Diff of the two buildlogs: -- --- b1/build.log 2022-01-10 01:48:14.170634569 +0000 +++ b2/build.log 2022-01-10 04:32:24.866446148 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 11 19:36:58 -12 2023 -I: pbuilder-time-stamp: 1676187418 +I: Current time: Mon Jan 10 15:48:21 +14 2022 +I: pbuilder-time-stamp: 1641779301 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./spades_3.13.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.M9ftsnOO/trustedkeys.kbx': General error -gpgv: Signature made Thu Nov 21 21:49:38 2019 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.6FdvCLj5/trustedkeys.kbx': General error +gpgv: Signature made Fri Nov 22 23:49:38 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key @@ -45,135 +45,169 @@ dpkg-source: info: applying yaml_load.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1777496/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/696983/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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/696983/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/696983/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3191333a33a94739977cb5084186d29b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1777496' - PS1='# ' - PS2='> ' + INVOCATION_ID=60165f42cb91484ea47951b5cc5009b7 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=696983 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.QpjsReePDq/pbuilderrc_2hAm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QpjsReePDq/b1 --logfile b1/build.log spades_3.13.1+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.QpjsReePDq/pbuilderrc_P554 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QpjsReePDq/b2 --logfile b2/build.log spades_3.13.1+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 9 03:46 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1777496/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jan 10 15:49 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 7 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/696983/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -369,7 +403,7 @@ Get: 120 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4 [213 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] -Fetched 67.1 MB in 1s (62.4 MB/s) +Fetched 67.1 MB in 5s (12.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -888,7 +922,8 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/spades-3.13.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_3.13.1+dfsg-2_source.changes +hostname: Name or service not known +I: Running cd /build/spades-3.13.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_3.13.1+dfsg-2_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.13.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -11871,7 +11906,7 @@ System information: SPAdes version: 3.13.1 Python version: 3.9.2 - OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31 + OS: Linux-5.10.0-10-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-3.13.1+dfsg/spades_test Mode: read error correction and assembling @@ -11913,59 +11948,59 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info - 0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset - 0:00:00.001 4M / 4M INFO General (main.cpp : 92) Determined value is 33 - 0:00:00.001 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] - 0:00:00.001 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes + 0:00:00.007 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.007 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb + 0:00:00.007 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset + 0:00:00.027 4M / 4M INFO General (main.cpp : 92) Determined value is 33 + 0:00:00.028 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] + 0:00:00.028 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === - 0:00:00.001 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:03.921 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:04.040 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:04.142 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed - 0:00:04.682 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.090 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. - 0:00:05.090 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.121 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:05.514 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:05.515 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). - 0:00:05.515 64M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order - 0:00:05.558 64M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. - 0:00:05.674 64M / 8G INFO General (main.cpp : 155) Extracting clusters - 0:00:05.742 64M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 - 0:00:05.742 64M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. - 0:00:05.742 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:05.838 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:05.942 64M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. - 0:00:05.942 64M / 8G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. - 0:00:05.942 64M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 - 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) - 0:00:05.966 64M / 8G INFO General (main.cpp : 178) Finished clustering. - 0:00:05.966 64M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. - 0:00:06.082 64M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. - 0:00:06.082 64M / 8G INFO General (main.cpp : 222) Solid k-mers finalized - 0:00:06.082 64M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. - 0:00:06.082 64M / 8G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:06.311 408M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. - 0:00:06.348 408M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 - 0:00:06.353 408M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 - 0:00:06.432 64M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. - 0:00:06.432 64M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. - 0:00:06.432 64M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml - 0:00:06.432 64M / 8G INFO General (main.cpp : 262) All done. Exiting. + 0:00:00.028 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.028 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.028 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.028 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:00.219 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:00.451 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:00.607 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed + 0:00:01.113 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.303 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. + 0:00:01.303 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.350 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:02.279 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:02.280 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). + 0:00:02.280 60M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order + 0:00:02.339 60M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. + 0:00:02.427 60M / 8G INFO General (main.cpp : 155) Extracting clusters + 0:00:02.512 60M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 + 0:00:02.512 60M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. + 0:00:02.512 60M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:02.679 60M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:02.851 60M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. + 0:00:02.851 60M / 8G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. + 0:00:02.851 60M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 + 0:00:02.915 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) + 0:00:02.915 60M / 8G INFO General (main.cpp : 178) Finished clustering. + 0:00:02.915 60M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 15 threads. + 0:00:03.155 60M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. + 0:00:03.155 60M / 8G INFO General (main.cpp : 222) Solid k-mers finalized + 0:00:03.155 60M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 15 threads. + 0:00:03.155 60M / 8G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:04.433 388M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. + 0:00:04.483 388M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 + 0:00:04.509 388M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 + 0:00:05.080 60M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. + 0:00:05.080 60M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. + 0:00:05.081 60M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml + 0:00:05.081 60M / 8G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) @@ -11981,195 +12016,195 @@ == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K21/configs/config.info - 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.001 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A - 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 - 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=21 - 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.001 4M / 4M INFO General (launch.hpp : 52) SPAdes started - 0:00:00.001 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction - 0:00:00.001 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads - 0:00:00.135 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written - 0:00:00.137 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:00.333 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.334 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:00.560 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.567 4M / 140M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.567 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.567 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.567 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.568 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.568 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.568 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:04.527 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:05.069 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:05.069 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.455 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. - 0:00:05.455 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.492 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:05.492 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:05.492 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:05.492 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:05.492 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:05.492 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:09.055 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. - 0:00:09.585 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.935 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. - 0:00:09.935 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.963 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.631 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:10.632 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). - 0:00:10.632 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:10.687 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:10.687 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:10.687 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:10.687 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:10.763 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper - 0:00:10.763 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:10.763 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:10.779 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:10.807 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:10.827 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:10.887 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:10.887 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.887 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:11.267 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). - 0:00:11.267 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:11.339 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:11.391 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 - 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 - 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 - 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model - 0:00:11.591 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 - 0:00:11.877 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 - 0:00:12.328 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 - 0:00:13.025 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 - 0:00:14.162 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 - 0:00:16.925 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 - 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 - 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 - 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 - 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 - 0:00:16.927 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 342.845 - 0:00:16.927 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171 - 0:00:16.927 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:16.927 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:16.927 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:16.928 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:16.928 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:16.951 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:16.951 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:16.999 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:16.999 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:17.039 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:17.039 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:17.067 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:17.067 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:17.067 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:17.067 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:17.067 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:17.067 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.099 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.099 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.131 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.131 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.175 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.175 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.199 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.199 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.227 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.227 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:17.227 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:17.227 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled - 0:00:17.227 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled - 0:00:17.227 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:17.227 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.255 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.255 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.271 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.271 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.295 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.295 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.319 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.319 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:17.319 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:17.339 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:17.339 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:17.339 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 - 0:00:17.339 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:17.339 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta - 0:00:17.339 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:17.339 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 17 seconds + 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb + 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A + 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 + 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=21 + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started + 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction + 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 + 0:00:00.010 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) + 0:00:00.010 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads + 0:00:00.434 124M / 132M INFO General (binary_converter.hpp : 117) 2054 reads written + 0:00:00.477 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:01.274 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:01.333 4M / 196M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:02.009 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:02.058 4M / 196M INFO General (construction.cpp : 111) Max read length 100 + 0:00:02.058 4M / 196M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:02.058 4M / 196M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:02.058 4M / 196M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:02.059 4M / 196M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:02.059 4M / 196M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:02.059 4M / 196M INFO General (kmer_splitters.hpp : 97) Using cell size of 298261 + 0:00:02.341 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:02.692 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:02.693 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.821 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. + 0:00:02.821 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.854 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:02.855 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:02.855 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:02.855 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:02.855 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:02.855 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:03.121 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. + 0:00:03.576 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:03.681 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. + 0:00:03.681 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:03.727 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:04.625 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:04.626 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). + 0:00:04.626 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:04.673 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:04.673 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:04.673 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:04.673 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:04.749 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper + 0:00:04.749 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:04.749 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:04.805 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:04.845 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:04.885 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:04.969 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:04.969 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:04.969 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:05.609 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (74.7967 bits per kmer). + 0:00:05.609 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:05.653 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:05.709 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:05.710 60M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 + 0:00:05.710 60M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 + 0:00:05.710 60M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 + 0:00:05.710 60M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model + 0:00:06.435 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 + 0:00:07.953 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 + 0:00:10.056 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 + 0:00:12.864 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 + 0:00:16.949 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 + 0:00:26.484 60M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 + 0:00:26.498 60M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 + 0:00:26.498 60M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 + 0:00:26.498 60M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 + 0:00:26.498 60M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 + 0:00:26.498 60M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 342.845 + 0:00:26.498 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171 + 0:00:26.498 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:26.498 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:26.498 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:26.498 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:26.498 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:26.521 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:26.521 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:26.553 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:26.553 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:26.585 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:26.585 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:26.625 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:26.625 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:26.625 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:26.625 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:26.625 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:26.625 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.665 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.665 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.709 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.709 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.776 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.776 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.776 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.776 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:26.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.813 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.813 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.849 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.849 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:26.893 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:26.893 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:26.893 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:26.893 60M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled + 0:00:26.893 60M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled + 0:00:26.893 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:26.893 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:26.925 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:26.925 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:26.973 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:26.973 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:27.009 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:27.009 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:27.045 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:27.045 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:27.045 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:27.077 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:27.077 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:27.077 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 + 0:00:27.077 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:27.077 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta + 0:00:27.077 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:27.077 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 27 seconds Max read length detected as 100 == Running assembler: K33 @@ -12179,505 +12214,505 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=33 - 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected + 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. + 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:03.913 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:04.575 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:04.575 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.028 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. - 0:00:05.028 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.053 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:05.053 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:05.053 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:05.053 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:05.053 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:05.053 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:08.949 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. - 0:00:09.550 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.944 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. - 0:00:09.944 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.336 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:10.338 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). - 0:00:10.338 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:10.460 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:10.460 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:10.460 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:10.460 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:10.572 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper - 0:00:10.572 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:10.572 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:10.612 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:10.644 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:10.676 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:10.744 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:10.744 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.744 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:11.156 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). - 0:00:11.156 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:11.244 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:11.293 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 - 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 - 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 - 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model - 0:00:11.390 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 - 0:00:11.565 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 - 