Diff of the two buildlogs: -- --- b1/build.log 2021-12-15 09:08:17.754939827 +0000 +++ b2/build.log 2021-12-15 09:42:45.574596659 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 17 02:57:29 -12 2023 -I: pbuilder-time-stamp: 1673967449 +I: Current time: Wed Dec 15 23:08:20 +14 2021 +I: pbuilder-time-stamp: 1639559300 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 17 06:27:53 2019 -12 +gpgv: Signature made Fri Jan 18 08:27:53 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./spades_3.13.0+dfsg2-2.dsc @@ -42,136 +42,170 @@ dpkg-source: info: applying gcc7.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3267546/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2692573/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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/2692573/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2692573/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 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all 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='f64921964c7541d2be74fb0a991a5e77' - 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='3267546' - PS1='# ' - PS2='> ' + INVOCATION_ID=102dac920c2d445d9f30460c774d2c00 + 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=2692573 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.C91g8wCCqd/pbuilderrc_Mhyd --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.C91g8wCCqd/b1 --logfile b1/build.log spades_3.13.0+dfsg2-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.C91g8wCCqd/pbuilderrc_yfpG --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.C91g8wCCqd/b2 --logfile b2/build.log spades_3.13.0+dfsg2-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 ionos15-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 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/3267546/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 15 23:08 sh -> bash + lrwxrwxrwx 1 root root 4 Nov 8 11:58 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/2692573/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -381,7 +415,7 @@ Get: 134 http://deb.debian.org/debian buster/main amd64 python-all-dev amd64 2.7.16-1 [1068 B] Get: 135 http://deb.debian.org/debian buster/main amd64 python-joblib all 0.13.0-2 [190 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 python-yaml amd64 3.13-2 [127 kB] -Fetched 93.9 MB in 2s (62.1 MB/s) +Fetched 93.9 MB in 1s (64.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -961,7 +995,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/spades-3.13.0+dfsg2/ && 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_3.13.0+dfsg2-2_source.changes +hostname: Name or service not known +I: Running cd /build/spades-3.13.0+dfsg2/ && 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_3.13.0+dfsg2-2_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.13.0+dfsg2-2 dpkg-buildpackage: info: source distribution unstable @@ -2690,7 +2725,7 @@ System information: SPAdes version: 3.13.0 Python version: 2.7.16 - OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-debian-10.11 + OS: Linux-5.10.0-9-amd64-x86_64-with-debian-10.11 Output dir: /build/spades-3.13.0+dfsg2/spades_test Mode: read error correction and assembling @@ -2731,60 +2766,60 @@ == Running read error correction tool: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-hammer /build/spades-3.13.0+dfsg2/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 - 0:00:00.004 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.0+dfsg2/spades_test/corrected/configs/config.info - 0:00:00.004 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.005 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.005 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset - 0:00:00.005 4M / 4M INFO General (main.cpp : 92) Determined value is 33 - 0:00:00.005 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] - 0:00:00.005 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-3.13.0+dfsg2/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 + 0:00:00.000 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 === - 0:00:00.005 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 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 262144 - 0:00:05.092 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:05.206 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:05.294 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed - 0:00:05.747 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:06.442 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. - 0:00:06.442 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:06.475 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:06.894 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:06.895 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). - 0:00:06.895 64M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order - 0:00:06.942 64M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. - 0:00:07.018 64M / 8G INFO General (main.cpp : 155) Extracting clusters - 0:00:07.066 64M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 - 0:00:07.066 64M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. - 0:00:07.067 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:07.162 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:07.299 64M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. - 0:00:07.299 64M / 8G INFO K-mer Counting (kmer_data.cpp : 403) There are 1974 kmers in total. Among them 0 (0%) are singletons. - 0:00:07.299 64M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 - 0:00:07.330 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 - 0:00:07.330 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)) - 0:00:07.330 64M / 8G INFO General (main.cpp : 178) Finished clustering. - 0:00:07.330 64M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. - 0:00:07.490 64M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. - 0:00:07.490 64M / 8G INFO General (main.cpp : 222) Solid k-mers finalized - 0:00:07.490 64M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. - 0:00:07.490 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 - 0:00:08.171 408M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. - 0:00:08.234 408M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 - 0:00:08.240 408M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 - 0:00:08.625 64M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. - 0:00:08.625 64M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. - 0:00:08.625 64M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml - 0:00:08.626 64M / 8G INFO General (main.cpp : 262) All done. Exiting. + 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 240 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 279620 + 0:00:00.064 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:00.123 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:00.183 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed + 0:00:00.315 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.412 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. + 0:00:00.412 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.434 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.558 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.559 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). + 0:00:00.559 60M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order + 0:00:00.582 60M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. + 0:00:00.642 60M / 8G INFO General (main.cpp : 155) Extracting clusters + 0:00:00.698 60M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 + 0:00:00.698 60M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. + 0:00:00.698 60M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:00.738 60M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:00.786 60M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. + 0:00:00.786 60M / 8G INFO K-mer Counting (kmer_data.cpp : 403) There are 1974 kmers in total. Among them 0 (0%) are singletons. + 0:00:00.786 60M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 + 0:00:00.810 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 + 0:00:00.810 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)) + 0:00:00.810 60M / 8G INFO General (main.cpp : 178) Finished clustering. + 0:00:00.810 60M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 15 threads. + 0:00:00.862 60M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. + 0:00:00.862 60M / 8G INFO General (main.cpp : 222) Solid k-mers finalized + 0:00:00.862 60M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 15 threads. + 0:00:00.862 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 + 0:00:01.162 388M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. + 0:00:01.198 388M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 + 0:00:01.207 388M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 + 0:00:01.335 60M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. + 0:00:01.335 60M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. + 0:00:01.335 60M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml + 0:00:01.335 60M / 8G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) @@ -2802,722 +2837,722 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K21/configs/config.info 0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.002 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from N/A, git revision N/A - 0:00:00.003 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 - 0:00:00.003 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.0+dfsg2/spades_test/dataset.info) with K=21 - 0:00:00.003 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.003 4M / 4M INFO General (launch.hpp : 51) SPAdes started - 0:00:00.003 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction - 0:00:00.003 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 - 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) - 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads - 0:00:00.443 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written - 0:00:00.454 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:01.345 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:01.357 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:02.277 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:02.288 4M / 140M INFO General (construction.cpp : 111) Max read length 100 - 0:00:02.289 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:02.289 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:02.289 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:02.294 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:02.294 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:02.294 