -feature swap of score: 8.18599279864096 instead of 2.60795576265215 -feature swap of score: 2.76036024994831 instead of 2.6280402089626 -feature swap of score: 2.78975398090645 instead of 2.52452585220658 -feature swap of score: 5.70170805496546 instead of 2.70128062823008 -feature swap of score: 6.87652323963527 instead of 2.79468492671997 -feature swap of score: 4.71280683574267 instead of 2.80710350724438 -feature swap of score: 6.42029834953629 instead of 2.89783213550355 -feature swap of score: 3.9594827259518 instead of 2.9183140313711 -feature swap of score: 6.01133451489541 instead of 2.7100692411109 -feature swap of score: 4.5815814811534 instead of 2.88758235874201 -num feature swaps: 101 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scoring.+-.pl --features_plus stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.features --features_minus stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.-.features --atg_position 20 > stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores -round: 1 -round: 2 -round: 3 -round: 4 -round: 5 * Running CMD: /build/transdecoder-5.0.1/util/PWM/feature_scores_to_ROC.pl stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores > stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc -parsing scores * Running CMD: /build/transdecoder-5.0.1/util/PWM/plot_ROC.Rscript stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.feature.scores.roc Can't exec "Rscript": No such file or directory at /build/transdecoder-5.0.1/util/PWM/compute_AUC.pl line 82. * Running CMD: /build/transdecoder-5.0.1/util/PWM/make_seqLogo.Rscript stringtie_merged.transcripts.fasta.transdecoder_dir/start_refinement.enhanced.+.pwm || : /usr/bin/env: 'Rscript': No such file or directory * Running CMD: /build/transdecoder-5.0.1/util/start_codon_refinement.pl --transcripts stringtie_merged.transcripts.fasta --gff3_file stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 > stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 -indexing [Gene.2979::MSTRG.1.1::g.2979] -indexing [Gene.3929::MSTRG.10.1::g.3929] -indexing [Gene.292::MSTRG.1000.4::g.292] -indexing [Gene.910::MSTRG.1001.1::g.910] -indexing [Gene.913::MSTRG.1001.2::g.913] -indexing [Gene.4046::MSTRG.1005.1::g.4046] -indexing [Gene.4042::MSTRG.1005.2::g.4042] -indexing [Gene.4038::MSTRG.1005.3::g.4038] -indexing [Gene.2536::MSTRG.1009.2::g.2536] -indexing [Gene.1979::MSTRG.101.1::g.1979] -indexing [Gene.392::MSTRG.1012.1::g.392] -indexing [Gene.398::MSTRG.1012.3::g.398] -indexing [Gene.394::MSTRG.1012.4::g.394] -indexing [Gene.2490::MSTRG.1017.1::g.2490] -indexing [Gene.3075::MSTRG.1021.3::g.3075] -indexing [Gene.1660::MSTRG.1023.2::g.1660] -indexing [Gene.1658::MSTRG.1023.3::g.1658] -indexing [Gene.1662::MSTRG.1023.4::g.1662] -indexing [Gene.4267::MSTRG.1024.2::g.4267] -indexing [Gene.573::MSTRG.1025.1::g.573] -indexing [Gene.547::MSTRG.1025.12::g.547] -indexing [Gene.558::MSTRG.1025.2::g.558] -indexing [Gene.551::MSTRG.1025.3::g.551] -indexing [Gene.552::MSTRG.1025.4::g.552] -indexing [Gene.555::MSTRG.1025.5::g.555] -indexing [Gene.562::MSTRG.1025.6::g.562] -indexing [Gene.3132::MSTRG.1028.1::g.3132] -indexing [Gene.3374::MSTRG.1029.1::g.3374] -indexing [Gene.3389::MSTRG.1029.11::g.3389] -indexing [Gene.3368::MSTRG.1029.12::g.3368] -indexing [Gene.3361::MSTRG.1029.2::g.3361] -indexing [Gene.3384::MSTRG.1029.3::g.3384] -indexing [Gene.3377::MSTRG.1029.4::g.3377] -indexing [Gene.1340::MSTRG.1034.2::g.1340] -indexing [Gene.1949::MSTRG.1036.1::g.1949] -indexing [Gene.3592::MSTRG.1037.1::g.3592] -indexing [Gene.3591::MSTRG.1037.8::g.3591] -indexing [Gene.3217::MSTRG.1040.3::g.3217] -indexing [Gene.3149::MSTRG.1041.4::g.3149] -indexing [Gene.3167::MSTRG.1041.5::g.3167] -indexing [Gene.3154::MSTRG.1041.6::g.3154] -indexing [Gene.3163::MSTRG.1041.7::g.3163] -indexing [Gene.3147::MSTRG.1041.8::g.3147] -indexing [Gene.3168::MSTRG.1041.9::g.3168] -indexing [Gene.1064::MSTRG.1042.1::g.1064] -indexing [Gene.1060::MSTRG.1042.2::g.1060] -indexing [Gene.1062::MSTRG.1042.3::g.1062] -indexing [Gene.1710::MSTRG.1045.1::g.1710] -indexing [Gene.2715::MSTRG.1049.1::g.2715] -indexing [Gene.368::MSTRG.1055.1::g.368] -indexing [Gene.365::MSTRG.1055.2::g.365] -indexing [Gene.3572::MSTRG.1069.1::g.3572] -indexing [Gene.2943::MSTRG.1070.2::g.2943] -indexing [Gene.3406::MSTRG.1073.3::g.3406] -indexing [Gene.2770::MSTRG.1074.1::g.2770] -indexing [Gene.2767::MSTRG.1074.10::g.2767] -indexing [Gene.2761::MSTRG.1074.11::g.2761] -indexing [Gene.2788::MSTRG.1074.12::g.2788] -indexing [Gene.2775::MSTRG.1074.13::g.2775] -indexing [Gene.2759::MSTRG.1074.14::g.2759] -indexing [Gene.2776::MSTRG.1074.2::g.2776] -indexing [Gene.2782::MSTRG.1074.3::g.2782] -indexing [Gene.2774::MSTRG.1074.4::g.2774] -indexing [Gene.2779::MSTRG.1074.5::g.2779] -indexing [Gene.2765::MSTRG.1074.6::g.2765] -indexing [Gene.2791::MSTRG.1074.7::g.2791] -indexing [Gene.2785::MSTRG.1074.8::g.2785] -indexing [Gene.2763::MSTRG.1074.9::g.2763] -indexing [Gene.4074::MSTRG.108.1::g.4074] -indexing [Gene.4063::MSTRG.108.2::g.4063] -indexing [Gene.4067::MSTRG.108.3::g.4067] -indexing [Gene.2448::MSTRG.109.1::g.2448] -indexing [Gene.2452::MSTRG.109.10::g.2452] -indexing [Gene.2455::MSTRG.109.7::g.2455] -indexing [Gene.2453::MSTRG.109.9::g.2453] -indexing [Gene.433::MSTRG.110.1::g.433] -indexing [Gene.431::MSTRG.110.10::g.431] -indexing [Gene.425::MSTRG.110.11::g.425] -indexing [Gene.427::MSTRG.110.2::g.427] -indexing [Gene.426::MSTRG.110.4::g.426] -indexing [Gene.422::MSTRG.110.5::g.422] -indexing [Gene.432::MSTRG.110.6::g.432] -indexing [Gene.434::MSTRG.110.7::g.434] -indexing [Gene.424::MSTRG.110.8::g.424] -indexing [Gene.429::MSTRG.110.9::g.429] -indexing [Gene.2238::MSTRG.113.1::g.2238] -indexing [Gene.2237::MSTRG.113.4::g.2237] -indexing [Gene.926::MSTRG.116.5::g.926] -indexing [Gene.3952::MSTRG.124.1::g.3952] -indexing [Gene.3953::MSTRG.124.2::g.3953] -indexing [Gene.3954::MSTRG.124.3::g.3954] -indexing [Gene.3951::MSTRG.124.7::g.3951] -indexing [Gene.3956::MSTRG.124.8::g.3956] -indexing [Gene.3950::MSTRG.124.9::g.3950] -indexing [Gene.2842::MSTRG.125.1::g.2842] -indexing [Gene.2548::MSTRG.128.1::g.2548] -indexing [Gene.2546::MSTRG.128.2::g.2546] -indexing [Gene.2542::MSTRG.128.4::g.2542] -indexing [Gene.2551::MSTRG.128.5::g.2551] -indexing [Gene.1205::MSTRG.131.4::g.1205] -indexing [Gene.1206::MSTRG.131.5::g.1206] -indexing [Gene.1203::MSTRG.131.6::g.1203] -indexing [Gene.3109::MSTRG.137.3::g.3109] -indexing [Gene.3237::MSTRG.14.1::g.3237] -indexing [Gene.263::MSTRG.142.5::g.263] -indexing [Gene.2750::MSTRG.143.2::g.2750] -indexing [Gene.183::MSTRG.144.1::g.183] -indexing [Gene.1723::MSTRG.147.2::g.1723] -indexing [Gene.1727::MSTRG.147.3::g.1727] -indexing [Gene.1724::MSTRG.147.4::g.1724] -indexing [Gene.502::MSTRG.151.1::g.502] -indexing [Gene.503::MSTRG.151.5::g.503] -indexing [Gene.496::MSTRG.151.6::g.496] -indexing [Gene.497::MSTRG.151.7::g.497] -indexing [Gene.2721::MSTRG.159.5::g.2721] -indexing [Gene.2724::MSTRG.159.6::g.2724] -indexing [Gene.3117::MSTRG.16.1::g.3117] -indexing [Gene.2730::MSTRG.161.2::g.2730] -indexing [Gene.2729::MSTRG.161.3::g.2729] -indexing [Gene.2911::MSTRG.166.5::g.2911] -indexing [Gene.4247::MSTRG.17.1::g.4247] -indexing [Gene.4253::MSTRG.17.2::g.4253] -indexing [Gene.4263::MSTRG.17.6::g.4263] -indexing [Gene.4249::MSTRG.17.7::g.4249] -indexing [Gene.4246::MSTRG.17.8::g.4246] -indexing [Gene.3301::MSTRG.172.1::g.3301] -indexing [Gene.4016::MSTRG.178.3::g.4016] -indexing [Gene.4015::MSTRG.178.4::g.4015] -indexing [Gene.4012::MSTRG.178.5::g.4012] -indexing [Gene.4014::MSTRG.178.6::g.4014] -indexing [Gene.2540::MSTRG.179.1::g.2540] -indexing [Gene.4316::MSTRG.181.1::g.4316] -indexing [Gene.1354::MSTRG.183.2::g.1354] -indexing [Gene.525::MSTRG.187.1::g.525] -indexing [Gene.1132::MSTRG.189.1::g.1132] -indexing [Gene.1130::MSTRG.189.10::g.1130] -indexing [Gene.1129::MSTRG.189.11::g.1129] -indexing [Gene.1141::MSTRG.189.7::g.1141] -indexing [Gene.1139::MSTRG.189.8::g.1139] -indexing [Gene.1134::MSTRG.189.9::g.1134] -indexing [Gene.24::MSTRG.191.1::g.24] -indexing [Gene.3640::MSTRG.195.1::g.3640] -indexing [Gene.1150::MSTRG.2.1::g.1150] -indexing [Gene.2325::MSTRG.205.1::g.2325] -indexing [Gene.2327::MSTRG.205.2::g.2327] -indexing [Gene.2326::MSTRG.205.3::g.2326] -indexing [Gene.491::MSTRG.207.1::g.491] -indexing [Gene.4180::MSTRG.208.2::g.4180] -indexing [Gene.4175::MSTRG.208.3::g.4175] -indexing [Gene.4173::MSTRG.208.4::g.4173] -indexing [Gene.2965::MSTRG.209.5::g.2965] -indexing [Gene.2970::MSTRG.209.6::g.2970] -indexing [Gene.2969::MSTRG.209.7::g.2969] -indexing [Gene.2967::MSTRG.209.8::g.2967] -indexing [Gene.2972::MSTRG.209.9::g.2972] -indexing [Gene.358::MSTRG.215.2::g.358] -indexing [Gene.4137::MSTRG.216.1::g.4137] -indexing [Gene.4141::MSTRG.216.5::g.4141] -indexing [Gene.2200::MSTRG.221.1::g.2200] -indexing [Gene.2219::MSTRG.222.1::g.2219] -indexing [Gene.2230::MSTRG.222.2::g.2230] -indexing [Gene.967::MSTRG.227.1::g.967] -indexing [Gene.3450::MSTRG.230.5::g.3450] -indexing [Gene.3452::MSTRG.230.6::g.3452] -indexing [Gene.3445::MSTRG.230.7::g.3445] -indexing [Gene.3797::MSTRG.232.1::g.3797] -indexing [Gene.3801::MSTRG.232.2::g.3801] -indexing [Gene.4244::MSTRG.234.1::g.4244] -indexing [Gene.879::MSTRG.236.1::g.879] -indexing [Gene.877::MSTRG.236.3::g.877] -indexing [Gene.4134::MSTRG.239.1::g.4134] -indexing [Gene.641::MSTRG.248.1::g.641] -indexing [Gene.1576::MSTRG.250.1::g.1576] -indexing [Gene.1579::MSTRG.250.5::g.1579] -indexing [Gene.3325::MSTRG.251.1::g.3325] -indexing [Gene.986::MSTRG.254.1::g.986] -indexing [Gene.3681::MSTRG.258.8::g.3681] -indexing [Gene.3691::MSTRG.258.9::g.3691] -indexing [Gene.261::MSTRG.26.2::g.261] -indexing [Gene.1832::MSTRG.265.3::g.1832] -indexing [Gene.1830::MSTRG.265.4::g.1830] -indexing [Gene.4130::MSTRG.266.4::g.4130] -indexing [Gene.4121::MSTRG.266.5::g.4121] -indexing [Gene.3515::MSTRG.268.1::g.3515] -indexing [Gene.3513::MSTRG.268.2::g.3513] -indexing [Gene.3517::MSTRG.268.3::g.3517] -indexing [Gene.3501::MSTRG.268.4::g.3501] -indexing [Gene.3506::MSTRG.268.5::g.3506] -indexing [Gene.3520::MSTRG.268.6::g.3520] -indexing [Gene.3507::MSTRG.268.7::g.3507] -indexing [Gene.810::MSTRG.275.2::g.810] -indexing [Gene.802::MSTRG.275.3::g.802] -indexing [Gene.813::MSTRG.275.4::g.813] -indexing [Gene.821::MSTRG.275.6::g.821] -indexing [Gene.818::MSTRG.275.7::g.818] -indexing [Gene.1810::MSTRG.276.2::g.1810] -indexing [Gene.4231::MSTRG.277.1::g.4231] -indexing [Gene.248::MSTRG.279.1::g.248] -indexing [Gene.252::MSTRG.279.10::g.252] -indexing [Gene.238::MSTRG.279.11::g.238] -indexing [Gene.242::MSTRG.279.2::g.242] -indexing [Gene.244::MSTRG.279.3::g.244] -indexing [Gene.254::MSTRG.279.4::g.254] -indexing [Gene.250::MSTRG.279.5::g.250] -indexing [Gene.240::MSTRG.279.6::g.240] -indexing [Gene.236::MSTRG.279.7::g.236] -indexing [Gene.234::MSTRG.279.8::g.234] -indexing [Gene.2494::MSTRG.281.1::g.2494] -indexing [Gene.2167::MSTRG.284.1::g.2167] -indexing [Gene.2175::MSTRG.284.5::g.2175] -indexing [Gene.2197::MSTRG.292.4::g.2197] -indexing [Gene.2192::MSTRG.292.5::g.2192] -indexing [Gene.3404::MSTRG.293.1::g.3404] -indexing [Gene.2701::MSTRG.294.4::g.2701] -indexing [Gene.2599::MSTRG.301.2::g.2599] -indexing [Gene.2595::MSTRG.301.3::g.2595] -indexing [Gene.538::MSTRG.302.4::g.538] -indexing [Gene.539::MSTRG.302.5::g.539] -indexing [Gene.530::MSTRG.302.6::g.530] -indexing [Gene.537::MSTRG.302.7::g.537] -indexing [Gene.3580::MSTRG.303.1::g.3580] -indexing [Gene.1029::MSTRG.305.1::g.1029] -indexing [Gene.1040::MSTRG.305.6::g.1040] -indexing [Gene.1047::MSTRG.305.7::g.1047] -indexing [Gene.1037::MSTRG.305.8::g.1037] -indexing [Gene.1761::MSTRG.306.1::g.1761] -indexing [Gene.1759::MSTRG.306.3::g.1759] -indexing [Gene.3137::MSTRG.308.1::g.3137] -indexing [Gene.3136::MSTRG.308.3::g.3136] -indexing [Gene.3139::MSTRG.308.4::g.3139] -indexing [Gene.1319::MSTRG.311.2::g.1319] -indexing [Gene.1323::MSTRG.311.3::g.1323] -indexing [Gene.3457::MSTRG.314.1::g.3457] -indexing [Gene.4277::MSTRG.32.1::g.4277] -indexing [Gene.4289::MSTRG.32.4::g.4289] -indexing [Gene.3620::MSTRG.320.1::g.3620] -indexing [Gene.3619::MSTRG.320.2::g.3619] -indexing [Gene.3616::MSTRG.320.3::g.3616] -indexing [Gene.3615::MSTRG.320.4::g.3615] -indexing [Gene.3613::MSTRG.320.5::g.3613] -indexing [Gene.3618::MSTRG.320.8::g.3618] -indexing [Gene.958::MSTRG.324.2::g.958] -indexing [Gene.2076::MSTRG.325.1::g.2076] -indexing [Gene.2083::MSTRG.325.4::g.2083] -indexing [Gene.3534::MSTRG.326.1::g.3534] -indexing [Gene.3532::MSTRG.326.2::g.3532] -indexing [Gene.3535::MSTRG.326.3::g.3535] -indexing [Gene.1518::MSTRG.327.3::g.1518] -indexing [Gene.657::MSTRG.329.1::g.657] -indexing [Gene.892::MSTRG.331.1::g.892] -indexing [Gene.894::MSTRG.331.2::g.894] -indexing [Gene.890::MSTRG.331.3::g.890] -indexing [Gene.896::MSTRG.331.4::g.896] -indexing [Gene.2606::MSTRG.336.10::g.2606] -indexing [Gene.2605::MSTRG.336.9::g.2605] -indexing [Gene.527::MSTRG.337.1::g.527] -indexing [Gene.3038::MSTRG.338.5::g.3038] -indexing [Gene.3034::MSTRG.338.6::g.3034] -indexing 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[Gene.4177::NM_152787::g.4177] -indexing [Gene.2011::NM_152856::g.2011] -indexing [Gene.1591::NM_152869::g.1591] -indexing [Gene.1304::NM_153183::g.1304] -indexing [Gene.1327::NM_153252::g.1327] -indexing [Gene.870::NM_153270::g.870] -indexing [Gene.2501::NM_153280::g.2501] -indexing [Gene.2057::NM_153333::g.2057] -indexing [Gene.1156::NM_153346::g.1156] -indexing [Gene.232::NM_153380::g.232] -indexing [Gene.2328::NM_153448::g.2328] -indexing [Gene.966::NM_153477::g.966] -indexing [Gene.494::NM_153488::g.494] -indexing [Gene.493::NM_153488_dup1::g.493] -indexing [Gene.2359::NM_153834::g.2359] -indexing [Gene.2876::NM_170750::g.2876] -indexing [Gene.3724::NM_171998::g.3724] -indexing [Gene.3522::NM_172245::g.3522] -indexing [Gene.1277::NM_172246::g.1277] -indexing [Gene.2961::NM_172247::g.2961] -indexing [Gene.2260::NM_172249::g.2260] -indexing [Gene.2441::NM_172377::g.2441] -indexing [Gene.647::NM_173078::g.647] -indexing [Gene.630::NM_173358::g.630] -indexing 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[Gene.2736::NM_174951::g.2736] -indexing [Gene.3293::NM_175569::g.3293] -indexing [Gene.3822::NM_175698::g.3822] -indexing [Gene.3821::NM_175698_dup1::g.3821] -indexing [Gene.1213::NM_175723::g.1213] -indexing [Gene.3018::NM_175729::g.3018] -indexing [Gene.3019::NM_175729_dup1::g.3019] -indexing [Gene.3880::NM_175742::g.3880] -indexing [Gene.3879::NM_175742_dup1::g.3879] -indexing [Gene.968::NM_175743::g.968] -indexing [Gene.969::NM_175743_dup1::g.969] -indexing [Gene.1201::NM_175859::g.1201] -indexing [Gene.668::NM_175868::g.668] -indexing [Gene.3408::NM_176786::g.3408] -indexing [Gene.3487::NM_176819::g.3487] -indexing [Gene.2047::NM_177404::g.2047] -indexing [Gene.3009::NM_177415::g.3009] -indexing [Gene.3924::NM_177433::g.3924] -indexing [Gene.531::NM_177439::g.531] -indexing [Gene.3918::NM_177456::g.3918] -indexing [Gene.3813::NM_177535_dup1::g.3813] -indexing [Gene.2186::NM_177537::g.2186] -indexing [Gene.3817::NM_177537_dup1::g.3817] -indexing [Gene.3480::NM_177556::g.3480] -indexing [Gene.3471::NM_177557::g.3471] -indexing [Gene.1617::NM_177947::g.1617] -indexing [Gene.1620::NM_177948::g.1620] -indexing [Gene.2641::NM_177949::g.2641] -indexing [Gene.2666::NM_178124::g.2666] -indexing [Gene.3238::NM_178129::g.3238] -indexing [Gene.1614::NM_178151::g.1614] -indexing [Gene.1154::NM_178152::g.1154] -indexing [Gene.2507::NM_178153::g.2507] -indexing [Gene.464::NM_178175::g.464] -indexing [Gene.2056::NM_178270::g.2056] -indexing [Gene.277::NM_178470::g.277] -indexing [Gene.2757::NM_178471::g.2757] -indexing [Gene.188::NM_178813::g.188] -indexing [Gene.3308::NM_181303::g.3308] -indexing [Gene.3366::NM_181311::g.3366] -indexing [Gene.3390::NM_181312::g.3390] -indexing [Gene.3383::NM_181313::g.3383] -indexing [Gene.290::NM_181332::g.290] -indexing [Gene.2848::NM_181532::g.2848] -indexing [Gene.2649::NM_181672::g.2649] -indexing [Gene.2655::NM_181673::g.2655] -indexing [Gene.469::NM_181762::g.469] -indexing [Gene.2935::NM_182314::g.2935] -indexing 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-indexing [Gene.1551::NM_201599::g.1551] -indexing [Gene.2379::NM_203281::g.2379] -indexing [Gene.2974::NM_203391::g.2974] -indexing [Gene.702::NM_203407::g.702] -indexing [Gene.2794::NM_203408::g.2794] -indexing [Gene.1045::NM_203473::g.1045] -indexing [Gene.1033::NM_203474::g.1033] -indexing [Gene.1043::NM_203475::g.1043] -indexing [Gene.1084::NM_205833::g.1084] -indexing [Gene.3469::NM_205849::g.3469] -indexing [Gene.707::NM_205856::g.707] -indexing [Gene.706::NM_205856_dup1::g.706] -indexing [Gene.282::NM_206915::g.282] -indexing [Gene.284::NM_206917::g.284] -indexing [Gene.3312::NM_206923::g.3312] -indexing [Gene.3945::NM_207318::g.3945] -indexing [Gene.3099::NM_207320::g.3099] -indexing [Gene.4029::NM_207339::g.4029] -indexing [Gene.1071::NM_207422::g.1071] -indexing [Gene.970::NM_212559::g.970] -indexing [Gene.195::NR_001564::g.195] -indexing [Gene.3028::NR_002191::g.3028] -indexing [Gene.3342::NR_002216::g.3342] -indexing [Gene.2372::NR_002308::g.2372] -indexing [Gene.2927::NR_002309::g.2927] -indexing [Gene.4096::NR_002718::g.4096] -indexing [Gene.2053::NR_002784::g.2053] -indexing [Gene.4326::NR_003255::g.4326] -indexing [Gene.2535::NR_003539::g.2535] -indexing [Gene.29::NR_015353::g.29] -indexing [Gene.3379::NR_024048::g.3379] -indexing [Gene.3090::NR_024062::g.3090] -indexing [Gene.852::NR_024359::g.852] -indexing [Gene.185::NR_024608::g.185] -indexing [Gene.1027::NR_026545::g.1027] -indexing [Gene.3948::NR_026551::g.3948] -indexing [Gene.3577::NR_026594::g.3577] -indexing [Gene.2626::NR_026594_dup1::g.2626] -indexing [Gene.3123::NR_026710::g.3123] -indexing [Gene.3111::NR_026711::g.3111] -indexing [Gene.3133::NR_026742::g.3133] -indexing [Gene.3581::NR_026935::g.3581] -indexing [Gene.941::NR_026975::g.941] -indexing [Gene.2059::NR_027121::g.2059] -indexing [Gene.274::NR_027131::g.274] -indexing [Gene.506::NR_027141::g.506] -indexing [Gene.2897::NR_027250::g.2897] -indexing [Gene.618::NR_027291::g.618] -indexing [Gene.4273::NR_027383::g.4273] -indexing [Gene.2509::NR_027401::g.2509] -indexing [Gene.446::NR_027401_dup1::g.446] -indexing [Gene.1844::NR_027419::g.1844] -indexing [Gene.2743::NR_027455::g.2743] -indexing [Gene.2828::NR_027621::g.2828] -indexing [Gene.2718::NR_027760::g.2718] -indexing [Gene.1874::NR_027761::g.1874] -indexing [Gene.1808::NR_028057::g.1808] -indexing [Gene.2720::NR_028089::g.2720] -indexing [Gene.2560::NR_028119::g.2560] -indexing [Gene.3125::NR_028366::g.3125] -indexing [Gene.3046::NR_028407::g.3046] -indexing [Gene.1356::NR_028443::g.1356] -indexing [Gene.3714::NR_028476::g.3714] -indexing [Gene.3718::NR_028477::g.3718] -indexing [Gene.3916::NR_028597::g.3916] -indexing [Gene.1190::NR_029423::g.1190] -indexing [Gene.2079::NR_029427::g.2079] -indexing [Gene.654::NR_030727::g.654] -indexing [Gene.920::NR_030737::g.920] -indexing [Gene.3104::NR_030774::g.3104] -indexing [Gene.1847::NR_033181::g.1847] -indexing [Gene.2615::NR_033212::g.2615] -indexing [Gene.1347::NR_033262::g.1347] -indexing [Gene.1940::NR_033348::g.1940] -indexing [Gene.3540::NR_033349::g.3540] -indexing [Gene.1736::NR_033699::g.1736] -indexing [Gene.1741::NR_033700::g.1741] -indexing [Gene.1706::NR_033714::g.1706] -indexing [Gene.1705::NR_033715::g.1705] -indexing [Gene.2068::NR_033717::g.2068] -indexing [Gene.1766::NR_033742::g.1766] -indexing [Gene.935::NR_033772::g.935] -indexing [Gene.938::NR_033772_dup1::g.938] -indexing [Gene.3145::NR_033773::g.3145] -indexing [Gene.3142::NR_033773_dup1::g.3142] -indexing [Gene.927::NR_033835::g.927] -indexing [Gene.929::NR_033836::g.929] -indexing [Gene.1416::NR_034031::g.1416] -indexing [Gene.632::NR_034116::g.632] -indexing [Gene.633::NR_034116_dup1::g.633] -indexing [Gene.1503::NR_037183::g.1503] -indexing [Gene.3934::NR_037859::g.3934] -indexing [Gene.4319::NR_037916::g.4319] -indexing [Gene.2846::NR_037927::g.2846] -indexing [Gene.4185::NR_045044::g.4185] -indexing [Gene.797::NR_045260::g.797] -indexing [Gene.965::NR_045559::g.965] -indexing [Gene.964::NR_045560::g.964] -indexing [Gene.3048::NR_045861::g.3048] -indexing [Gene.3049::NR_045864::g.3049] -indexing [Gene.2931::NR_046750::g.2931] -indexing [Gene.1838::NR_051952::g.1838] -indexing [Gene.3473::NR_073148::g.3473] -indexing [Gene.3472::NR_073149::g.3472] -indexing [Gene.3778::NR_073156::g.3778] -indexing [Gene.445::NR_073393::g.445] -indexing [Gene.2367::NR_073450::g.2367] -indexing [Gene.2505::NR_102268::g.2505] -indexing [Gene.2579::NR_102272::g.2579] -indexing [Gene.944::NR_103708::g.944] -indexing [Gene.942::NR_103709::g.942] -indexing [Gene.3074::NR_103715::g.3074] -indexing [Gene.2017::NR_104107::g.2017] -indexing [Gene.2622::NR_104109::g.2622] -indexing [Gene.3052::NR_104114::g.3052] -indexing [Gene.2370::NR_104121::g.2370] -indexing [Gene.1097::NR_104128::g.1097] -indexing [Gene.2408::NR_104387::g.2408] -indexing [Gene.2417::NR_104388::g.2417] -indexing [Gene.2399::NR_104389::g.2399] -indexing [Gene.2390::NR_104390::g.2390] -indexing [Gene.2410::NR_104391::g.2410] -indexing [Gene.2403::NR_104392::g.2403] -indexing [Gene.2397::NR_104393::g.2397] -indexing [Gene.2414::NR_104394::g.2414] -indexing [Gene.2394::NR_104395::g.2394] -indexing [Gene.3966::NR_109776::g.3966] -indexing [Gene.4004::NR_110021::g.4004] -indexing [Gene.3997::NR_110022::g.3997] -indexing [Gene.4003::NR_110023::g.4003] -indexing [Gene.4346::NR_110311::g.4346] -indexing [Gene.4200::NR_110385::g.4200] -indexing [Gene.1915::NR_110506::g.1915] -indexing [Gene.4210::NR_110830::g.4210] -indexing [Gene.3679::NR_111960::g.3679] -indexing [Gene.3864::NR_120493::g.3864] -indexing [Gene.3865::NR_120493_dup1::g.3865] -indexing [Gene.1366::NR_120494::g.1366] -indexing [Gene.1365::NR_120494_dup1::g.1365] -indexing [Gene.994::NR_120499::g.994] -indexing [Gene.995::NR_120499_dup1::g.995] -indexing [Gene.3601::NR_126093::g.3601] -indexing [Gene.3124::NR_130733::g.3124] -indexing [Gene.3358::NR_130768::g.3358] -indexing [Gene.1249::NR_132647::g.1249] -number of revised start positions: 236 CMD: cp stringtie_merged.transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3.revised_starts.gff3 stringtie_merged.transcripts.fasta.transdecoder.gff3 CMD: /build/transdecoder-5.0.1/util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.gff3 > stringtie_merged.transcripts.fasta.transdecoder.bed -indexing [Gene.2979::MSTRG.1.1::g.2979] -indexing [Gene.3929::MSTRG.10.1::g.3929] -indexing [Gene.292::MSTRG.1000.4::g.292] -indexing [Gene.910::MSTRG.1001.1::g.910] -indexing [Gene.913::MSTRG.1001.2::g.913] -indexing [Gene.4046::MSTRG.1005.1::g.4046] -indexing [Gene.4042::MSTRG.1005.2::g.4042] -indexing [Gene.4038::MSTRG.1005.3::g.4038] -indexing [Gene.2536::MSTRG.1009.2::g.2536] -indexing [Gene.1979::MSTRG.101.1::g.1979] -indexing [Gene.392::MSTRG.1012.1::g.392] -indexing [Gene.398::MSTRG.1012.3::g.398] -indexing [Gene.394::MSTRG.1012.4::g.394] -indexing 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[Gene.1706::NR_033714::g.1706] -indexing [Gene.1705::NR_033715::g.1705] -indexing [Gene.2068::NR_033717::g.2068] -indexing [Gene.1766::NR_033742::g.1766] -indexing [Gene.935::NR_033772::g.935] -indexing [Gene.938::NR_033772_dup1::g.938] -indexing [Gene.3145::NR_033773::g.3145] -indexing [Gene.3142::NR_033773_dup1::g.3142] -indexing [Gene.927::NR_033835::g.927] -indexing [Gene.929::NR_033836::g.929] -indexing [Gene.1416::NR_034031::g.1416] -indexing [Gene.632::NR_034116::g.632] -indexing [Gene.633::NR_034116_dup1::g.633] -indexing [Gene.1503::NR_037183::g.1503] -indexing [Gene.3934::NR_037859::g.3934] -indexing [Gene.4319::NR_037916::g.4319] -indexing [Gene.2846::NR_037927::g.2846] -indexing [Gene.4185::NR_045044::g.4185] -indexing [Gene.797::NR_045260::g.797] -indexing [Gene.965::NR_045559::g.965] -indexing [Gene.964::NR_045560::g.964] -indexing [Gene.3048::NR_045861::g.3048] -indexing [Gene.3049::NR_045864::g.3049] -indexing [Gene.2931::NR_046750::g.2931] -indexing [Gene.1838::NR_051952::g.1838] -indexing [Gene.3473::NR_073148::g.3473] -indexing [Gene.3472::NR_073149::g.3472] -indexing [Gene.3778::NR_073156::g.3778] -indexing [Gene.445::NR_073393::g.445] -indexing [Gene.2367::NR_073450::g.2367] -indexing [Gene.2505::NR_102268::g.2505] -indexing [Gene.2579::NR_102272::g.2579] -indexing [Gene.944::NR_103708::g.944] -indexing [Gene.942::NR_103709::g.942] -indexing [Gene.3074::NR_103715::g.3074] -indexing [Gene.2017::NR_104107::g.2017] -indexing [Gene.2622::NR_104109::g.2622] -indexing [Gene.3052::NR_104114::g.3052] -indexing [Gene.2370::NR_104121::g.2370] -indexing [Gene.1097::NR_104128::g.1097] -indexing [Gene.2408::NR_104387::g.2408] -indexing [Gene.2417::NR_104388::g.2417] -indexing [Gene.2399::NR_104389::g.2399] -indexing [Gene.2390::NR_104390::g.2390] -indexing [Gene.2410::NR_104391::g.2410] -indexing [Gene.2403::NR_104392::g.2403] -indexing [Gene.2397::NR_104393::g.2397] -indexing [Gene.2414::NR_104394::g.2414] -indexing [Gene.2394::NR_104395::g.2394] -indexing [Gene.3966::NR_109776::g.3966] -indexing [Gene.4004::NR_110021::g.4004] -indexing [Gene.3997::NR_110022::g.3997] -indexing [Gene.4003::NR_110023::g.4003] -indexing [Gene.4346::NR_110311::g.4346] -indexing [Gene.4200::NR_110385::g.4200] -indexing [Gene.1915::NR_110506::g.1915] -indexing [Gene.4210::NR_110830::g.4210] -indexing [Gene.3679::NR_111960::g.3679] -indexing [Gene.3864::NR_120493::g.3864] -indexing [Gene.3865::NR_120493_dup1::g.3865] -indexing [Gene.1366::NR_120494::g.1366] -indexing [Gene.1365::NR_120494_dup1::g.1365] -indexing [Gene.994::NR_120499::g.994] -indexing [Gene.995::NR_120499_dup1::g.995] -indexing [Gene.3601::NR_126093::g.3601] -indexing [Gene.3124::NR_130733::g.3124] -indexing [Gene.3358::NR_130768::g.3358] -indexing [Gene.1249::NR_132647::g.1249] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta > stringtie_merged.transcripts.fasta.transdecoder.pep -indexing [Gene.2979::MSTRG.1.1::g.2979] -indexing [Gene.3929::MSTRG.10.1::g.3929] -indexing [Gene.292::MSTRG.1000.4::g.292] -indexing [Gene.910::MSTRG.1001.1::g.910] -indexing [Gene.913::MSTRG.1001.2::g.913] -indexing [Gene.4046::MSTRG.1005.1::g.4046] -indexing [Gene.4042::MSTRG.1005.2::g.4042] -indexing [Gene.4038::MSTRG.1005.3::g.4038] -indexing [Gene.2536::MSTRG.1009.2::g.2536] -indexing [Gene.1979::MSTRG.101.1::g.1979] -indexing [Gene.392::MSTRG.1012.1::g.392] -indexing [Gene.398::MSTRG.1012.3::g.398] -indexing [Gene.394::MSTRG.1012.4::g.394] -indexing [Gene.2490::MSTRG.1017.1::g.2490] -indexing [Gene.3075::MSTRG.1021.3::g.3075] -indexing [Gene.1660::MSTRG.1023.2::g.1660] -indexing [Gene.1658::MSTRG.1023.3::g.1658] -indexing [Gene.1662::MSTRG.1023.4::g.1662] -indexing [Gene.4267::MSTRG.1024.2::g.4267] -indexing [Gene.573::MSTRG.1025.1::g.573] -indexing [Gene.547::MSTRG.1025.12::g.547] -indexing [Gene.558::MSTRG.1025.2::g.558] 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[Gene.3099::NM_207320::g.3099] -indexing [Gene.4029::NM_207339::g.4029] -indexing [Gene.1071::NM_207422::g.1071] -indexing [Gene.970::NM_212559::g.970] -indexing [Gene.195::NR_001564::g.195] -indexing [Gene.3028::NR_002191::g.3028] -indexing [Gene.3342::NR_002216::g.3342] -indexing [Gene.2372::NR_002308::g.2372] -indexing [Gene.2927::NR_002309::g.2927] -indexing [Gene.4096::NR_002718::g.4096] -indexing [Gene.2053::NR_002784::g.2053] -indexing [Gene.4326::NR_003255::g.4326] -indexing [Gene.2535::NR_003539::g.2535] -indexing [Gene.29::NR_015353::g.29] -indexing [Gene.3379::NR_024048::g.3379] -indexing [Gene.3090::NR_024062::g.3090] -indexing [Gene.852::NR_024359::g.852] -indexing [Gene.185::NR_024608::g.185] -indexing [Gene.1027::NR_026545::g.1027] -indexing [Gene.3948::NR_026551::g.3948] -indexing [Gene.3577::NR_026594::g.3577] -indexing [Gene.2626::NR_026594_dup1::g.2626] -indexing [Gene.3123::NR_026710::g.3123] -indexing [Gene.3111::NR_026711::g.3111] -indexing [Gene.3133::NR_026742::g.3133] -indexing [Gene.3581::NR_026935::g.3581] -indexing [Gene.941::NR_026975::g.941] -indexing [Gene.2059::NR_027121::g.2059] -indexing [Gene.274::NR_027131::g.274] -indexing [Gene.506::NR_027141::g.506] -indexing [Gene.2897::NR_027250::g.2897] -indexing [Gene.618::NR_027291::g.618] -indexing [Gene.4273::NR_027383::g.4273] -indexing [Gene.2509::NR_027401::g.2509] -indexing [Gene.446::NR_027401_dup1::g.446] -indexing [Gene.1844::NR_027419::g.1844] -indexing [Gene.2743::NR_027455::g.2743] -indexing [Gene.2828::NR_027621::g.2828] -indexing [Gene.2718::NR_027760::g.2718] -indexing [Gene.1874::NR_027761::g.1874] -indexing [Gene.1808::NR_028057::g.1808] -indexing [Gene.2720::NR_028089::g.2720] -indexing [Gene.2560::NR_028119::g.2560] -indexing [Gene.3125::NR_028366::g.3125] -indexing [Gene.3046::NR_028407::g.3046] -indexing [Gene.1356::NR_028443::g.1356] -indexing [Gene.3714::NR_028476::g.3714] -indexing [Gene.3718::NR_028477::g.3718] -indexing 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[Gene.632::NR_034116::g.632] -indexing [Gene.633::NR_034116_dup1::g.633] -indexing [Gene.1503::NR_037183::g.1503] -indexing [Gene.3934::NR_037859::g.3934] -indexing [Gene.4319::NR_037916::g.4319] -indexing [Gene.2846::NR_037927::g.2846] -indexing [Gene.4185::NR_045044::g.4185] -indexing [Gene.797::NR_045260::g.797] -indexing [Gene.965::NR_045559::g.965] -indexing [Gene.964::NR_045560::g.964] -indexing [Gene.3048::NR_045861::g.3048] -indexing [Gene.3049::NR_045864::g.3049] -indexing [Gene.2931::NR_046750::g.2931] -indexing [Gene.1838::NR_051952::g.1838] -indexing [Gene.3473::NR_073148::g.3473] -indexing [Gene.3472::NR_073149::g.3472] -indexing [Gene.3778::NR_073156::g.3778] -indexing [Gene.445::NR_073393::g.445] -indexing [Gene.2367::NR_073450::g.2367] -indexing [Gene.2505::NR_102268::g.2505] -indexing [Gene.2579::NR_102272::g.2579] -indexing [Gene.944::NR_103708::g.944] -indexing [Gene.942::NR_103709::g.942] -indexing [Gene.3074::NR_103715::g.3074] -indexing [Gene.2017::NR_104107::g.2017] -indexing [Gene.2622::NR_104109::g.2622] -indexing [Gene.3052::NR_104114::g.3052] -indexing [Gene.2370::NR_104121::g.2370] -indexing [Gene.1097::NR_104128::g.1097] -indexing [Gene.2408::NR_104387::g.2408] -indexing [Gene.2417::NR_104388::g.2417] -indexing [Gene.2399::NR_104389::g.2399] -indexing [Gene.2390::NR_104390::g.2390] -indexing [Gene.2410::NR_104391::g.2410] -indexing [Gene.2403::NR_104392::g.2403] -indexing [Gene.2397::NR_104393::g.2397] -indexing [Gene.2414::NR_104394::g.2414] -indexing [Gene.2394::NR_104395::g.2394] -indexing [Gene.3966::NR_109776::g.3966] -indexing [Gene.4004::NR_110021::g.4004] -indexing [Gene.3997::NR_110022::g.3997] -indexing [Gene.4003::NR_110023::g.4003] -indexing [Gene.4346::NR_110311::g.4346] -indexing [Gene.4200::NR_110385::g.4200] -indexing [Gene.1915::NR_110506::g.1915] -indexing [Gene.4210::NR_110830::g.4210] -indexing [Gene.3679::NR_111960::g.3679] -indexing [Gene.3864::NR_120493::g.3864] -indexing [Gene.3865::NR_120493_dup1::g.3865] -indexing [Gene.1366::NR_120494::g.1366] -indexing [Gene.1365::NR_120494_dup1::g.1365] -indexing [Gene.994::NR_120499::g.994] -indexing [Gene.995::NR_120499_dup1::g.995] -indexing [Gene.3601::NR_126093::g.3601] -indexing [Gene.3124::NR_130733::g.3124] -indexing [Gene.3358::NR_130768::g.3358] -indexing [Gene.1249::NR_132647::g.1249] CMD: /build/transdecoder-5.0.1/util/gff3_file_to_proteins.pl --gff3 stringtie_merged.transcripts.fasta.transdecoder.gff3 --fasta stringtie_merged.transcripts.fasta --seqType CDS > stringtie_merged.transcripts.fasta.transdecoder.cds -indexing [Gene.2979::MSTRG.1.1::g.2979] -indexing [Gene.3929::MSTRG.10.1::g.3929] -indexing [Gene.292::MSTRG.1000.4::g.292] -indexing [Gene.910::MSTRG.1001.1::g.910] -indexing [Gene.913::MSTRG.1001.2::g.913] -indexing [Gene.4046::MSTRG.1005.1::g.4046] -indexing [Gene.4042::MSTRG.1005.2::g.4042] -indexing [Gene.4038::MSTRG.1005.3::g.4038] -indexing [Gene.2536::MSTRG.1009.2::g.2536] -indexing 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[Gene.1741::NR_033700::g.1741] -indexing [Gene.1706::NR_033714::g.1706] -indexing [Gene.1705::NR_033715::g.1705] -indexing [Gene.2068::NR_033717::g.2068] -indexing [Gene.1766::NR_033742::g.1766] -indexing [Gene.935::NR_033772::g.935] -indexing [Gene.938::NR_033772_dup1::g.938] -indexing [Gene.3145::NR_033773::g.3145] -indexing [Gene.3142::NR_033773_dup1::g.3142] -indexing [Gene.927::NR_033835::g.927] -indexing [Gene.929::NR_033836::g.929] -indexing [Gene.1416::NR_034031::g.1416] -indexing [Gene.632::NR_034116::g.632] -indexing [Gene.633::NR_034116_dup1::g.633] -indexing [Gene.1503::NR_037183::g.1503] -indexing [Gene.3934::NR_037859::g.3934] -indexing [Gene.4319::NR_037916::g.4319] -indexing [Gene.2846::NR_037927::g.2846] -indexing [Gene.4185::NR_045044::g.4185] -indexing [Gene.797::NR_045260::g.797] -indexing [Gene.965::NR_045559::g.965] -indexing [Gene.964::NR_045560::g.964] -indexing [Gene.3048::NR_045861::g.3048] -indexing [Gene.3049::NR_045864::g.3049] -indexing [Gene.2931::NR_046750::g.2931] -indexing [Gene.1838::NR_051952::g.1838] -indexing [Gene.3473::NR_073148::g.3473] -indexing [Gene.3472::NR_073149::g.3472] -indexing [Gene.3778::NR_073156::g.3778] -indexing [Gene.445::NR_073393::g.445] -indexing [Gene.2367::NR_073450::g.2367] -indexing [Gene.2505::NR_102268::g.2505] -indexing [Gene.2579::NR_102272::g.2579] -indexing [Gene.944::NR_103708::g.944] -indexing [Gene.942::NR_103709::g.942] -indexing [Gene.3074::NR_103715::g.3074] -indexing [Gene.2017::NR_104107::g.2017] -indexing [Gene.2622::NR_104109::g.2622] -indexing [Gene.3052::NR_104114::g.3052] -indexing [Gene.2370::NR_104121::g.2370] -indexing [Gene.1097::NR_104128::g.1097] -indexing [Gene.2408::NR_104387::g.2408] -indexing [Gene.2417::NR_104388::g.2417] -indexing [Gene.2399::NR_104389::g.2399] -indexing [Gene.2390::NR_104390::g.2390] -indexing [Gene.2410::NR_104391::g.2410] -indexing [Gene.2403::NR_104392::g.2403] -indexing [Gene.2397::NR_104393::g.2397] -indexing [Gene.2414::NR_104394::g.2414] -indexing [Gene.2394::NR_104395::g.2394] -indexing [Gene.3966::NR_109776::g.3966] -indexing [Gene.4004::NR_110021::g.4004] -indexing [Gene.3997::NR_110022::g.3997] -indexing [Gene.4003::NR_110023::g.4003] -indexing [Gene.4346::NR_110311::g.4346] -indexing [Gene.4200::NR_110385::g.4200] -indexing [Gene.1915::NR_110506::g.1915] -indexing [Gene.4210::NR_110830::g.4210] -indexing [Gene.3679::NR_111960::g.3679] -indexing [Gene.3864::NR_120493::g.3864] -indexing [Gene.3865::NR_120493_dup1::g.3865] -indexing [Gene.1366::NR_120494::g.1366] -indexing [Gene.1365::NR_120494_dup1::g.1365] -indexing [Gene.994::NR_120499::g.994] -indexing [Gene.995::NR_120499_dup1::g.995] -indexing [Gene.3601::NR_126093::g.3601] -indexing [Gene.3124::NR_130733::g.3124] -indexing [Gene.3358::NR_130768::g.3358] -indexing [Gene.1249::NR_132647::g.1249] transdecoder is finished. See output files stringtie_merged.transcripts.fasta.transdecoder.* ## convert to genome coordinates ../../util/cdna_alignment_orf_to_genome_orf.pl stringtie_merged.transcripts.fasta.transdecoder.gff3 stringtie_merged.gff3 stringtie_merged.transcripts.fasta > stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 -indexing [Gene.2979::MSTRG.1.1::g.2979] -indexing [Gene.3929::MSTRG.10.1::g.3929] -indexing [Gene.292::MSTRG.1000.4::g.292] -indexing [Gene.910::MSTRG.1001.1::g.910] -indexing [Gene.913::MSTRG.1001.2::g.913] -indexing [Gene.4046::MSTRG.1005.1::g.4046] -indexing [Gene.4042::MSTRG.1005.2::g.4042] -indexing [Gene.4038::MSTRG.1005.3::g.4038] -indexing [Gene.2536::MSTRG.1009.2::g.2536] -indexing [Gene.1979::MSTRG.101.1::g.1979] -indexing [Gene.392::MSTRG.1012.1::g.392] -indexing [Gene.398::MSTRG.1012.3::g.398] -indexing [Gene.394::MSTRG.1012.4::g.394] -indexing [Gene.2490::MSTRG.1017.1::g.2490] -indexing [Gene.3075::MSTRG.1021.3::g.3075] -indexing [Gene.1660::MSTRG.1023.2::g.1660] -indexing [Gene.1658::MSTRG.1023.3::g.1658] -indexing [Gene.1662::MSTRG.1023.4::g.1662] -indexing [Gene.4267::MSTRG.1024.2::g.4267] -indexing [Gene.573::MSTRG.1025.1::g.573] -indexing [Gene.547::MSTRG.1025.12::g.547] -indexing [Gene.558::MSTRG.1025.2::g.558] -indexing [Gene.551::MSTRG.1025.3::g.551] -indexing [Gene.552::MSTRG.1025.4::g.552] -indexing [Gene.555::MSTRG.1025.5::g.555] -indexing [Gene.562::MSTRG.1025.6::g.562] -indexing [Gene.3132::MSTRG.1028.1::g.3132] -indexing [Gene.3374::MSTRG.1029.1::g.3374] -indexing [Gene.3389::MSTRG.1029.11::g.3389] -indexing [Gene.3368::MSTRG.1029.12::g.3368] -indexing [Gene.3361::MSTRG.1029.2::g.3361] -indexing [Gene.3384::MSTRG.1029.3::g.3384] -indexing [Gene.3377::MSTRG.1029.4::g.3377] -indexing [Gene.1340::MSTRG.1034.2::g.1340] -indexing [Gene.1949::MSTRG.1036.1::g.1949] -indexing [Gene.3592::MSTRG.1037.1::g.3592] -indexing [Gene.3591::MSTRG.1037.8::g.3591] -indexing [Gene.3217::MSTRG.1040.3::g.3217] -indexing [Gene.3149::MSTRG.1041.4::g.3149] -indexing [Gene.3167::MSTRG.1041.5::g.3167] -indexing [Gene.3154::MSTRG.1041.6::g.3154] -indexing [Gene.3163::MSTRG.1041.7::g.3163] -indexing [Gene.3147::MSTRG.1041.8::g.3147] -indexing [Gene.3168::MSTRG.1041.9::g.3168] -indexing [Gene.1064::MSTRG.1042.1::g.1064] -indexing [Gene.1060::MSTRG.1042.2::g.1060] -indexing [Gene.1062::MSTRG.1042.3::g.1062] -indexing [Gene.1710::MSTRG.1045.1::g.1710] -indexing [Gene.2715::MSTRG.1049.1::g.2715] -indexing [Gene.368::MSTRG.1055.1::g.368] -indexing [Gene.365::MSTRG.1055.2::g.365] -indexing [Gene.3572::MSTRG.1069.1::g.3572] -indexing [Gene.2943::MSTRG.1070.2::g.2943] -indexing [Gene.3406::MSTRG.1073.3::g.3406] -indexing [Gene.2770::MSTRG.1074.1::g.2770] -indexing [Gene.2767::MSTRG.1074.10::g.2767] -indexing [Gene.2761::MSTRG.1074.11::g.2761] -indexing [Gene.2788::MSTRG.1074.12::g.2788] -indexing [Gene.2775::MSTRG.1074.13::g.2775] -indexing [Gene.2759::MSTRG.1074.14::g.2759] -indexing [Gene.2776::MSTRG.1074.2::g.2776] -indexing [Gene.2782::MSTRG.1074.3::g.2782] -indexing [Gene.2774::MSTRG.1074.4::g.2774] -indexing [Gene.2779::MSTRG.1074.5::g.2779] -indexing [Gene.2765::MSTRG.1074.6::g.2765] -indexing [Gene.2791::MSTRG.1074.7::g.2791] -indexing [Gene.2785::MSTRG.1074.8::g.2785] -indexing [Gene.2763::MSTRG.1074.9::g.2763] -indexing [Gene.4074::MSTRG.108.1::g.4074] -indexing [Gene.4063::MSTRG.108.2::g.4063] -indexing [Gene.4067::MSTRG.108.3::g.4067] -indexing [Gene.2448::MSTRG.109.1::g.2448] -indexing [Gene.2452::MSTRG.109.10::g.2452] -indexing [Gene.2455::MSTRG.109.7::g.2455] -indexing [Gene.2453::MSTRG.109.9::g.2453] -indexing [Gene.433::MSTRG.110.1::g.433] -indexing [Gene.431::MSTRG.110.10::g.431] -indexing [Gene.425::MSTRG.110.11::g.425] -indexing [Gene.427::MSTRG.110.2::g.427] -indexing [Gene.426::MSTRG.110.4::g.426] -indexing [Gene.422::MSTRG.110.5::g.422] -indexing [Gene.432::MSTRG.110.6::g.432] -indexing [Gene.434::MSTRG.110.7::g.434] -indexing [Gene.424::MSTRG.110.8::g.424] -indexing [Gene.429::MSTRG.110.9::g.429] -indexing [Gene.2238::MSTRG.113.1::g.2238] -indexing [Gene.2237::MSTRG.113.4::g.2237] -indexing [Gene.926::MSTRG.116.5::g.926] -indexing [Gene.3952::MSTRG.124.1::g.3952] -indexing [Gene.3953::MSTRG.124.2::g.3953] -indexing [Gene.3954::MSTRG.124.3::g.3954] -indexing [Gene.3951::MSTRG.124.7::g.3951] -indexing [Gene.3956::MSTRG.124.8::g.3956] -indexing [Gene.3950::MSTRG.124.9::g.3950] -indexing [Gene.2842::MSTRG.125.1::g.2842] -indexing [Gene.2548::MSTRG.128.1::g.2548] -indexing [Gene.2546::MSTRG.128.2::g.2546] -indexing [Gene.2542::MSTRG.128.4::g.2542] -indexing [Gene.2551::MSTRG.128.5::g.2551] -indexing [Gene.1205::MSTRG.131.4::g.1205] -indexing [Gene.1206::MSTRG.131.5::g.1206] -indexing [Gene.1203::MSTRG.131.6::g.1203] -indexing [Gene.3109::MSTRG.137.3::g.3109] -indexing [Gene.3237::MSTRG.14.1::g.3237] -indexing [Gene.263::MSTRG.142.5::g.263] -indexing [Gene.2750::MSTRG.143.2::g.2750] -indexing [Gene.183::MSTRG.144.1::g.183] -indexing [Gene.1723::MSTRG.147.2::g.1723] -indexing [Gene.1727::MSTRG.147.3::g.1727] -indexing [Gene.1724::MSTRG.147.4::g.1724] -indexing [Gene.502::MSTRG.151.1::g.502] -indexing [Gene.503::MSTRG.151.5::g.503] -indexing [Gene.496::MSTRG.151.6::g.496] -indexing [Gene.497::MSTRG.151.7::g.497] -indexing [Gene.2721::MSTRG.159.5::g.2721] -indexing [Gene.2724::MSTRG.159.6::g.2724] -indexing [Gene.3117::MSTRG.16.1::g.3117] -indexing [Gene.2730::MSTRG.161.2::g.2730] -indexing [Gene.2729::MSTRG.161.3::g.2729] -indexing [Gene.2911::MSTRG.166.5::g.2911] -indexing [Gene.4247::MSTRG.17.1::g.4247] -indexing [Gene.4253::MSTRG.17.2::g.4253] -indexing [Gene.4263::MSTRG.17.6::g.4263] -indexing [Gene.4249::MSTRG.17.7::g.4249] -indexing [Gene.4246::MSTRG.17.8::g.4246] -indexing [Gene.3301::MSTRG.172.1::g.3301] -indexing [Gene.4016::MSTRG.178.3::g.4016] -indexing [Gene.4015::MSTRG.178.4::g.4015] -indexing [Gene.4012::MSTRG.178.5::g.4012] -indexing [Gene.4014::MSTRG.178.6::g.4014] -indexing [Gene.2540::MSTRG.179.1::g.2540] -indexing [Gene.4316::MSTRG.181.1::g.4316] -indexing [Gene.1354::MSTRG.183.2::g.1354] -indexing [Gene.525::MSTRG.187.1::g.525] -indexing [Gene.1132::MSTRG.189.1::g.1132] -indexing [Gene.1130::MSTRG.189.10::g.1130] -indexing [Gene.1129::MSTRG.189.11::g.1129] -indexing [Gene.1141::MSTRG.189.7::g.1141] -indexing [Gene.1139::MSTRG.189.8::g.1139] -indexing [Gene.1134::MSTRG.189.9::g.1134] -indexing [Gene.24::MSTRG.191.1::g.24] -indexing [Gene.3640::MSTRG.195.1::g.3640] -indexing [Gene.1150::MSTRG.2.1::g.1150] -indexing [Gene.2325::MSTRG.205.1::g.2325] -indexing [Gene.2327::MSTRG.205.2::g.2327] -indexing [Gene.2326::MSTRG.205.3::g.2326] -indexing [Gene.491::MSTRG.207.1::g.491] -indexing [Gene.4180::MSTRG.208.2::g.4180] -indexing [Gene.4175::MSTRG.208.3::g.4175] -indexing [Gene.4173::MSTRG.208.4::g.4173] -indexing [Gene.2965::MSTRG.209.5::g.2965] -indexing [Gene.2970::MSTRG.209.6::g.2970] -indexing 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[Gene.986::MSTRG.254.1::g.986] -indexing [Gene.3681::MSTRG.258.8::g.3681] -indexing [Gene.3691::MSTRG.258.9::g.3691] -indexing [Gene.261::MSTRG.26.2::g.261] -indexing [Gene.1832::MSTRG.265.3::g.1832] -indexing [Gene.1830::MSTRG.265.4::g.1830] -indexing [Gene.4130::MSTRG.266.4::g.4130] -indexing [Gene.4121::MSTRG.266.5::g.4121] -indexing [Gene.3515::MSTRG.268.1::g.3515] -indexing [Gene.3513::MSTRG.268.2::g.3513] -indexing [Gene.3517::MSTRG.268.3::g.3517] -indexing [Gene.3501::MSTRG.268.4::g.3501] -indexing [Gene.3506::MSTRG.268.5::g.3506] -indexing [Gene.3520::MSTRG.268.6::g.3520] -indexing [Gene.3507::MSTRG.268.7::g.3507] -indexing [Gene.810::MSTRG.275.2::g.810] -indexing [Gene.802::MSTRG.275.3::g.802] -indexing [Gene.813::MSTRG.275.4::g.813] -indexing [Gene.821::MSTRG.275.6::g.821] -indexing [Gene.818::MSTRG.275.7::g.818] -indexing [Gene.1810::MSTRG.276.2::g.1810] -indexing [Gene.4231::MSTRG.277.1::g.4231] -indexing [Gene.248::MSTRG.279.1::g.248] -indexing [Gene.252::MSTRG.279.10::g.252] -indexing [Gene.238::MSTRG.279.11::g.238] -indexing [Gene.242::MSTRG.279.2::g.242] -indexing [Gene.244::MSTRG.279.3::g.244] -indexing [Gene.254::MSTRG.279.4::g.254] -indexing [Gene.250::MSTRG.279.5::g.250] -indexing [Gene.240::MSTRG.279.6::g.240] -indexing [Gene.236::MSTRG.279.7::g.236] -indexing [Gene.234::MSTRG.279.8::g.234] -indexing [Gene.2494::MSTRG.281.1::g.2494] -indexing [Gene.2167::MSTRG.284.1::g.2167] -indexing [Gene.2175::MSTRG.284.5::g.2175] -indexing [Gene.2197::MSTRG.292.4::g.2197] -indexing [Gene.2192::MSTRG.292.5::g.2192] -indexing [Gene.3404::MSTRG.293.1::g.3404] -indexing [Gene.2701::MSTRG.294.4::g.2701] -indexing [Gene.2599::MSTRG.301.2::g.2599] -indexing [Gene.2595::MSTRG.301.3::g.2595] -indexing [Gene.538::MSTRG.302.4::g.538] -indexing [Gene.539::MSTRG.302.5::g.539] -indexing [Gene.530::MSTRG.302.6::g.530] -indexing [Gene.537::MSTRG.302.7::g.537] -indexing [Gene.3580::MSTRG.303.1::g.3580] -indexing [Gene.1029::MSTRG.305.1::g.1029] -indexing [Gene.1040::MSTRG.305.6::g.1040] -indexing [Gene.1047::MSTRG.305.7::g.1047] -indexing [Gene.1037::MSTRG.305.8::g.1037] -indexing [Gene.1761::MSTRG.306.1::g.1761] -indexing [Gene.1759::MSTRG.306.3::g.1759] -indexing [Gene.3137::MSTRG.308.1::g.3137] -indexing [Gene.3136::MSTRG.308.3::g.3136] -indexing [Gene.3139::MSTRG.308.4::g.3139] -indexing [Gene.1319::MSTRG.311.2::g.1319] -indexing [Gene.1323::MSTRG.311.3::g.1323] -indexing [Gene.3457::MSTRG.314.1::g.3457] -indexing [Gene.4277::MSTRG.32.1::g.4277] -indexing [Gene.4289::MSTRG.32.4::g.4289] -indexing [Gene.3620::MSTRG.320.1::g.3620] -indexing [Gene.3619::MSTRG.320.2::g.3619] -indexing [Gene.3616::MSTRG.320.3::g.3616] -indexing [Gene.3615::MSTRG.320.4::g.3615] -indexing [Gene.3613::MSTRG.320.5::g.3613] -indexing [Gene.3618::MSTRG.320.8::g.3618] -indexing [Gene.958::MSTRG.324.2::g.958] -indexing [Gene.2076::MSTRG.325.1::g.2076] -indexing [Gene.2083::MSTRG.325.4::g.2083] -indexing [Gene.3534::MSTRG.326.1::g.3534] -indexing 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[Gene.4200::NR_110385::g.4200] -indexing [Gene.1915::NR_110506::g.1915] -indexing [Gene.4210::NR_110830::g.4210] -indexing [Gene.3679::NR_111960::g.3679] -indexing [Gene.3864::NR_120493::g.3864] -indexing [Gene.3865::NR_120493_dup1::g.3865] -indexing [Gene.1366::NR_120494::g.1366] -indexing [Gene.1365::NR_120494_dup1::g.1365] -indexing [Gene.994::NR_120499::g.994] -indexing [Gene.995::NR_120499_dup1::g.995] -indexing [Gene.3601::NR_126093::g.3601] -indexing [Gene.3124::NR_130733::g.3124] -indexing [Gene.3358::NR_130768::g.3358] -indexing [Gene.1249::NR_132647::g.1249] Done. 2649 / 2649 transcript orfs could be propagated to the genome ## make bed files for viewing with GenomeView # covert cufflinks gtf to bed ../../util/cufflinks_gtf_to_bed.pl stringtie_merged.gtf > stringtie_merged.bed # convert the genome-based gene-gff3 file to bed ../../util/gff3_file_to_bed.pl stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 > stringtie_merged.transcripts.fasta.transdecoder.genome.bed -indexing [MSTRG.1045] -indexing [MSTRG.512] -indexing [MSTRG.515] -indexing [MSTRG.541] -indexing [MSTRG.463] -indexing [NM_001170963] -indexing [MSTRG.849] -indexing [NM_001184771] -indexing [MSTRG.853] -indexing [MSTRG.715] -indexing [NM_001139501] -indexing [NM_001161529] -indexing [MSTRG.759] -indexing [MSTRG.743] -indexing [MSTRG.1006] -indexing [NM_001141920] -indexing [NM_001097642] -indexing [MSTRG.559] -indexing [MSTRG.389] -indexing [NM_000054] -indexing [MSTRG.427] -indexing [MSTRG.1039] -indexing [NM_024885] -indexing [MSTRG.211] -indexing [MSTRG.26] -indexing [NM_001184834] -indexing [NM_001109879] -indexing [MSTRG.987] -indexing [NM_020994] -indexing [NM_001171252] -indexing [NM_005296] -indexing [MSTRG.564] -indexing [MSTRG.17] -indexing [MSTRG.764] -indexing [NM_016267] -indexing [MSTRG.388] -indexing [NM_001291535] -indexing [MSTRG.558] -indexing [MSTRG.247] -indexing [NR_120499] -indexing [MSTRG.110] -indexing [NM_001170751] -indexing [NM_033641] -indexing [NM_001291868] -indexing [MSTRG.985] -indexing [MSTRG.848] -indexing [MSTRG.688] -indexing [MSTRG.466] -indexing [NM_001193281] -indexing [NM_001143981] -indexing [NM_152226] -indexing [NM_182541] -indexing [NM_001080144] -indexing [NM_001080851] -indexing [NM_203407] -indexing [NM_001169574] -indexing [NM_001163278] -indexing [NM_152869] -indexing [NM_152761] -indexing [MSTRG.183] -indexing [MSTRG.717] -indexing [MSTRG.216] -indexing [NM_005636] -indexing [MSTRG.181] -indexing [NM_001303514] -indexing [NM_001171111] -indexing [MSTRG.1069] -indexing [NM_001080138] -indexing [NM_001037968] -indexing [NM_001011544] -indexing [NM_133179] -indexing [NM_020742] -indexing [NM_001195553] -indexing [MSTRG.151] -indexing [NM_001303516] -indexing [NM_001256789] -indexing [MSTRG.317] -indexing [NM_000133] -indexing [NM_001017930] -indexing [NR_027761] -indexing [MSTRG.149] -indexing [NM_001080146] -indexing [MSTRG.83] -indexing [MSTRG.658] -indexing [MSTRG.32] -indexing [NM_001291540] -indexing [NM_000032] -indexing [MSTRG.87] -indexing [MSTRG.646] -indexing [NM_174951] -indexing [NM_001011548] -indexing [NM_152278] -indexing [NM_001195577] -indexing [NM_022567] -indexing [MSTRG.62] -indexing [NM_001939] -indexing [NM_001128172] -indexing [MSTRG.346] -indexing [MSTRG.148] -indexing [MSTRG.364] -indexing [MSTRG.156] -indexing [NR_030727] -indexing [NM_001271805] -indexing [NM_001171191] -indexing [MSTRG.957] -indexing [NM_000266] -indexing [MSTRG.664] -indexing [NM_173495] -indexing [NM_001184836] -indexing [NM_014253] -indexing [NM_001048164] -indexing [NM_007231] -indexing [MSTRG.615] -indexing [MSTRG.789] -indexing [MSTRG.641] -indexing [MSTRG.589] -indexing [NM_139289] -indexing [NM_001184703] -indexing [NM_001282146] -indexing [MSTRG.1041] -indexing [MSTRG.250] -indexing [NM_001163265] -indexing [NM_001102576] -indexing [MSTRG.1003] -indexing [NM_152630] -indexing [MSTRG.904] -indexing [MSTRG.312] -indexing [NM_033085] -indexing [NM_006240] -indexing [MSTRG.10] -indexing [NR_033772] -indexing [NM_001166400] -indexing [MSTRG.661] -indexing [MSTRG.61] -indexing [NM_003147] -indexing [NM_001079860] -indexing [NM_001141919] -indexing [NM_014728] -indexing [NM_003785] -indexing [MSTRG.489] -indexing [NR_033348] -indexing [MSTRG.102] -indexing [NM_006307] -indexing [MSTRG.663] -indexing [NM_021796] -indexing [MSTRG.105] -indexing [MSTRG.929] -indexing [NM_177456] -indexing [MSTRG.997] -indexing [NM_001271682] -indexing [NM_001145140] -indexing [NM_178153] -indexing [MSTRG.168] -indexing [MSTRG.290] -indexing [NM_012253] -indexing [MSTRG.877] -indexing [NR_073393] -indexing [MSTRG.837] -indexing [MSTRG.1031] -indexing [MSTRG.327] -indexing [NM_020721] -indexing [MSTRG.903] -indexing [NM_153448] -indexing [NM_001129896] -indexing [NM_178151] -indexing [NM_175729] -indexing [NM_021637] -indexing [MSTRG.872] -indexing [NM_001201538] -indexing [NM_001166387] -indexing [MSTRG.832] -indexing [NM_003604] -indexing [MSTRG.191] -indexing [NM_031907] -indexing [NM_000513] -indexing [MSTRG.325] -indexing [MSTRG.875] -indexing [NR_033349] -indexing [MSTRG.666] -indexing [MSTRG.488] -indexing [MSTRG.700] -indexing [NM_033031] -indexing [MSTRG.193] -indexing [NM_001303613] -indexing [MSTRG.366] -indexing [MSTRG.239] -indexing [MSTRG.279] -indexing [NM_001136533] -indexing [MSTRG.906] -indexing [NM_001128168] -indexing [MSTRG.820] -indexing [MSTRG.330] -indexing [MSTRG.370] -indexing [MSTRG.992] -indexing [NM_016153] -indexing [MSTRG.670] -indexing [MSTRG.107] -indexing [MSTRG.630] -indexing [NM_172246] -indexing [NM_138960] -indexing [NM_130467] -indexing [NM_022053] -indexing [NM_033290] -indexing [NM_024539] -indexing [MSTRG.598] -indexing [MSTRG.570] -indexing [MSTRG.530] -indexing [NM_015075] -indexing [NM_001144886] -indexing [NM_002367] -indexing [NM_001136024] -indexing [NR_027250] -indexing [MSTRG.221] -indexing [NM_001100431] -indexing [MSTRG.1065] -indexing [MSTRG.267] -indexing [MSTRG.209] -indexing [NR_003539] -indexing [NM_001144005] -indexing [MSTRG.976] -indexing [NR_002718] -indexing [MSTRG.868] -indexing [MSTRG.446] -indexing [MSTRG.525] -indexing [MSTRG.725] -indexing [MSTRG.458] -indexing [NM_012471] -indexing [MSTRG.522] -indexing [NM_173571] -indexing [NM_001128166] -indexing [MSTRG.137] -indexing [NM_001144009] -indexing [MSTRG.722] -indexing [MSTRG.600] -indexing [NM_152224] -indexing [MSTRG.1035] -indexing [NM_001303475] -indexing [MSTRG.265] -indexing [NR_110830] -indexing [MSTRG.262] -indexing [NM_020871] -indexing [MSTRG.1015] -indexing [MSTRG.599] -indexing [MSTRG.172] -indexing [NM_033670] -indexing [NM_018159] -indexing [MSTRG.799] -indexing [NM_001145139] -indexing [NM_178470] -indexing [MSTRG.1049] -indexing [NM_001099686] -indexing [NM_001032726] -indexing [MSTRG.561] -indexing [MSTRG.51] -indexing [MSTRG.443] -indexing [MSTRG.459] -indexing [NM_021014] -indexing [MSTRG.869] -indexing [MSTRG.71] -indexing [NM_002362] -indexing [MSTRG.933] -indexing [NM_031442] -indexing [MSTRG.973] -indexing [NM_005634] -indexing [NM_001586] -indexing [MSTRG.763] -indexing [NM_001287760] -indexing [NM_002578] -indexing [NM_002365] -indexing [MSTRG.4] -indexing [MSTRG.208] -indexing [MSTRG.120] -indexing [NR_045260] -indexing [MSTRG.979] -indexing [NM_198465] -indexing [NM_147175] -indexing [MSTRG.939] -indexing [NM_016383] -indexing [MSTRG.507] -indexing [NM_001161531] -indexing [MSTRG.451] -indexing [MSTRG.1012] -indexing [NM_001316889] -indexing [NM_198511] -indexing [NM_001282628] -indexing [NM_001031705] -indexing [NM_013452] -indexing [MSTRG.292] -indexing [NM_001242922] -indexing [MSTRG.453] -indexing [NM_001291543] -indexing [NM_001278000] -indexing [MSTRG.637] -indexing [MSTRG.100] -indexing [NM_005140] -indexing [MSTRG.677] -indexing [NM_172249] -indexing [NM_032498] -indexing [NM_001013403] -indexing [MSTRG.554] -indexing [NM_001282754] -indexing [NM_001278691] -indexing [MSTRG.591] -indexing [MSTRG.337] -indexing [NR_033717] -indexing [MSTRG.791] -indexing [NM_016610] -indexing [NM_020061] -indexing [MSTRG.684] -indexing [NM_153488] -indexing [NM_017863] -indexing [MSTRG.990] -indexing [MSTRG.866] -indexing [MSTRG.448] -indexing [NM_002063] -indexing [NR_046750] -indexing [NM_001145346] -indexing [MSTRG.1062] -indexing [MSTRG.456] -indexing [NM_032461] -indexing [MSTRG.672] -indexing [NM_032512] -indexing [MSTRG.825] -indexing [MSTRG.335] -indexing [MSTRG.978] -indexing [NM_001142395] -indexing [MSTRG.332] -indexing [NM_001004486] -indexing [MSTRG.822] -indexing [MSTRG.702] -indexing [MSTRG.502] -indexing [NM_207339] -indexing [MSTRG.705] -indexing [NM_001145933] -indexing [MSTRG.505] -indexing [NM_001287758] -indexing [MSTRG.320] -indexing [NM_138702] -indexing [MSTRG.830] -indexing [NM_005462] -indexing [NR_120494] -indexing [NM_020922] -indexing [NM_001282848] -indexing [MSTRG.796] -indexing [NM_001013628] -indexing [NM_001164417] -indexing [NM_001146151] -indexing [NM_001118885] -indexing [MSTRG.229] -indexing [NM_015419] -indexing [NM_152694] -indexing [NM_001171877] -indexing [MSTRG.271] -indexing [NM_001282502] -indexing [NM_000640] -indexing [NM_001079858] -indexing [MSTRG.396] -indexing [MSTRG.605] -indexing [MSTRG.163] -indexing [MSTRG.520] -indexing [MSTRG.602] -indexing [NM_001184767] -indexing [MSTRG.914] -indexing [MSTRG.1067] -indexing [MSTRG.305] -indexing [NM_001103150] -indexing [MSTRG.161] -indexing [MSTRG.11] -indexing [MSTRG.302] -indexing [MSTRG.772] -indexing [MSTRG.965] -indexing [MSTRG.127] -indexing [MSTRG.732] -indexing [MSTRG.199] -indexing [NM_177415] -indexing [NM_000555] -indexing [MSTRG.572] -indexing [NM_001145718] -indexing [NM_080873] -indexing [NM_001099681] -indexing [MSTRG.575] -indexing [MSTRG.144] -indexing [MSTRG.800] -indexing [NM_173523] -indexing [NM_182607] -indexing [NM_001251828] -indexing [MSTRG.47] -indexing [NM_001136233] -indexing [MSTRG.43] -indexing [MSTRG.668] -indexing [MSTRG.486] -indexing [NM_175723] -indexing [MSTRG.967] -indexing [MSTRG.125] -indexing [MSTRG.909] -indexing [MSTRG.654] -indexing [MSTRG.537] -indexing [NM_001163335] -indexing [NM_001012979] -indexing [MSTRG.391] -indexing [MSTRG.777] -indexing [MSTRG.276] -indexing [MSTRG.1037] -indexing [MSTRG.122] -indexing [MSTRG.693] -indexing [MSTRG.236] -indexing [NM_001257403] -indexing [NM_001144010] -indexing [MSTRG.166] -indexing [NM_001002916] -indexing [MSTRG.691] -indexing [MSTRG.1017] -indexing [NM_001001888] -indexing [MSTRG.393] -indexing [NM_001173489] -indexing [MSTRG.607] -indexing [MSTRG.669] -indexing [MSTRG.170] -indexing [NM_001142504] -indexing [MSTRG.923] -indexing [MSTRG.1034] -indexing [NM_145662] -indexing [NM_004988] -indexing [NM_004845] -indexing [MSTRG.369] -indexing [MSTRG.307] -indexing [NR_103715] -indexing [MSTRG.921] -indexing [NM_018558] -indexing [MSTRG.260] -indexing [NM_001011645] -indexing [MSTRG.653] -indexing [MSTRG.889] -indexing [MSTRG.781] -indexing [MSTRG.649] -indexing [NM_001522] -indexing [NM_001079900] -indexing [MSTRG.351] -indexing [NM_001144003] -indexing [MSTRG.694] -indexing [NM_001184702] -indexing [NM_001171879] -indexing [MSTRG.916] -indexing [NM_005367] -indexing [MSTRG.353] -indexing [NM_006883] -indexing [MSTRG.583] -indexing [NM_130776] -indexing [NM_153183] -indexing [NM_001168474] -indexing [NM_001174068] -indexing [MSTRG.651] -indexing [MSTRG.117] -indexing [MSTRG.1056] -indexing [MSTRG.285] -indexing [MSTRG.924] -indexing [MSTRG.1044] -indexing [NM_001177465] -indexing [NM_001099921] -indexing [NM_139058] -indexing [MSTRG.437] -indexing [MSTRG.477] -indexing [NM_001012977] -indexing [NM_001172288] -indexing [MSTRG.945] -indexing [NM_001099855] -indexing [MSTRG.942] -indexing [NM_001004308] -indexing [MSTRG.77] -indexing [MSTRG.586] -indexing [MSTRG.164] -indexing [MSTRG.57] -indexing [MSTRG.786] -indexing [MSTRG.53] -indexing [NM_001080790] -indexing [MSTRG.234] -indexing [NM_001128173] -indexing [MSTRG.913] -indexing [MSTRG.475] -indexing [NM_014467] -indexing [NM_175742] -indexing [MSTRG.60] -indexing [MSTRG.143] -indexing [MSTRG.159] -indexing [NM_001727] -indexing [NM_001142447] -indexing [NM_000808] -indexing [MSTRG.1038] -indexing [NM_007003] -indexing [MSTRG.980] -indexing [MSTRG.112] -indexing [NM_005365] -indexing [MSTRG.1018] -indexing [NM_001139498] -indexing [NM_212559] -indexing [NM_005362] -indexing [MSTRG.1] -indexing [MSTRG.115] -indexing [NM_006517] -indexing [MSTRG.496] -indexing [NM_001169154] -indexing [NM_001013736] -indexing [MSTRG.402] -indexing [MSTRG.189] -indexing [NR_033262] -indexing [NM_001327] -indexing [NM_001278702] -indexing [NM_001316887] -indexing [MSTRG.405] -indexing [NM_001184831] -indexing [NM_198270] -indexing [MSTRG.686] -indexing [MSTRG.468] -indexing [MSTRG.67] -indexing [MSTRG.858] -indexing [MSTRG.63] -indexing [MSTRG.1073] -indexing [NM_004114] -indexing [MSTRG.556] -indexing [NM_012069] -indexing [NR_120493] -indexing [MSTRG.748] -indexing [NM_194463] -indexing [NM_001205201] -indexing [NM_001195272] -indexing [MSTRG.82] -indexing [NM_004961] -indexing [NM_001193278] -indexing [NM_205856] -indexing [NM_001171706] -indexing [NM_001012428] -indexing [NM_001282505] -indexing [NM_001011719] -indexing [MSTRG.491] -indexing [NM_152632] -indexing [MSTRG.1023] -indexing [NM_153346] -indexing [NM_001171942] -indexing [NM_014289] -indexing [NM_000044] -indexing [MSTRG.610] -indexing [MSTRG.252] -indexing [MSTRG.454] -indexing [MSTRG.1042] -indexing [MSTRG.864] -indexing [NM_000533] -indexing [MSTRG.594] -indexing [NM_001170962] -indexing [NM_205849] -indexing [MSTRG.1040] -indexing [NM_001080141] -indexing [NM_001164415] -indexing [MSTRG.794] -indexing [MSTRG.383] -indexing [MSTRG.549] -indexing [MSTRG.841] -indexing [MSTRG.681] -indexing [MSTRG.8] -indexing [NM_018666] -indexing [NM_000531] -indexing [MSTRG.859] -indexing [NM_003413] -indexing [MSTRG.683] -indexing [MSTRG.407] -indexing [MSTRG.469] -indexing [MSTRG.551] -indexing [NR_029423] -indexing [NM_001170574] -indexing [NM_178152] -indexing [NM_174901] -indexing [MSTRG.1051] -indexing [NM_080737] -indexing [NM_001142503] -indexing [MSTRG.1002] -indexing [NM_001847] -indexing [MSTRG.860] -indexing [MSTRG.996] -indexing [NM_001080140] -indexing [MSTRG.614] -indexing [MSTRG.1021] -indexing [MSTRG.450] -indexing [NM_001163279] -indexing [NM_001080145] -indexing [NM_052926] -indexing [NM_001244892] -indexing [NM_198510] -indexing [NR_026935] -indexing [MSTRG.308] -indexing [NM_020766] -indexing [MSTRG.129] -indexing [MSTRG.905] -indexing [NM_001099682] -indexing [MSTRG.314] -indexing [MSTRG.362] -indexing [MSTRG.101] -indexing [MSTRG.626] -indexing [MSTRG.538] -indexing [NM_177404] -indexing [MSTRG.34] -indexing [MSTRG.365] -indexing [MSTRG.578] -indexing [MSTRG.1000] -indexing [MSTRG.790] -indexing [NM_001282501] -indexing [NM_001111125] -indexing [NM_001171095] -indexing [MSTRG.876] -indexing [MSTRG.326] -indexing [NM_001009613] -indexing [MSTRG.665] -indexing [NM_001303515] -indexing [MSTRG.88] -indexing [NM_173494] -indexing [NM_001282535] -indexing [MSTRG.991] -indexing [MSTRG.128] -indexing [MSTRG.309] -indexing [NM_000444] -indexing [NM_000074] -indexing [MSTRG.993] -indexing [NM_175569] -indexing [NM_001282145] -indexing [NM_001278697] -indexing [NM_001136234] -indexing [MSTRG.609] -indexing [MSTRG.954] -indexing [NM_001109878] -indexing [MSTRG.873] -indexing [NM_032946] -indexing [MSTRG.1071] -indexing [NM_194277] -indexing [NM_001184835] -indexing [NM_004224] -indexing [NM_001166386] -indexing [NM_173078] -indexing [NM_001184830] -indexing [MSTRG.739] -indexing [MSTRG.831] -indexing [NM_001282631] -indexing [MSTRG.195] -indexing [MSTRG.907] -indexing [NM_001555] -indexing [NM_012274] -indexing [MSTRG.230] -indexing [NM_001271804] -indexing [MSTRG.270] -indexing [MSTRG.829] -indexing [MSTRG.339] -indexing [NM_001145934] -indexing [NM_130388] -indexing [NM_002625] -indexing [MSTRG.416] -indexing [MSTRG.521] -indexing [NM_172247] -indexing [NM_001304963] -indexing [NM_032428] -indexing [NM_001128167] -indexing [NM_005491] -indexing [MSTRG.298] -indexing [MSTRG.723] -indexing [NM_207320] -indexing [NM_001144064] -indexing [MSTRG.984] -indexing [NM_001034832] -indexing [MSTRG.803] -indexing [NM_019117] -indexing [NM_022052] -indexing [MSTRG.222] -indexing [MSTRG.424] -indexing [MSTRG.567] -indexing [MSTRG.709] -indexing [MSTRG.266] -indexing [NM_001144887] -indexing [NM_001163264] -indexing [NM_001161532] -indexing [MSTRG.937] -indexing [MSTRG.977] -indexing [MSTRG.411] -indexing [MSTRG.526] -indexing [NM_004615] -indexing [MSTRG.299] -indexing [NM_001277423] -indexing [MSTRG.638] -indexing [MSTRG.85] -indexing [MSTRG.227] -indexing [NM_022148] -indexing [MSTRG.442] -indexing [NM_001101357] -indexing [MSTRG.390] -indexing [NM_002363] -indexing [MSTRG.74] -indexing [MSTRG.972] -indexing [MSTRG.565] -indexing [MSTRG.338] -indexing [MSTRG.828] -indexing [MSTRG.762] -indexing [MSTRG.935] -indexing [NM_001011549] -indexing [MSTRG.690] -indexing [MSTRG.1007] -indexing [MSTRG.562] -indexing [MSTRG.892] -indexing [MSTRG.714] -indexing [NM_152423] -indexing [NM_001184750] -indexing [MSTRG.171] -indexing [MSTRG.514] -indexing [MSTRG.1025] -indexing [MSTRG.131] -indexing [MSTRG.1055] -indexing [MSTRG.508] -indexing [NM_005756] -indexing [NM_172245] -indexing [MSTRG.480] -indexing [NM_001080139] -indexing [NM_001173490] -indexing [NM_001172732] -indexing [NM_001171109] -indexing [NM_001012288] -indexing [MSTRG.1004] -indexing [MSTRG.1029] -indexing [MSTRG.350] -indexing [MSTRG.580] -indexing [NM_021015] -indexing [NM_001077188] -indexing [MSTRG.780] -indexing [NM_022661] -indexing [MSTRG.1059] -indexing [NM_001143983] -indexing [MSTRG.212] -indexing [NM_001011550] -indexing [NM_001313913] -indexing [NM_138780] -indexing [NM_002364] -indexing [NM_005448] -indexing [MSTRG.241] -indexing [NM_007268] -indexing [NM_001144006] -indexing [MSTRG.215] -indexing [MSTRG.2] -indexing [NR_028089] -indexing [NM_005635] -indexing [NM_001278701] -indexing [MSTRG.513] -indexing [MSTRG.855] -indexing [NM_033053] -indexing [MSTRG.187] -indexing [NM_001144885] -indexing [NM_052817] -indexing [NM_001184749] -indexing [NM_198451] -indexing [MSTRG.852] -indexing [MSTRG.711] -indexing [MSTRG.76] -indexing [MSTRG.819] -indexing [MSTRG.174] -indexing [MSTRG.426] -indexing [MSTRG.511] -indexing [NM_001201539] -indexing [MSTRG.134] -indexing [MSTRG.742] -indexing [NM_031894] -indexing [MSTRG.986] -indexing [NM_001195081] -indexing [MSTRG.910] -indexing [MSTRG.467] -indexing [NM_001395] -indexing [NM_001195578] -indexing [NM_001204811] -indexing [MSTRG.185] -indexing [NM_001080142] -indexing [MSTRG.258] -indexing [NM_001170961] -indexing [NM_001170331] -indexing [MSTRG.747] -indexing [NM_001099685] -indexing [MSTRG.724] -indexing [NM_001135740] -indexing [NM_033289] -indexing [NM_021785] -indexing [MSTRG.524] -indexing [NM_181332] -indexing [MSTRG.804] -indexing [MSTRG.983] -indexing [NM_001040612] -indexing [NM_006089] -indexing [NM_017711] -indexing [NM_016379] -indexing [NM_001171184] -indexing [MSTRG.981] -indexing [NM_001171092] -indexing [NM_033048] -indexing [NR_110385] -indexing [NM_001103151] -indexing [MSTRG.516] -indexing [NM_033642] -indexing [NM_001080137] -indexing [NM_001303512] -indexing [NM_001037967] -indexing [NM_005393] -indexing [NM_001171020] -indexing [NM_145234] -indexing [NM_001304548] -indexing [NM_001171186] -indexing [NM_001282607] -indexing [MSTRG.994] -indexing [NM_001171193] -indexing [NM_001270458] -indexing [NM_001195576] -indexing [NM_001162936] -indexing [MSTRG.324] -indexing [NM_024082] -indexing [NM_001002838] -indexing [NM_152578] -indexing [MSTRG.874] -indexing [MSTRG.288] -indexing [NM_005369] -indexing [MSTRG.347] -indexing [NM_001172739] -indexing [NM_001291867] -indexing [NM_054021] -indexing [MSTRG.647] -indexing [MSTRG.887] -indexing [NM_016954] -indexing [NM_022076] -indexing [MSTRG.152] -indexing [NR_024062] -indexing [NM_001201583] -indexing [MSTRG.948] -indexing [NM_001007551] -indexing [NM_001128834] -indexing [NM_001001344] -indexing [MSTRG.342] -indexing [NM_001002254] -indexing [NM_001144008] -indexing [MSTRG.345] -indexing [MSTRG.311] -indexing [NM_020717] -indexing [MSTRG.642] -indexing [MSTRG.438] -indexing [MSTRG.478] -indexing [NM_001305004] -indexing [NR_033773] -indexing [NM_001009609] -indexing [NM_001098413] -indexing [NM_138289] -indexing [NM_001161530] -indexing [NM_001144004] -indexing [MSTRG.680] -indexing [MSTRG.840] -indexing [NM_013364] -indexing [NR_002784] -indexing [NM_024689] -indexing [MSTRG.104] -indexing [NM_001184837] -indexing [NM_139250] -indexing [NM_173493] -indexing [MSTRG.380] -indexing [MSTRG.750] -indexing [MSTRG.118] -indexing [MSTRG.283] -indexing [NM_130777] -indexing [NM_001287759] -indexing [NM_024859] -indexing [NM_021804] -indexing [NM_005366] -indexing [NM_001184704] -indexing [MSTRG.1036] -indexing [NM_005193] -indexing [NM_000898] -indexing [NM_001282849] -indexing [MSTRG.540] -indexing [MSTRG.116] -indexing [NM_001013579] -indexing [MSTRG.281] -indexing [NM_021083] -indexing [NM_001170553] -indexing [MSTRG.917] -indexing [NM_032539] -indexing [MSTRG.147] -indexing [MSTRG.92] -indexing [MSTRG.476] -indexing [MSTRG.124] -indexing [MSTRG.655] -indexing [NM_001017438] -indexing [NM_001097605] -indexing [NM_139282] -indexing [MSTRG.352] -indexing [MSTRG.1009] -indexing [MSTRG.958] -indexing [NM_001184880] -indexing [NM_001193277] -indexing [MSTRG.574] -indexing [MSTRG.111] -indexing [MSTRG.16] -indexing [MSTRG.145] -indexing [NM_001173486] -indexing [MSTRG.1058] -indexing [MSTRG.734] -indexing [NM_175743] -indexing [MSTRG.142] -indexing [NM_005361] -indexing [MSTRG.657] -indexing [MSTRG.1028] -indexing [NR_027419] -indexing [MSTRG.113] -indexing [MSTRG.286] -indexing [NM_005363] -indexing [NM_001011543] -indexing [NM_001316888] -indexing [MSTRG.471] -indexing [NR_002191] -indexing [NM_130775] -indexing [MSTRG.431] -indexing [MSTRG.604] -indexing [NM_000451] -indexing [MSTRG.433] -indexing [MSTRG.473] -indexing [MSTRG.180] -indexing [NM_001039582] -indexing [MSTRG.912] -indexing [NM_001171192] -indexing [MSTRG.915] -indexing [MSTRG.9] -indexing [MSTRG.704] -indexing [NM_001163334] -indexing [NM_001015038] -indexing [NM_203408] -indexing [NM_057162] -indexing [NM_001256790] -indexing [NM_001097596] -indexing [MSTRG.518] -indexing [MSTRG.718] -indexing [NR_027121] -indexing [NM_173358] -indexing [NM_001013742] -indexing [NM_001312891] -indexing [NM_001303513] -indexing [NM_001306193] -indexing [NM_001184924] -indexing [NM_000307] -indexing [NM_001009615] -indexing [NM_006140] -indexing [NM_001271752] -indexing [NM_001163257] -indexing [MSTRG.816] -indexing [NR_027760] -indexing [NM_003446] -indexing [NM_021118] -indexing [MSTRG.497] -indexing [MSTRG.387] -indexing [NM_001139502] -indexing [MSTRG.248] -indexing [NM_022144] -indexing [MSTRG.401] -indexing [MSTRG.634] -indexing [NM_000354] -indexing [MSTRG.403] -indexing [NM_000166] -indexing [MSTRG.687] -indexing [MSTRG.824] -indexing [MSTRG.334] -indexing [NM_021048] -indexing [MSTRG.1063] -indexing [NM_001080143] -indexing [NM_018969] -indexing [MSTRG.428] -indexing [MSTRG.813] -indexing [NM_001184833] -indexing [MSTRG.382] -indexing [MSTRG.552] -indexing [NM_001118886] -indexing [MSTRG.988] -indexing [MSTRG.685] -indexing [MSTRG.845] -indexing [NM_001017978] -indexing [MSTRG.719] -indexing [MSTRG.519] -indexing [MSTRG.45] -indexing [NM_153834] -indexing [NM_138382] -indexing [MSTRG.682] -indexing [MSTRG.842] -indexing [NM_001143982] -indexing [NM_172377] -indexing [NM_021049] -indexing [NM_001079855] -indexing [MSTRG.1033] -indexing [MSTRG.640] -indexing [MSTRG.406] -indexing [MSTRG.79] -indexing [NM_001166401] -indexing [MSTRG.251] -indexing [NM_032803] -indexing [NM_000273] -indexing [NM_001079859] -indexing [NM_152631] -indexing [MSTRG.294] -indexing [MSTRG.340] -indexing [NM_001122716] -indexing [MSTRG.249] -indexing [MSTRG.253] -indexing [NM_001098624] -indexing [NM_015686] -indexing [NM_021949] -indexing [NM_001170752] -indexing [NM_001013435] -indexing [MSTRG.1020] -indexing [MSTRG.814] -indexing [MSTRG.179] -indexing [MSTRG.592] -indexing [NM_001042506] -indexing [MSTRG.139] -indexing [MSTRG.1050] -indexing [MSTRG.795] -indexing [NM_001024452] -indexing [MSTRG.595] -indexing [NM_173699] -indexing [NM_016249] -indexing [MSTRG.207] -indexing [MSTRG.706] -indexing [MSTRG.419] -indexing [MSTRG.1043] -indexing [MSTRG.291] -indexing [NM_001172285] -indexing [MSTRG.376] -indexing [MSTRG.75] -indexing [NM_198512] -indexing [NM_138636] -indexing [MSTRG.826] -indexing [MSTRG.336] -indexing [MSTRG.528] -indexing [MSTRG.1052] -indexing [MSTRG.68] -indexing [MSTRG.865] -indexing [NM_013453] -indexing [MSTRG.293] -indexing [MSTRG.636] -indexing [MSTRG.676] -indexing [MSTRG.455] -indexing [MSTRG.728] -indexing [MSTRG.862] -indexing [NM_175698] -indexing [MSTRG.1001] -indexing [NM_000475] -indexing [MSTRG.254] -indexing [NM_005183] -indexing [MSTRG.190] -indexing [MSTRG.503] -indexing [MSTRG.268] -indexing [NR_037183] -indexing [NM_182506] -indexing [NR_102268] -indexing [NM_004143] -indexing [NR_002216] -indexing [NM_173698] -indexing [NM_138703] -indexing [MSTRG.457] -indexing [MSTRG.701] -indexing [MSTRG.867] -indexing [MSTRG.1072] -indexing [NM_001164416] -indexing [MSTRG.138] -indexing [MSTRG.178] -indexing [NR_034116] -indexing [NM_000047] -indexing [NR_033742] -indexing [NM_144967] -indexing [MSTRG.729] -indexing [MSTRG.821] -indexing [MSTRG.331] -indexing [MSTRG.597] -indexing [MSTRG.371] -indexing [MSTRG.633] -indexing [MSTRG.797] -indexing [MSTRG.529] -indexing [MSTRG.1070] -indexing [MSTRG.673] -indexing [NM_001017931] -indexing [NM_004042] -indexing [MSTRG.404] -indexing [MSTRG.671] -indexing [NM_000240] -indexing [MSTRG.373] -indexing [MSTRG.205] -indexing [NM_001171878] -indexing [MSTRG.418] -indexing [MSTRG.333] -indexing [NM_003886] -indexing [NM_001177466] -indexing [MSTRG.697] -indexing [NM_032882] -indexing [MSTRG.573] -indexing [MSTRG.629] -indexing [NM_080832] -indexing [NM_205833] -indexing [MSTRG.963] -indexing [NM_001282504] -indexing [MSTRG.397] -indexing [NM_014725] -indexing [MSTRG.531] -indexing [NM_001171110] -indexing [MSTRG.329] -indexing [MSTRG.731] -indexing [MSTRG.839] -indexing [NM_020384] -indexing [MSTRG.108] -indexing [NM_005364] -indexing [NM_000381] -indexing [MSTRG.91] -indexing [MSTRG.961] -indexing [MSTRG.1074] -indexing [NM_173798] -indexing [MSTRG.14] -indexing [MSTRG.999] -indexing [NM_001170750] -indexing [NM_001195522] -indexing [MSTRG.301] -indexing [MSTRG.487] -indexing [MSTRG.603] -indexing [NM_031273] -indexing [NM_001171876] -indexing [MSTRG.474] -indexing [MSTRG.126] -indexing [MSTRG.272] -indexing [MSTRG.232] -indexing [NR_102272] -indexing [NM_152582] -indexing [NM_012216] -indexing [NM_001193280] -indexing [MSTRG.601] -indexing [MSTRG.303] -indexing [MSTRG.275] -indexing [MSTRG.284] -indexing [MSTRG.109] -indexing [MSTRG.167] -indexing [MSTRG.925] -indexing [NM_001193279] -indexing [MSTRG.838] -indexing [MSTRG.328] -indexing [MSTRG.1024] -indexing [MSTRG.922] -indexing [MSTRG.1046] -indexing [NM_003918] -indexing [NM_176819] -indexing [MSTRG.890] -indexing [MSTRG.1005] -indexing [MSTRG.628] -indexing [MSTRG.277] -indexing [NM_178471] -indexing [NM_004683] -indexing [MSTRG.237] -indexing [MSTRG.576] -indexing [NM_001243963] -indexing [NM_001172743] -indexing [MSTRG.695] -indexing [MSTRG.306] -indexing [MSTRG.1057] -indexing [MSTRG.760] -indexing [NM_000950] -indexing [NM_175868] -indexing [MSTRG.560] -indexing [NR_024359] -indexing [MSTRG.692] -indexing [NM_001048181] -indexing [MSTRG.606] -indexing [NM_001105243] -indexing [MSTRG.998] -indexing [NR_073450] -indexing [NM_199478] -indexing [NM_001139500] # Done! Coding region genome annotations provided as: transcripts.fasta.transdecoder.genome.\* exit 0 make[4]: Leaving directory '/build/transdecoder-5.0.1/sample_data/stringtie_example' make[3]: Leaving directory '/build/transdecoder-5.0.1/sample_data' make[2]: Leaving directory '/build/transdecoder-5.0.1' cd ./sample_data && for script in ./*/cleanme.pl; do $($script); done -removing file: blastp.outfmt6 -removing file: pfam.domtblout -removing file: pipeliner.7560.cmds -removing file: pipeliner.7835.cmds -removing file: test.genome.fasta -removing file: transcripts.bed -removing file: transcripts.fasta -removing file: transcripts.fasta.transdecoder.bed -removing file: transcripts.fasta.transdecoder.cds -removing file: transcripts.fasta.transdecoder.genome.bed -removing file: transcripts.fasta.transdecoder.genome.gff3 -removing file: transcripts.fasta.transdecoder.gff3 -removing file: transcripts.fasta.transdecoder.pep -removing file: transcripts.fasta.transdecoder_dir -removing file: transcripts.fasta.transdecoder_dir.__checkpoints -removing file: transcripts.gff3 -removing file: transcripts.gtf -removing file: genome.fasta -removing file: pasa.gene_trans_map.txt -removing file: pasa_assemblies.fasta -removing file: pasa_assemblies.fasta.transdecoder.bed -removing file: pasa_assemblies.fasta.transdecoder.cds -removing file: pasa_assemblies.fasta.transdecoder.genome.gff3 -removing file: pasa_assemblies.fasta.transdecoder.gff3 -removing file: pasa_assemblies.fasta.transdecoder.pep -removing file: pasa_assemblies.fasta.transdecoder_dir -removing file: pasa_assemblies.fasta.transdecoder_dir.__checkpoints -removing file: pasa_assemblies.gff3 -removing file: pasa_assemblies_described.txt -removing file: pipeliner.17667.cmds -removing file: pipeliner.19074.cmds -removing file: genome_alignments.gmap.gff3 -removing file: pipeliner.27300.cmds -removing file: pipeliner.29900.cmds -removing file: Trinity.fasta -removing file: Trinity.fasta.transdecoder.bed -removing file: Trinity.fasta.transdecoder.cds -removing file: Trinity.fasta.transdecoder.genome.gff3 -removing file: Trinity.fasta.transdecoder.gff3 -removing file: Trinity.fasta.transdecoder.pep -removing file: Trinity.fasta.transdecoder_dir -removing file: Trinity.fasta.transdecoder_dir.__checkpoints -removing file: pipeliner.20857.cmds -removing file: pipeliner.31664.cmds -removing file: stringtie_merged.bed -removing file: stringtie_merged.gff3 -removing file: stringtie_merged.transcripts.fasta.transdecoder.bed -removing file: stringtie_merged.transcripts.fasta.transdecoder.cds -removing file: stringtie_merged.transcripts.fasta.transdecoder.genome.bed -removing file: stringtie_merged.transcripts.fasta.transdecoder.genome.gff3 -removing file: stringtie_merged.transcripts.fasta.transdecoder.gff3 -removing file: stringtie_merged.transcripts.fasta.transdecoder.pep -removing file: stringtie_merged.transcripts.fasta.transdecoder_dir -removing file: stringtie_merged.transcripts.fasta.transdecoder_dir.__checkpoints make[1]: Leaving directory '/build/transdecoder-5.0.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/transdecoder-5.0.1' dh_install find debian/transdecoder -name '*.p?' | xargs sed -i \ 's=^#!/usr/local/bin/perl=#!/usr/bin/perl=' find debian/*/usr/lib/transdecoder -type d -empty -delete make[1]: Leaving directory '/build/transdecoder-5.0.1' debian/rules override_dh_installdocs make[1]: Entering directory '/build/transdecoder-5.0.1' dh_installdocs for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/transdecoder/usr/lib/transdecoder/util/__pwm_tests/pasa_assemblies.fasta.gz: No such file or directory make[1]: Leaving directory '/build/transdecoder-5.0.1' dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/transdecoder-5.0.1' pod2man --section=1 --center="Transcriptome Protein Prediction" \ --release="5.0.1" TransDecoder.LongOrfs > \ debian/TransDecoder.LongOrfs.1 pod2man --section=1 --center="Transcriptome Protein Prediction" \ --release="5.0.1" TransDecoder.Predict > \ debian/TransDecoder.Predict.1 dh_installman make[1]: Leaving directory '/build/transdecoder-5.0.1' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/transdecoder-5.0.1' dh_fixperms chmod -x debian/transdecoder/usr/lib/transdecoder/PerlLib/Fasta_retriever.pm find debian -name Process_cmd.pm -exec chmod -x \{\} \; make[1]: Leaving directory '/build/transdecoder-5.0.1' dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'transdecoder' in '../transdecoder_5.0.1-2_all.deb'. dpkg-deb: building package 'transdecoder-doc' in '../transdecoder-doc_5.0.1-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../transdecoder_5.0.1-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/2479/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2479/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2479 and its subdirectories I: Current time: Thu Nov 5 16:23:27 +14 2020 I: pbuilder-time-stamp: 1604543007