0:00:11.757 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 - 0:00:11.936 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 - 0:00:12.274 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 - 0:00:12.967 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 - 0:00:14.437 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 - 0:00:16.275 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 - 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 - 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 - 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 - 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 - 0:00:16.277 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 108.181 - 0:00:16.277 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 3 - 0:00:16.277 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:16.277 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:16.277 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:16.277 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:16.277 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:16.300 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:16.300 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:16.340 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:16.340 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:16.376 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:16.376 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:16.404 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:16.404 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:16.404 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:16.404 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:16.404 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:16.404 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.432 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.432 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.456 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.456 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.500 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.500 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.512 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.512 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.524 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.524 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:16.524 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:16.524 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled - 0:00:16.524 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled - 0:00:16.524 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:16.524 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.540 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.540 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.557 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.557 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.580 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.580 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.592 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.592 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:16.592 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:16.604 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:16.604 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:16.604 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 - 0:00:16.604 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:16.604 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta - 0:00:16.605 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:16.605 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 16 seconds + 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.451 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:01.009 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:01.009 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.148 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. + 0:00:01.148 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.185 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.185 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.185 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.186 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.186 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.186 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.559 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. + 0:00:02.085 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.307 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. + 0:00:02.307 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.357 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:03.304 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:03.304 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). + 0:00:03.304 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:03.363 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:03.364 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:03.364 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:03.364 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:03.451 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper + 0:00:03.451 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:03.452 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:03.476 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:03.519 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:03.563 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:03.647 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:03.647 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:03.647 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:04.255 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (75.7202 bits per kmer). + 0:00:04.255 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:04.307 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:04.356 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:04.356 60M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 + 0:00:04.356 60M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 + 0:00:04.356 60M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 + 0:00:04.356 60M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model + 0:00:04.605 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 + 0:00:05.033 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 + 0:00:05.534 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 + 0:00:06.202 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 + 0:00:07.666 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 + 0:00:10.503 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 + 0:00:16.249 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 + 0:00:23.604 60M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 + 0:00:23.604 60M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 + 0:00:23.604 60M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 + 0:00:23.604 60M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 + 0:00:23.604 60M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 + 0:00:23.604 60M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 108.181 + 0:00:23.604 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 3 + 0:00:23.604 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:23.604 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:23.604 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:23.604 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:23.604 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:23.615 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:23.615 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:23.663 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:23.663 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:23.703 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:23.703 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:23.750 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:23.750 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:23.750 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:23.750 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:23.750 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:23.750 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.783 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.783 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.828 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.828 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.867 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.867 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:23.867 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.867 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.867 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.868 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:23.868 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:23.899 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:23.899 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:23.939 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:23.939 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:23.975 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:23.976 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:23.976 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:23.976 60M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled + 0:00:23.976 60M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled + 0:00:23.976 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:23.976 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:24.015 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:24.015 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:24.043 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:24.043 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:24.083 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:24.083 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:24.115 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:24.115 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:24.116 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:24.164 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:24.165 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:24.165 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 + 0:00:24.165 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:24.165 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta + 0:00:24.165 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:24.165 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 24 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K55/configs/config.info - 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A - 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 - 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=55 - 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started - 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction - 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.000 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected - 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:03.672 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:04.206 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:04.206 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:04.624 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:04.624 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:04.647 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:04.656 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:04.656 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:04.656 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:04.656 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:04.656 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:08.401 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. - 0:00:08.972 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.324 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. - 0:00:09.324 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.350 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:09.772 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:09.772 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). - 0:00:09.773 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:09.850 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:09.851 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:09.851 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:09.884 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted - 0:00:09.916 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:09.940 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:09.980 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:09.980 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:09.980 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.312 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:10.312 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:10.356 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:10.412 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 - 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 - 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 - 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model - 0:00:10.489 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 - 0:00:10.533 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 - 0:00:10.652 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 - 0:00:10.833 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 - 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 - 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 - 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 - 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 - 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 - 0:00:10.992 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 13.7375 - 0:00:10.992 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 1 - 0:00:10.992 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:10.992 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:10.992 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:10.992 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.992 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:10.993 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:10.993 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:10.993 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:14.596 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. - 0:00:15.125 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:15.472 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:15.472 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:15.499 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:15.800 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:15.801 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:15.801 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:15.848 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:15.848 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:15.848 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:15.884 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:15.884 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:15.884 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:15.884 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates - 0:00:15.924 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:15.924 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:15.924 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:15.924 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:15.956 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:15.956 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:15.996 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:15.996 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:16.032 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:16.032 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:16.060 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times - 0:00:16.060 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:16.060 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:16.060 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:16.060 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:16.060 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.088 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times - 0:00:16.088 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.120 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.120 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.192 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.192 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.216 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.216 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.240 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.240 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:16.240 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:16.240 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:16.240 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:16.240 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:16.240 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:16.240 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:19.956 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:20.519 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:20.896 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. - 0:00:20.896 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:20.926 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:21.320 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:21.320 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). - 0:00:21.321 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:21.368 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:21.369 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:21.369 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:21.438 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:21.438 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:21.438 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:21.438 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:21.488 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:21.488 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:21.488 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled - 0:00:21.488 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled - 0:00:21.488 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:21.488 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.532 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.532 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.584 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.584 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.624 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.624 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.664 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:21.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:21.684 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:21.684 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:21.684 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 - 0:00:21.684 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction - 0:00:21.684 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:21.684 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:21.718 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions - 0:00:21.718 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed - 0:00:21.718 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides - 0:00:21.718 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:21.718 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:21.718 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta - 0:00:21.719 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg - 0:00:21.719 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta - 0:00:21.719 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting - 0:00:21.719 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:21.719 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:21.719 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 945 - 0:00:21.719 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 - 0:00:21.719 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:21.932 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:22.811 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:22.916 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:22.916 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges - 0:00:22.919 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 - 0:00:23.028 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 - 0:00:23.029 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:23.045 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:23.045 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 - 0:00:23.045 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) - 0:00:23.045 256M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 2, rounding threshold 0 - 0:00:23.058 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:23.076 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:23.087 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation - 0:00:23.087 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:23.087 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:23.087 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:23.096 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:23.096 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:23.136 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:23.179 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:23.179 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index - 0:00:23.179 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator - 0:00:23.188 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:23.188 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:23.188 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:23.188 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index - 0:00:23.188 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving - 0:00:23.188 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 - 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 - 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library - 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library - 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:23.188 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished - 0:00:23.188 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:23.188 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:23.188 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta - 0:00:23.188 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg - 0:00:23.188 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths - 0:00:23.189 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths - 0:00:23.189 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:23.189 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 23 seconds + 0:00:00.017 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb + 0:00:00.017 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A + 0:00:00.017 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 + 0:00:00.017 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=55 + 0:00:00.017 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.017 4M / 4M INFO General (launch.hpp : 52) SPAdes started + 0:00:00.017 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction + 0:00:00.017 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 + 0:00:00.017 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached + 0:00:00.017 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.018 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected + 0:00:00.018 4M / 4M INFO General (construction.cpp : 111) Max read length 100 + 0:00:00.018 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:00.018 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:00.018 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:00.019 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.019 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.019 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.373 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.894 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.894 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.065 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:01.065 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.111 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.111 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.111 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.112 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.112 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.112 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.421 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. + 0:00:01.894 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.045 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. + 0:00:02.045 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.089 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:03.121 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:03.122 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). + 0:00:03.122 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:03.165 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:03.166 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:03.166 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:03.209 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted + 0:00:03.257 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:03.297 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:03.401 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:03.401 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:03.401 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:04.057 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9168 bytes occupied (77.2856 bits per kmer). + 0:00:04.057 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:04.105 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:04.134 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:04.134 60M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 + 0:00:04.134 60M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 + 0:00:04.134 60M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 + 0:00:04.134 60M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model + 0:00:04.209 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 + 0:00:04.406 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 + 0:00:05.015 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 + 0:00:05.763 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 + 0:00:06.338 60M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 + 0:00:06.338 60M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 + 0:00:06.338 60M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 + 0:00:06.338 60M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 + 0:00:06.338 60M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 + 0:00:06.338 60M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 13.7375 + 0:00:06.338 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 1 + 0:00:06.338 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:06.338 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:06.338 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:06.339 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:06.339 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:06.339 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:06.339 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:06.339 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:06.667 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. + 0:00:07.133 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:07.257 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:07.257 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:07.305 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:08.077 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:08.078 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). + 0:00:08.078 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:08.110 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:08.110 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:08.110 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:08.141 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:08.141 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:08.141 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:08.141 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates + 0:00:08.177 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:08.177 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:08.178 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:08.178 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:08.209 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:08.209 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:08.245 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:08.245 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:08.281 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:08.281 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:08.317 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times + 0:00:08.317 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:08.317 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:08.317 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:08.317 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:08.317 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.369 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times + 0:00:08.369 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.385 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.385 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.433 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.433 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.433 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.433 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.433 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.434 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.434 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.434 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.434 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.434 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.434 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:08.434 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.469 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.469 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.501 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.501 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.545 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.545 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:08.546 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:08.546 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:08.546 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:08.546 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:08.546 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:08.546 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:08.983 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:09.436 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:09.557 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. + 0:00:09.557 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:09.592 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:10.417 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:10.418 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). + 0:00:10.418 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:10.446 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:10.446 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:10.446 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:10.494 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:10.494 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:10.494 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:10.494 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:10.529 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:10.529 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:10.529 60M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled + 0:00:10.529 60M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled + 0:00:10.529 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:10.529 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:10.581 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:10.581 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:10.601 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:10.602 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:10.657 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:10.657 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:10.677 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:10.677 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:10.677 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:10.725 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:10.725 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:10.725 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 + 0:00:10.725 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction + 0:00:10.725 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:10.726 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:10.748 60M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions + 0:00:10.748 60M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed + 0:00:10.748 60M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides + 0:00:10.748 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:10.748 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:10.749 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta + 0:00:10.749 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg + 0:00:10.749 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta + 0:00:10.749 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting + 0:00:10.749 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:10.749 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:10.749 60M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 945 + 0:00:10.749 60M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 + 0:00:10.749 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:11.535 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:14.674 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:15.103 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:15.104 316M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges + 0:00:15.253 60M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 + 0:00:15.931 252M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 + 0:00:15.931 252M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:15.949 252M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:15.950 252M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 + 0:00:15.950 252M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) + 0:00:15.950 252M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 2, rounding threshold 0 + 0:00:16.019 264M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:16.057 264M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:16.229 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation + 0:00:16.229 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:16.229 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:16.229 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:16.245 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:16.245 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:16.245 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:16.245 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:16.245 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:16.245 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:16.333 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:16.417 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:16.417 60M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index + 0:00:16.417 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator + 0:00:16.469 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:16.469 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:16.469 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:16.469 60M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index + 0:00:16.469 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving + 0:00:16.469 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:16.469 60M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started + 0:00:16.469 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:16.470 60M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 + 0:00:16.470 60M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 + 0:00:16.470 60M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library + 0:00:16.470 60M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library + 0:00:16.470 60M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:16.470 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:16.470 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:16.470 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:16.470 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:16.470 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:16.470 60M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished + 0:00:16.470 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:16.470 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:16.470 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta + 0:00:16.470 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg + 0:00:16.470 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths + 0:00:16.470 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths + 0:00:16.471 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:16.471 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 16 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 @@ -12702,7 +12737,7 @@ System information: SPAdes version: 3.13.1 Python version: 3.9.2 - OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31 + OS: Linux-5.10.0-10-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-3.13.1+dfsg/spades_test Mode: read error correction and assembling @@ -12743,71 +12778,71 @@ == Running read error correction tool: /build/spades-3.13.1+dfsg/install_spades/bin/spades-hammer /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A - 0:00:00.008 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info - 0:00:00.009 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.009 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.009 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset - 0:00:00.009 4M / 4M INFO General (main.cpp : 92) Determined value is 33 - 0:00:00.009 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] - 0:00:00.009 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes + 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info + 0:00:00.000 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb + 0:00:00.000 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset + 0:00:00.001 4M / 4M INFO General (main.cpp : 92) Determined value is 33 + 0:00:00.001 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] + 0:00:00.001 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === - 0:00:00.009 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count - 0:00:00.167 260M / 260M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:00.244 320M / 320M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:00.280 320M / 320M INFO K-mer Counting (kmer_data.cpp : 299) Total 4108 reads processed - 0:00:01.095 64M / 320M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers + 0:00:00.001 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count + 0:00:00.965 244M / 244M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:01.103 300M / 300M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:01.211 300M / 300M INFO K-mer Counting (kmer_data.cpp : 299) Total 4108 reads processed + 0:00:04.299 60M / 300M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers 38 8 0 nslots: 1073741824 bits per slot: 8 range: 0000004000000000 - 0:00:01.095 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:01.332 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:01.500 1G / 1G INFO K-mer Counting (kmer_data.cpp : 331) Total 4108 reads processed - 0:00:01.500 1G / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:01.500 1G / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:01.500 1G / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:01.500 1G / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.951416 Gb - 0:00:01.500 1G / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:05.229 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:05.308 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:05.388 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed - 0:00:05.913 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:06.308 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. - 0:00:06.308 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:06.344 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:06.892 1G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:06.893 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). - 0:00:06.906 64M / 10G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order - 0:00:06.920 64M / 10G INFO General (main.cpp : 148) Clustering Hamming graph. - 0:00:06.972 64M / 10G INFO General (main.cpp : 155) Extracting clusters - 0:00:07.012 64M / 10G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 - 0:00:07.012 64M / 10G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. - 0:00:07.012 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:07.100 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:07.200 64M / 10G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. - 0:00:07.200 64M / 10G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. - 0:00:07.200 64M / 10G INFO General (main.cpp : 173) Subclustering Hamming graph - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 - 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) - 0:00:07.220 64M / 10G INFO General (main.cpp : 178) Finished clustering. - 0:00:07.220 64M / 10G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. - 0:00:07.344 64M / 10G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. - 0:00:07.344 64M / 10G INFO General (main.cpp : 222) Solid k-mers finalized - 0:00:07.344 64M / 10G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. - 0:00:07.344 64M / 10G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:07.567 408M / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. - 0:00:07.586 408M / 10G INFO General (hammer_tools.cpp : 175) Processed batch 0 - 0:00:07.592 408M / 10G INFO General (hammer_tools.cpp : 185) Written batch 0 - 0:00:07.672 64M / 10G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. - 0:00:07.672 64M / 10G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. - 0:00:07.672 64M / 10G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml - 0:00:07.672 64M / 10G INFO General (main.cpp : 262) All done. Exiting. + 0:00:04.299 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:04.599 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:04.875 1G / 1G INFO K-mer Counting (kmer_data.cpp : 331) Total 4108 reads processed + 0:00:04.875 1G / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:04.875 1G / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:04.875 1G / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:04.875 1G / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.01493 Gb + 0:00:04.876 1G / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:05.211 9G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:05.379 9G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:05.571 9G / 9G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed + 0:00:06.130 1G / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:06.343 1G / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. + 0:00:06.343 1G / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:06.390 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:07.351 1G / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:07.352 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). + 0:00:07.402 60M / 9G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order + 0:00:07.447 60M / 9G INFO General (main.cpp : 148) Clustering Hamming graph. + 0:00:07.551 60M / 9G INFO General (main.cpp : 155) Extracting clusters + 0:00:07.628 60M / 9G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 + 0:00:07.628 60M / 9G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. + 0:00:07.628 60M / 9G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:07.811 60M / 9G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:07.967 60M / 9G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. + 0:00:07.967 60M / 9G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. + 0:00:07.967 60M / 9G INFO General (main.cpp : 173) Subclustering Hamming graph + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 + 0:00:08.011 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) + 0:00:08.011 60M / 9G INFO General (main.cpp : 178) Finished clustering. + 0:00:08.011 60M / 9G INFO General (main.cpp : 197) Starting solid k-mers expansion in 15 threads. + 0:00:08.211 60M / 9G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. + 0:00:08.211 60M / 9G INFO General (main.cpp : 222) Solid k-mers finalized + 0:00:08.211 60M / 9G INFO General (hammer_tools.cpp : 220) Starting read correction in 15 threads. + 0:00:08.211 60M / 9G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:09.430 388M / 9G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. + 0:00:09.491 388M / 9G INFO General (hammer_tools.cpp : 175) Processed batch 0 + 0:00:09.513 388M / 9G INFO General (hammer_tools.cpp : 185) Written batch 0 + 0:00:09.852 60M / 9G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. + 0:00:09.852 60M / 9G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. + 0:00:09.852 60M / 9G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml + 0:00:09.853 60M / 9G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) @@ -12829,147 +12864,147 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=21 - 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.001 4M / 4M INFO General (launch.hpp : 52) SPAdes started - 0:00:00.001 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction - 0:00:00.001 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads - 0:00:00.130 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written - 0:00:00.132 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:00.332 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.333 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:00.545 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.548 4M / 140M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.548 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.548 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.548 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.549 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.549 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.549 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:04.442 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:05.035 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:05.035 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.460 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. - 0:00:05.460 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.497 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:05.497 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:05.497 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:05.498 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:05.498 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:05.498 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:09.216 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. - 0:00:09.855 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:10.212 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. - 0:00:10.212 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:10.232 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.628 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:10.629 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). - 0:00:10.629 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:10.700 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:10.701 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:10.701 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:10.701 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:10.772 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper - 0:00:10.773 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:10.773 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:10.788 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:10.820 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:10.836 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:10.884 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:10.884 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.884 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:11.101 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). - 0:00:11.101 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:11.168 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:11.216 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:11.216 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:11.216 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:11.216 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:11.247 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:11.247 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:11.279 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:11.279 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:11.308 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:11.308 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:11.352 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:11.352 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:11.352 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:11.353 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:11.353 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:11.353 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.376 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.376 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.401 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.401 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.440 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.440 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:11.440 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.440 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.441 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.441 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.459 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.459 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.475 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.475 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.490 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.490 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:11.490 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:11.490 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:11.490 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:11.506 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:11.507 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:11.522 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:11.523 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:11.539 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:11.544 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:11.553 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:11.553 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:11.587 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:11.587 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.603 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.603 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:11.617 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:11.617 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:11.635 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:11.635 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:11.665 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:11.665 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:11.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:11.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:11.724 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:11.724 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.738 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.744 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:11.754 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:11.754 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) - 0:00:11.768 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:11.768 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:11.784 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:11.784 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:11.784 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 - 0:00:11.784 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:11.785 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta - 0:00:11.785 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:11.785 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 11 seconds + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started + 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction + 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 + 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads + 0:00:00.537 124M / 132M INFO General (binary_converter.hpp : 117) 2054 reads written + 0:00:00.589 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:01.600 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:01.693 4M / 196M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:02.883 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:02.996 4M / 196M INFO General (construction.cpp : 111) Max read length 100 + 0:00:02.996 4M / 196M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:02.996 4M / 196M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:02.996 4M / 196M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:03.013 4M / 196M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:03.013 4M / 196M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:03.013 4M / 196M INFO General (kmer_splitters.hpp : 97) Using cell size of 298261 + 0:00:03.473 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:04.028 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:04.028 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:04.173 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. + 0:00:04.173 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:04.217 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:04.217 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:04.217 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:04.217 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:04.217 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:04.217 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:04.653 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. + 0:00:05.191 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:05.333 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. + 0:00:05.333 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:05.384 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:06.491 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:06.492 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). + 0:00:06.492 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:06.557 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:06.557 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:06.558 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:06.558 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:06.649 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper + 0:00:06.649 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:06.649 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:06.685 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:06.749 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:06.809 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:06.925 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:06.925 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:06.925 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:07.521 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (74.7967 bits per kmer). + 0:00:07.521 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:07.661 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:07.724 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:07.724 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:07.724 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:07.724 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:07.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:07.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:07.839 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:07.839 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:07.905 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:07.905 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:07.960 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:07.960 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:07.960 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:07.960 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:07.960 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:07.960 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:07.994 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:07.994 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.050 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.050 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.105 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.105 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.105 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:08.105 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.153 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.153 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.213 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.213 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.297 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.297 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:08.297 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:08.297 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:08.297 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:08.325 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:08.325 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:08.409 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:08.409 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:08.449 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:08.449 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:08.513 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:08.513 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.577 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.577 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:08.637 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:08.637 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.713 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.713 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:08.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:08.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:08.837 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:08.837 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:08.901 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:08.901 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:08.959 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:08.959 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:09.005 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:09.005 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.077 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.077 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:09.113 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:09.113 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.177 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.177 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:09.209 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:09.209 60M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) + 0:00:09.277 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:09.277 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:09.337 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:09.337 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:09.337 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 + 0:00:09.337 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:09.338 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta + 0:00:09.338 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:09.338 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 9 seconds Max read length detected as 100 == Running assembler: K33 @@ -12981,141 +13016,141 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=33 - 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. + 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:03.320 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:03.871 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:03.872 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:04.290 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. - 0:00:04.290 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:04.305 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:04.310 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:04.310 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:04.310 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:04.310 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:04.310 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:07.911 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. - 0:00:08.523 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:08.894 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. - 0:00:08.894 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:08.918 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:09.478 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:09.479 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). - 0:00:09.479 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:09.546 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:09.546 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:09.546 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:09.546 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:09.602 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper - 0:00:09.602 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:09.602 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:09.614 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:09.626 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:09.650 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:09.674 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:09.674 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:09.674 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.066 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). - 0:00:10.066 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:10.122 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:10.151 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:10.151 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:10.151 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:10.151 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:10.182 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:10.182 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:10.226 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:10.226 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:10.258 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:10.258 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:10.294 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:10.294 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:10.294 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:10.294 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:10.294 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:10.294 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.330 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.330 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.354 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.354 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.378 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.378 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.378 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.402 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.402 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.426 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.426 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.450 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.450 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:10.450 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:10.450 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:10.450 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:10.474 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:10.474 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:10.498 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:10.498 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:10.522 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:10.522 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:10.542 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:10.542 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.566 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.566 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:10.574 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:10.574 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.590 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.590 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:10.606 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:10.606 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:10.626 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:10.627 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:10.642 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:10.642 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:10.654 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:10.654 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:10.670 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:10.670 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.686 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.686 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:10.710 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:10.710 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.718 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.718 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:10.734 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:10.734 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) - 0:00:10.750 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:10.750 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:10.766 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:10.766 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:10.766 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 - 0:00:10.766 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:10.766 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta - 0:00:10.767 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:10.767 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 10 seconds + 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.579 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:01.317 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:01.317 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.519 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. + 0:00:01.519 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.592 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.592 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.592 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.592 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.592 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.592 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:02.015 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. + 0:00:02.689 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.807 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. + 0:00:02.807 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.853 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:03.723 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:03.724 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). + 0:00:03.724 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:03.759 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:03.759 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:03.759 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:03.759 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:03.863 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper + 0:00:03.863 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:03.863 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:03.914 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:03.967 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:03.996 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:04.119 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:04.119 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:04.119 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:04.743 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (75.7202 bits per kmer). + 0:00:04.743 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:04.791 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:04.847 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:04.847 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:04.847 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:04.847 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:04.871 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:04.871 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:04.922 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:04.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:04.951 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:04.951 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:04.998 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:04.999 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:04.999 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:04.999 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:04.999 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:04.999 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:05.051 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:05.051 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:05.103 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:05.103 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:05.155 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:05.155 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:05.155 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:05.155 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:05.203 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:05.203 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:05.259 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:05.259 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:05.307 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:05.307 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:05.307 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:05.307 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:05.307 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:05.354 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:05.355 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:05.382 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:05.383 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:05.411 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:05.411 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:05.487 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:05.487 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:05.538 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:05.539 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:05.587 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:05.587 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:05.638 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:05.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:05.690 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:05.691 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:05.739 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:05.739 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:05.791 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:05.791 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:05.867 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:05.867 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:05.891 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:05.891 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:05.967 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:05.967 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:06.015 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:06.015 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.071 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.071 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:06.119 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:06.119 60M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) + 0:00:06.170 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:06.171 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:06.194 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:06.195 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:06.195 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 + 0:00:06.195 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:06.195 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta + 0:00:06.195 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:06.195 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 6 seconds == Running assembler: K55 @@ -13126,410 +13161,410 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=55 - 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected - 0:00:00.005 4M / 4M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.005 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.005 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.005 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.005 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.005 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.005 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:03.829 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:04.418 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:04.418 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:04.829 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:04.829 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:04.865 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:04.865 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:04.865 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:04.866 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:04.866 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:04.866 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:08.410 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. - 0:00:08.937 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.285 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. - 0:00:09.285 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.301 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:09.777 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:09.778 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). - 0:00:09.778 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:09.833 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:09.833 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:09.833 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:09.869 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted - 0:00:09.913 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:09.933 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:09.977 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:09.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:09.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.489 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:10.489 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:10.513 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:10.546 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:10.546 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:10.546 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.546 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:10.546 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:10.546 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:10.546 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:14.325 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. - 0:00:14.914 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:15.265 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:15.265 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:15.290 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:15.721 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:15.722 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:15.722 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:15.757 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:15.758 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:15.758 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:15.793 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:15.793 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:15.793 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:15.793 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates - 0:00:15.813 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:15.813 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:15.813 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:15.837 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:15.837 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:15.861 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:15.861 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:15.881 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:15.881 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage - 0:00:15.893 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 0 times - 0:00:15.893 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:15.917 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times - 0:00:15.917 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification - 0:00:15.917 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:15.917 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:15.917 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:15.917 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.929 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times - 0:00:15.929 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.941 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.941 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.965 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.965 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.965 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.981 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.981 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.997 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.997 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.017 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.017 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:16.017 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:16.017 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:16.017 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:16.017 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:16.017 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:16.017 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:19.893 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:20.557 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:20.979 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. - 0:00:20.979 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:20.999 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:21.477 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:21.478 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). - 0:00:21.478 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:21.509 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:21.510 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:21.510 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:21.541 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:21.541 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:21.541 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:21.541 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:21.569 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting - 0:00:21.569 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:21.569 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:21.569 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 - 0:00:21.569 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 - 0:00:21.569 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:21.889 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:22.878 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:22.979 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:22.979 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges - 0:00:22.982 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 - 0:00:23.092 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 - 0:00:23.093 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:23.106 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:23.106 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 - 0:00:23.106 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) - 0:00:23.106 256M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 - 0:00:23.120 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:23.138 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:23.151 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation - 0:00:23.151 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:23.151 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:23.151 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:23.157 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:23.157 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:23.197 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:23.241 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:23.241 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index - 0:00:23.241 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator - 0:00:23.265 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:23.265 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:23.265 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:23.265 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index - 0:00:23.265 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving - 0:00:23.265 64M / 8G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings - 0:00:23.265 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:23.265 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library - 0:00:23.265 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library - 0:00:23.265 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed - 0:00:23.265 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:23.266 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished - 0:00:23.266 64M / 8G INFO General (repeat_resolving.cpp : 75) Restoring initial path extend settings - 0:00:23.266 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:23.266 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta - 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg - 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths - 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths - 0:00:23.266 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Second Phase Setup - 0:00:23.266 64M / 8G INFO General (second_phase_setup.cpp : 20) Preparing second phase - 0:00:23.266 64M / 8G INFO General (second_phase_setup.cpp : 28) Moving preliminary contigs from /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta to /build/spades-3.13.1+dfsg/spades_test//K55/first_pe_contigs.fasta - 0:00:23.266 64M / 8G INFO General (second_phase_setup.cpp : 40) Ready to run second phase - 0:00:23.266 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:23.266 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:23.266 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:23.266 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:23.266 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:23.277 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:23.277 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:23.297 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:23.297 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:23.309 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:23.309 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:23.309 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:23.325 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:23.325 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:23.341 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:23.341 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:23.357 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:23.357 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:23.357 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:23.357 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:23.357 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:23.357 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:23.357 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:23.357 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:27.673 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:28.226 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:28.558 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. - 0:00:28.558 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:28.582 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:29.053 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:29.054 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). - 0:00:29.054 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:29.093 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:29.094 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:29.094 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:29.118 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:29.118 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:29.118 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:29.118 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:29.153 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:29.153 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:29.153 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:29.153 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:29.153 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:29.169 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:29.169 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:29.193 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:29.193 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:29.205 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:29.205 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:29.229 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:29.229 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:29.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:29.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:29.261 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:29.261 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:29.285 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:29.285 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:29.297 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:29.297 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:29.321 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:29.321 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:29.337 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:29.337 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:29.353 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:29.353 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:29.369 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:29.369 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:29.393 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:29.393 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:29.405 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:29.405 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:29.417 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:29.417 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:29.433 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:29.433 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:29.449 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:29.449 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:29.465 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:29.465 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) - 0:00:29.485 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:29.485 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:29.501 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:29.501 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:29.501 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 - 0:00:29.501 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction - 0:00:29.501 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:29.501 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:29.525 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions - 0:00:29.525 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed - 0:00:29.525 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides - 0:00:29.526 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:29.526 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:29.526 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta - 0:00:29.526 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg - 0:00:29.526 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta - 0:00:29.526 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting - 0:00:29.526 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:29.526 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:29.526 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 - 0:00:29.526 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 - 0:00:29.526 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:29.808 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:30.764 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:30.867 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:30.868 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges - 0:00:30.871 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 - 0:00:30.979 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 - 0:00:30.979 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:30.993 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:30.993 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 - 0:00:30.993 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) - 0:00:30.993 256M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 - 0:00:31.029 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:31.061 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:31.095 64M / 8G INFO General (pair_info_count.cpp : 330) Mapping contigs library #1 - 0:00:31.095 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:31.096 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 1 reads processed - 0:00:31.096 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation - 0:00:31.096 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:31.096 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:31.096 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:31.117 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:31.117 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:31.141 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:31.177 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:31.177 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index - 0:00:31.177 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator - 0:00:31.201 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:31.201 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:31.201 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:31.201 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index - 0:00:31.201 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving - 0:00:31.201 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 - 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library - 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library - 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 477) Using 1 single read library - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 359) Filling backbone edges for long reads scaffolding... - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 361) with long reads paths - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 370) Removing fake unique with paired-end libs - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 381) 0 unique edges - 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 389) Using 0 long reads scaffolding libraries - 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 399) Using additional coordinated coverage extender - 0:00:31.201 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:31.202 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished - 0:00:31.202 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:31.202 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta - 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg - 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths - 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths - 0:00:31.202 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:31.203 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 31 seconds + 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected + 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 + 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.420 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:01.040 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:01.040 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.171 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:01.171 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.221 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.221 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.221 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.221 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.221 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.221 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.671 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. + 0:00:02.221 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.331 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. + 0:00:02.331 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.392 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:03.371 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:03.372 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). + 0:00:03.372 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:03.439 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:03.439 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:03.439 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:03.483 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted + 0:00:03.531 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:03.575 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:03.671 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:03.671 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:03.671 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:04.411 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9168 bytes occupied (77.2856 bits per kmer). + 0:00:04.411 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:04.442 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:04.488 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:04.488 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:04.488 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:04.488 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:04.488 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:04.488 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:04.488 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:05.175 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. + 0:00:05.812 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:05.971 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:05.971 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:06.029 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:07.091 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:07.092 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). + 0:00:07.092 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:07.143 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:07.144 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:07.144 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:07.176 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:07.176 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:07.176 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:07.176 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates + 0:00:07.231 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:07.231 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:07.231 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:07.283 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:07.283 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:07.339 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:07.339 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:07.367 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:07.367 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage + 0:00:07.419 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 0 times + 0:00:07.419 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:07.475 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times + 0:00:07.475 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification + 0:00:07.475 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:07.475 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:07.475 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:07.475 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:07.531 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times + 0:00:07.531 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:07.559 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:07.559 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:07.611 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:07.611 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:07.611 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:07.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:07.667 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:07.667 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:07.695 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:07.695 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:07.747 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:07.747 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:07.747 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:07.747 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:07.747 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:07.747 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:07.747 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:07.747 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:08.247 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:08.871 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:08.972 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. + 0:00:08.972 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:09.014 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:09.808 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:09.808 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). + 0:00:09.808 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:09.883 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:09.884 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:09.884 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:09.935 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:09.935 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:09.935 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:09.935 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:09.979 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting + 0:00:09.979 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:09.979 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:09.979 60M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 + 0:00:09.979 60M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 + 0:00:09.979 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:11.268 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:14.273 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:14.724 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:14.724 316M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges + 0:00:14.864 60M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 + 0:00:15.781 252M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 + 0:00:15.782 252M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:15.804 252M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:15.804 252M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 + 0:00:15.804 252M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) + 0:00:15.804 252M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 + 0:00:15.927 264M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:15.972 264M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:16.199 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation + 0:00:16.199 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:16.199 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:16.199 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:16.235 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:16.235 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:16.235 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:16.235 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:16.235 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:16.235 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:16.327 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:16.443 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:16.443 60M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index + 0:00:16.443 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator + 0:00:16.491 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:16.491 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:16.491 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:16.491 60M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index + 0:00:16.491 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving + 0:00:16.491 60M / 8G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings + 0:00:16.491 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:16.491 60M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started + 0:00:16.491 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:16.491 60M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library + 0:00:16.491 60M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library + 0:00:16.491 60M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries + 0:00:16.491 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:16.492 60M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished + 0:00:16.492 60M / 8G INFO General (repeat_resolving.cpp : 75) Restoring initial path extend settings + 0:00:16.492 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:16.492 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:16.492 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta + 0:00:16.492 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg + 0:00:16.492 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths + 0:00:16.492 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths + 0:00:16.492 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Second Phase Setup + 0:00:16.492 60M / 8G INFO General (second_phase_setup.cpp : 20) Preparing second phase + 0:00:16.492 60M / 8G INFO General (second_phase_setup.cpp : 28) Moving preliminary contigs from /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta to /build/spades-3.13.1+dfsg/spades_test//K55/first_pe_contigs.fasta + 0:00:16.492 60M / 8G INFO General (second_phase_setup.cpp : 40) Ready to run second phase + 0:00:16.492 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:16.493 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:16.493 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:16.493 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:16.493 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:16.539 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:16.539 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:16.580 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:16.580 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:16.639 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:16.639 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:16.639 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:16.639 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:16.691 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:16.691 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:16.731 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:16.731 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:16.778 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:16.778 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:16.778 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:16.778 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:16.778 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:16.778 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:16.778 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:16.778 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:17.137 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:17.737 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:17.851 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. + 0:00:17.851 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:17.912 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:18.943 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:18.944 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). + 0:00:18.944 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:19.003 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:19.004 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:19.004 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:19.059 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:19.059 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:19.059 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:19.059 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:19.111 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:19.111 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:19.111 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:19.111 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:19.111 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:19.171 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:19.171 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:19.223 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:19.223 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:19.251 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:19.251 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:19.307 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:19.307 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:19.363 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:19.363 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:19.391 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:19.391 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:19.443 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:19.443 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:19.499 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:19.499 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:19.555 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:19.555 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:19.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:19.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:19.671 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:19.671 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:19.723 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:19.723 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:19.779 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:19.779 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:19.831 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:19.831 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:19.859 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:19.859 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:19.935 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:19.935 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:19.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:19.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:20.039 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:20.039 60M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) + 0:00:20.067 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:20.067 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:20.147 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:20.147 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:20.147 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 + 0:00:20.147 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction + 0:00:20.147 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:20.147 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:20.203 60M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions + 0:00:20.203 60M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed + 0:00:20.203 60M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides + 0:00:20.203 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:20.204 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:20.204 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta + 0:00:20.204 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg + 0:00:20.204 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta + 0:00:20.204 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting + 0:00:20.204 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:20.204 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:20.204 60M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 + 0:00:20.204 60M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 + 0:00:20.204 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:21.481 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:25.349 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:25.948 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:25.948 316M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges + 0:00:26.135 60M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 + 0:00:27.109 252M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 + 0:00:27.109 252M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:27.139 252M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:27.139 252M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 + 0:00:27.139 252M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) + 0:00:27.139 252M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 + 0:00:27.254 264M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:27.319 264M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:27.567 60M / 8G INFO General (pair_info_count.cpp : 330) Mapping contigs library #1 + 0:00:27.567 60M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:27.568 60M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 1 reads processed + 0:00:27.568 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation + 0:00:27.568 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:27.568 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:27.568 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:27.593 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:27.593 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:27.593 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:27.593 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:27.593 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:27.593 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:27.687 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:27.795 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:27.795 60M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index + 0:00:27.795 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator + 0:00:27.851 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:27.851 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:27.851 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:27.851 60M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index + 0:00:27.851 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving + 0:00:27.851 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:27.851 60M / 8G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 + 0:00:27.851 60M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library + 0:00:27.851 60M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library + 0:00:27.851 60M / 8G INFO General (extenders_logic.cpp : 477) Using 1 single read library + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 359) Filling backbone edges for long reads scaffolding... + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 361) with long reads paths + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 370) Removing fake unique with paired-end libs + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 381) 0 unique edges + 0:00:27.851 60M / 8G INFO General (extenders_logic.cpp : 389) Using 0 long reads scaffolding libraries + 0:00:27.851 60M / 8G INFO General (extenders_logic.cpp : 399) Using additional coordinated coverage extender + 0:00:27.851 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:27.852 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:27.852 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:27.852 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:27.852 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:27.852 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:27.852 60M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished + 0:00:27.852 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:27.852 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:27.852 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta + 0:00:27.852 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg + 0:00:27.852 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths + 0:00:27.852 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths + 0:00:27.852 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:27.853 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 27 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 @@ -13554,7 +13589,7 @@ System information: SPAdes version: 3.13.1 Python version: 3.9.2 - OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31 + OS: Linux-5.10.0-10-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-3.13.1+dfsg/spades_test Mode: ONLY assembling (without read error correction) @@ -13603,243 +13638,243 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=33 - 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads - 0:00:00.125 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written - 0:00:00.126 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:00.313 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.314 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:00.523 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.525 4M / 140M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.525 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1611 - 0:00:00.525 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.525 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.527 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.527 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.527 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:04.473 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:05.016 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:05.016 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.450 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 974 kmers in total. - 0:00:05.451 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.474 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:05.483 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:05.483 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:05.483 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:05.483 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:05.483 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:09.075 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 974 kmers. - 0:00:09.615 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.986 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 975 kmers in total. - 0:00:09.987 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:10.010 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.450 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:10.451 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.2133 bits per kmer). - 0:00:10.451 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:10.522 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:10.523 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:10.523 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:10.523 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:10.595 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 7 34-mers were removed by early tip clipper - 0:00:10.595 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:10.595 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:10.622 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:10.658 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:10.695 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:10.731 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:10.731 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.731 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:11.107 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.3614 bits per kmer). - 0:00:11.107 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:11.186 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:11.228 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:11.228 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 72 - 0:00:11.228 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage - 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 225.865 - 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 22.5865 - 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 22.5865 - 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:11.228 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:11.228 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:11.228 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:11.228 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:11.259 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:11.259 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges - 0:00:11.259 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT - 0:00:11.318 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times - 0:00:11.319 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges - 0:00:11.359 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times - 0:00:11.359 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:11.387 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:11.387 64M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections - 0:00:11.387 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:11.387 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:11.387 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:11.387 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:11.387 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:11.387 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.387 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:11.387 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.419 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.419 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.451 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.451 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.463 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.463 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.487 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.487 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.487 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:11.487 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.499 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.499 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.510 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.511 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.535 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.535 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.559 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.559 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.559 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:11.559 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.570 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.595 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.595 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.623 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.623 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.651 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.651 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.663 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.663 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.687 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.687 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.735 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.735 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.735 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:11.735 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.742 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.743 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.767 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.767 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.778 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.779 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.791 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.791 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.791 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:11.791 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.807 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.807 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.822 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.823 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.847 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.847 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.859 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.859 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.859 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:11.859 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.871 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.871 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.887 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.887 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.903 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.903 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.927 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.927 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.927 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:11.927 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.938 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.939 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:11.951 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:11.951 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.967 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.967 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.983 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:11.984 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.984 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:11.984 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:12.006 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:12.007 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:12.019 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:12.019 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:12.031 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:12.031 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:12.047 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:12.047 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:12.047 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:12.047 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:12.063 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:12.063 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:12.079 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:12.079 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:12.103 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:12.103 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:12.111 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:12.111 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:12.111 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:12.111 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:12.127 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:12.127 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:12.143 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:12.143 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:12.159 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:12.159 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:12.183 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:12.183 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:12.183 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:12.183 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled - 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled - 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:12.183 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover - 0:00:12.190 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times - 0:00:12.190 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:12.207 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:12.207 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:12.223 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:12.223 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:12.247 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:12.247 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:12.259 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:12.259 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:12.283 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:12.283 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:12.295 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:12.295 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:12.319 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:12.319 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover - 0:00:12.330 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times - 0:00:12.331 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:12.343 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:12.343 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:12.359 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:12.359 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:12.375 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:12.375 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:12.399 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:12.399 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:12.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:12.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:12.423 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:12.423 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:12.439 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:12.439 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:12.439 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:12.455 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:12.455 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:12.455 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.865 - 0:00:12.455 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:12.455 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta - 0:00:12.455 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:12.455 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 12 seconds + 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads + 0:00:00.850 124M / 132M INFO General (binary_converter.hpp : 117) 2054 reads written + 0:00:00.929 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:02.256 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:02.328 4M / 196M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:03.774 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:03.905 4M / 196M INFO General (construction.cpp : 111) Max read length 100 + 0:00:03.905 4M / 196M INFO General (construction.cpp : 117) Average read length 86.1611 + 0:00:03.905 4M / 196M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:03.905 4M / 196M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:03.905 4M / 196M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:03.905 4M / 196M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:03.905 4M / 196M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:04.511 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:05.246 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:05.246 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:05.383 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 974 kmers in total. + 0:00:05.383 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:05.442 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:05.442 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:05.442 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:05.442 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:05.442 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:05.442 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:05.936 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 974 kmers. + 0:00:06.549 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:06.647 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 975 kmers in total. + 0:00:06.647 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:06.708 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:07.681 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:07.682 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.2133 bits per kmer). + 0:00:07.682 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:07.715 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:07.716 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:07.716 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:07.716 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:07.827 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 7 34-mers were removed by early tip clipper + 0:00:07.827 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:07.827 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:07.883 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:07.947 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:07.975 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:08.063 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:08.063 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:08.063 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:08.763 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (75.5647 bits per kmer). + 0:00:08.763 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:08.847 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:08.888 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:08.888 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 72 + 0:00:08.888 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage + 0:00:08.888 60M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 225.865 + 0:00:08.888 60M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 22.5865 + 0:00:08.888 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 22.5865 + 0:00:08.888 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:08.888 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:08.888 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:08.888 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:08.888 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:08.939 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:08.939 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges + 0:00:08.939 60M / 8G INFO General (simplification.cpp : 76) Removing short polyAT + 0:00:09.047 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times + 0:00:09.047 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges + 0:00:09.075 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times + 0:00:09.075 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:09.131 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:09.131 60M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections + 0:00:09.131 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:09.131 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:09.131 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:09.131 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:09.131 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:09.131 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.131 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:09.131 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.175 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.175 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.199 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.207 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.220 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.220 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.235 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.235 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.235 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:09.235 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.250 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.250 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.263 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.263 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.279 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.279 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.291 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.291 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.291 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:09.291 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.303 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.303 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.319 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.319 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.335 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.335 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.351 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.351 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.351 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:09.351 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.367 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.367 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.383 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.383 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.399 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.399 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.415 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.415 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.415 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:09.415 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.431 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.431 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.447 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.447 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.463 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.463 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.479 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.479 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.479 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:09.479 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.495 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.495 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.511 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.511 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.527 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.527 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.543 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.543 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.543 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:09.543 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.559 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.559 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.571 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.571 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.583 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.583 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.599 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.599 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.599 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:09.599 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.615 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.615 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.631 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.631 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.647 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.647 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.663 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:09.663 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:09.663 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:09.663 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:09.679 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:09.679 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:09.695 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:09.695 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:09.707 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:09.707 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:09.719 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.468 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.468 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:12.468 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.479 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.479 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.527 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.527 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.567 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.567 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.611 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.611 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.611 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:12.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.635 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.635 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.666 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.666 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.695 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.695 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.739 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.739 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.739 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:12.739 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:12.739 60M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled + 0:00:12.739 60M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled + 0:00:12.739 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:12.739 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:12.739 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover + 0:00:12.767 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times + 0:00:12.767 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:12.807 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:12.807 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:12.847 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:12.847 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.903 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.903 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:12.975 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:12.975 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:13.023 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:13.023 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:13.095 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:13.095 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:13.135 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:13.135 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover + 0:00:13.187 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times + 0:00:13.187 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:13.223 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:13.223 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:13.287 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:13.287 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:13.319 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:13.319 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:13.367 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:13.367 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:13.411 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:13.411 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:13.451 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:13.451 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:13.507 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:13.507 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:13.507 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:13.543 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:13.543 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:13.543 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.865 + 0:00:13.543 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:13.543 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta + 0:00:13.543 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:13.543 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 13 seconds Max read length detected as 100 == Running assembler: K49 @@ -13847,388 +13882,388 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K49/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K49/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K49/configs/rna_mode.info - 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.001 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A - 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 - 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=49 - 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.001 4M / 4M INFO General (launch.hpp : 52) SPAdes started - 0:00:00.001 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction - 0:00:00.001 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 - 0:00:00.001 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached - 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected - 0:00:00.002 4M / 4M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.002 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1611 - 0:00:00.002 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.002 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:03.680 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:04.222 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:04.222 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:04.648 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. - 0:00:04.648 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:04.685 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:04.685 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:04.685 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:04.685 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:04.685 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:04.685 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:08.828 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 958 kmers. - 0:00:09.363 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.764 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 959 kmers in total. - 0:00:09.764 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.800 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.296 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:10.297 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (81.4849 bits per kmer). - 0:00:10.297 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:10.372 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:10.372 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:10.372 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:10.404 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5 sequences extracted - 0:00:10.416 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:10.436 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:10.484 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:10.484 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.484 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:10.900 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). - 0:00:10.900 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:10.948 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:10.984 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:10.984 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 53 - 0:00:10.984 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage - 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 162.219 - 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 16.2219 - 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 16.2219 - 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:10.984 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:10.984 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:10.985 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.985 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:10.985 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:10.985 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:10.985 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:14.976 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 10 sequences. - 0:00:15.535 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:15.916 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. - 0:00:15.916 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:15.946 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:16.336 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:16.337 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). - 0:00:16.337 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:16.388 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:16.388 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:16.388 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:16.424 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:16.424 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:16.424 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:16.424 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:16.456 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:16.456 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:16.456 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled - 0:00:16.456 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:16.492 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:16.492 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges - 0:00:16.492 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT - 0:00:16.544 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times - 0:00:16.544 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges - 0:00:16.572 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times - 0:00:16.572 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:16.596 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1 times - 0:00:16.596 64M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections - 0:00:16.596 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:16.596 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:16.596 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:16.596 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:16.596 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:16.596 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:16.596 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:16.596 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.612 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times - 0:00:16.612 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:16.640 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:16.640 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.687 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:16.687 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.687 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:16.687 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.708 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.708 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:16.732 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:16.732 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.760 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.760 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.780 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:16.780 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.780 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:16.780 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.804 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.804 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:16.828 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:16.828 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.852 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.852 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.876 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:16.876 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.876 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:16.876 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.896 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.896 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:16.912 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:16.912 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.928 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.928 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:16.944 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:16.944 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:16.944 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:16.944 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.960 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.960 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:16.976 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:16.976 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.992 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.992 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.008 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.008 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.008 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:17.008 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.024 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.024 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:17.040 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:17.040 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.056 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.056 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.072 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.072 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.072 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:17.072 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.088 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.088 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:17.104 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:17.104 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.120 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.120 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.136 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.136 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.136 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:17.136 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.156 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.156 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:17.172 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:17.172 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.188 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.188 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.204 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.204 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.204 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:17.204 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.228 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.228 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:17.240 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:17.240 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.264 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.264 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.276 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.276 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.276 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:17.276 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.288 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.288 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:17.304 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:17.304 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.320 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.320 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.336 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.336 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.336 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:17.336 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:17.356 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:17.356 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:17.368 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:17.368 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:17.384 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:17.384 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:17.400 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 - 0:00:17.400 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:17.400 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:17.400 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:17.400 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:17.400 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:17.400 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:17.400 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:17.400 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:21.000 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:21.566 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:21.944 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. - 0:00:21.944 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:21.983 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:22.384 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:22.385 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (82.103 bits per kmer). - 0:00:22.385 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:22.436 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:22.436 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:22.436 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:22.464 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:22.464 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:22.464 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:22.464 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:22.496 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:22.496 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled - 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled - 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance - 0:00:22.496 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover - 0:00:22.524 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times - 0:00:22.524 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:22.548 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:22.548 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:22.572 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:22.572 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:22.592 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:22.592 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:22.624 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:22.624 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:22.644 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:22.644 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:22.668 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:22.668 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:22.688 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:22.688 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover - 0:00:22.720 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times - 0:00:22.720 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:22.744 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:22.744 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:22.768 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:22.768 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:22.792 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:22.792 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:22.816 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:22.816 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:22.840 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:22.840 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:22.864 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:22.864 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:22.880 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:22.880 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:22.880 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:22.912 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:22.912 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:22.912 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 163.37 - 0:00:22.912 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction - 0:00:22.912 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:22.912 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:22.930 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions - 0:00:22.930 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed - 0:00:22.930 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides - 0:00:22.930 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:22.930 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa - 0:00:22.930 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta - 0:00:22.930 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg - 0:00:22.931 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/final_contigs.fasta - 0:00:22.931 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting - 0:00:22.931 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:22.931 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:22.931 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 951 - 0:00:22.931 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 - 0:00:22.931 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:23.108 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:23.922 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:24.023 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:24.023 336M / 8G INFO General (pair_info_count.cpp : 211) 1751 paired reads (85.2483% of all) aligned to long edges - 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100 - 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 - 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) - 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0 - 0:00:24.040 76M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:24.060 76M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:24.090 64M / 8G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #0 - 0:00:24.090 64M / 8G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well - 0:00:24.090 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:24.116 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 4108 reads processed - 0:00:24.116 64M / 8G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0 - 0:00:24.116 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation - 0:00:24.116 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:24.116 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:24.116 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:24.128 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:24.128 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:24.176 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:24.212 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 - 0:00:24.212 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving - 0:00:24.212 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:24.212 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library - 0:00:24.212 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library - 0:00:24.212 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 466) Finalizing paths - hard - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 466) Finalizing paths - soft - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 56 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 - 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 71 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 474) Finalizing main paths - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 81 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 111 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 - 0:00:24.213 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished - 0:00:24.213 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:24.213 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa - 0:00:24.213 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta - 0:00:24.213 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg - 0:00:24.213 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K49/transcripts.paths - 0:00:24.213 64M / 8G INFO General (launch.hpp : 151) SPAdes finished - 0:00:24.213 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 24 seconds + 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb + 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A + 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 + 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=49 + 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started + 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction + 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 + 0:00:00.000 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached + 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected + 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 + 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1611 + 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:00.013 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.014 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.014 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.395 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.883 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.883 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.013 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. + 0:00:01.013 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.059 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.059 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.059 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.059 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.059 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.059 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.386 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 958 kmers. + 0:00:01.878 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.965 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 959 kmers in total. + 0:00:01.966 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.008 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:02.846 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:02.847 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (81.4849 bits per kmer). + 0:00:02.847 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:02.917 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:02.918 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:02.918 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:03.021 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5 sequences extracted + 0:00:03.093 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:03.149 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:03.277 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:03.277 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:03.277 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:08.389 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9176 bytes occupied (76.6263 bits per kmer). + 0:00:08.389 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:08.449 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:08.518 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:08.518 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 53 + 0:00:08.518 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage + 0:00:08.518 60M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 162.219 + 0:00:08.518 60M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 16.2219 + 0:00:08.518 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 16.2219 + 0:00:08.518 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:08.518 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:08.518 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:08.518 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:08.518 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:08.518 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:08.518 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:08.518 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:09.070 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 10 sequences. + 0:00:09.722 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:09.869 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. + 0:00:09.869 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:09.924 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:10.721 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:10.722 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). + 0:00:10.722 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:10.766 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:10.766 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:10.766 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:10.805 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:10.805 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:10.805 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:10.805 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:10.854 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:10.854 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:10.854 60M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled + 0:00:10.854 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:10.905 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:10.905 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges + 0:00:10.905 60M / 8G INFO General (simplification.cpp : 76) Removing short polyAT + 0:00:10.981 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times + 0:00:10.981 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges + 0:00:11.033 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times + 0:00:11.033 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:11.093 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1 times + 0:00:11.093 60M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections + 0:00:11.093 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:11.093 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:11.094 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:11.094 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:11.094 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:11.094 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:11.094 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:11.094 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:11.125 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times + 0:00:11.125 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:11.191 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:11.191 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:11.226 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:11.297 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:11.297 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:11.297 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:11.297 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:11.349 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:11.349 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:11.381 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:11.381 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:11.445 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:11.445 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:11.496 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:11.496 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:11.496 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:11.496 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:11.545 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:11.545 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:11.593 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:11.593 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:11.621 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:11.621 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:11.661 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:11.661 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:11.661 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:11.661 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:11.717 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:11.717 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:11.773 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:11.773 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:11.833 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:11.833 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:11.865 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:11.865 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:11.865 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:11.865 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:11.909 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:11.909 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:11.965 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:11.965 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:11.997 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:11.997 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.049 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.049 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.049 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:12.049 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.093 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.093 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.141 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.141 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.177 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.177 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.199 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.199 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.199 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:12.199 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.313 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.313 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.337 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.337 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.415 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.415 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.415 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:12.415 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.453 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.453 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.517 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.517 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.567 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.567 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.593 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.593 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.593 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:12.593 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.649 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.649 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.689 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.689 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.733 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.733 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:12.777 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:12.777 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:12.777 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:12.777 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:12.845 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:12.845 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:12.893 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:12.893 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:12.977 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:12.977 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:13.021 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:13.021 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:13.021 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:13.021 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:13.041 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:13.041 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:13.065 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:13.065 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:13.089 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:13.089 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:13.097 60M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 + 0:00:13.097 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:13.097 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:13.097 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:13.097 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:13.097 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:26.626 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:26.626 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:26.626 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:27.281 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:27.928 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:28.035 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. + 0:00:28.035 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:28.069 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:28.961 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:28.962 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (82.103 bits per kmer). + 0:00:28.962 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:29.010 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:29.010 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:29.010 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:29.049 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:29.049 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:29.049 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:29.049 60M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:29.097 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:29.097 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:29.097 60M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled + 0:00:29.098 60M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled + 0:00:29.098 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:29.098 60M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance + 0:00:29.098 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover + 0:00:29.141 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times + 0:00:29.141 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:29.185 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:29.185 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:29.229 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:29.229 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:29.277 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:29.277 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:29.321 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:29.321 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:29.366 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:29.366 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:29.409 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:29.409 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:29.453 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:29.453 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover + 0:00:29.501 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times + 0:00:29.501 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:29.545 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:29.545 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:29.570 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:29.570 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:29.633 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:29.633 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:29.701 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:29.701 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:29.745 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:29.746 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:29.793 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:29.793 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:29.837 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:29.837 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:29.837 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:29.881 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:29.881 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:29.881 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 163.37 + 0:00:29.881 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction + 0:00:29.881 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:29.881 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:29.925 60M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions + 0:00:29.925 60M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed + 0:00:29.925 60M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides + 0:00:29.926 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:29.926 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa + 0:00:29.926 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta + 0:00:29.926 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg + 0:00:29.926 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/final_contigs.fasta + 0:00:29.926 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting + 0:00:29.926 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:29.926 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:29.926 60M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 951 + 0:00:29.926 60M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 + 0:00:29.926 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:31.222 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:32.980 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:33.081 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:33.081 316M / 8G INFO General (pair_info_count.cpp : 211) 1751 paired reads (85.2483% of all) aligned to long edges + 0:00:33.118 60M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100 + 0:00:33.118 60M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 + 0:00:33.118 60M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) + 0:00:33.118 60M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0 + 0:00:33.137 72M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:33.151 72M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:33.181 60M / 8G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #0 + 0:00:33.181 60M / 8G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well + 0:00:33.181 60M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:33.211 60M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 4108 reads processed + 0:00:33.211 60M / 8G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0 + 0:00:33.211 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation + 0:00:33.211 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:33.211 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:33.211 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:33.245 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:33.245 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:33.245 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:33.245 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:33.245 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:33.245 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:33.333 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:33.413 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 + 0:00:33.413 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving + 0:00:33.413 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:33.413 60M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:33.414 60M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library + 0:00:33.414 60M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library + 0:00:33.414 60M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 466) Finalizing paths - hard + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 466) Finalizing paths - soft + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 56 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 71 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 474) Finalizing main paths + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 81 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 + 0:00:33.414 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 + 0:00:33.415 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 111 + 0:00:33.415 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 + 0:00:33.415 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 + 0:00:33.415 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 + 0:00:33.415 60M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished + 0:00:33.415 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:33.415 60M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa + 0:00:33.415 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta + 0:00:33.415 60M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg + 0:00:33.415 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K49/transcripts.paths + 0:00:33.415 60M / 8G INFO General (launch.hpp : 151) SPAdes finished + 0:00:33.415 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 33 seconds ===== Assembling finished. Used k-mer sizes: 33, 49 @@ -14324,12 +14359,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/696983/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/696983/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/1777496 and its subdirectories -I: Current time: Sat Feb 11 20:11:15 -12 2023 -I: pbuilder-time-stamp: 1676189475 +I: removing directory /srv/workspace/pbuilder/696983 and its subdirectories +I: Current time: Mon Jan 10 18:32:23 +14 2022 +I: pbuilder-time-stamp: 1641789143