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:07.026 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:07.518 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:07.518 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:08.111 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. - 0:00:08.112 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:08.139 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:08.148 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:08.148 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:08.148 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:08.148 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:08.148 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:12.256 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. - 0:00:12.639 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:13.019 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. - 0:00:13.020 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:13.050 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:13.515 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:13.517 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). - 0:00:13.517 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:13.587 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:13.588 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:13.588 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:13.588 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:13.636 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper - 0:00:13.636 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:13.636 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:13.644 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:13.667 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:13.679 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:13.711 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:13.712 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:13.712 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:14.132 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). - 0:00:14.132 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:14.179 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:14.194 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:14.194 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 - 0:00:14.194 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 - 0:00:14.194 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 - 0:00:14.194 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model - 0:00:14.378 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 - 0:00:14.609 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 - 0:00:15.121 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 - 0:00:15.931 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 - 0:00:17.421 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 - 0:00:21.329 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 - 0:00:21.331 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 - 0:00:21.331 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 - 0:00:21.331 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 - 0:00:21.331 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 - 0:00:21.331 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 342.845 - 0:00:21.331 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171 - 0:00:21.331 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:21.331 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:21.331 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:21.331 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:21.331 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:21.344 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:21.344 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:21.368 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:21.368 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:21.392 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:21.392 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:21.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:21.412 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:21.412 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:21.412 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:21.412 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:21.412 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.432 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.432 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.448 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.448 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.468 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:21.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.487 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.488 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.504 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.504 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:21.520 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:21.520 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:21.520 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:21.520 64M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled - 0:00:21.520 64M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled - 0:00:21.520 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:21.520 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.539 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.540 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.557 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.557 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:21.571 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:21.572 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:21.588 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:21.588 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:21.588 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:21.600 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:21.600 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:21.600 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 - 0:00:21.600 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:21.600 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa - 0:00:21.600 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta - 0:00:21.600 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg - 0:00:21.600 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta - 0:00:21.600 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta - 0:00:21.600 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:21.600 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa - 0:00:21.600 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta - 0:00:21.600 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg - 0:00:21.600 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta - 0:00:21.601 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta - 0:00:21.601 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:21.601 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 21 seconds + 0:00:00.002 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 + 0:00:00.002 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.0+dfsg2/spades_test/dataset.info) with K=21 + 0:00:00.002 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.002 4M / 4M INFO General (launch.hpp : 51) SPAdes started + 0:00:00.002 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction + 0:00:00.002 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 + 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction + 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) + 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads + 0:00:00.156 124M / 132M INFO General (binary_converter.hpp : 117) 2054 reads written + 0:00:00.166 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:00.388 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:00.406 4M / 196M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:00.628 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:00.644 4M / 196M INFO General (construction.cpp : 111) Max read length 100 + 0:00:00.644 4M / 196M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:00.644 4M / 196M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:00.644 4M / 196M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:00.644 4M / 196M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.645 4M / 196M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.645 4M / 196M INFO General (kmer_splitters.hpp : 97) Using cell size of 298261 + 0:00:00.784 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.934 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.934 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.028 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. + 0:00:01.028 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.049 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.049 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.049 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.049 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.049 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.049 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:01.161 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. + 0:00:01.291 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.360 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. + 0:00:01.360 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.394 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.496 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:01.497 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). + 0:00:01.497 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:01.524 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:01.524 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:01.524 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:01.524 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:01.568 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper + 0:00:01.568 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:01.568 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:01.580 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:01.592 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:01.600 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:01.632 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:01.632 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.632 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.752 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (74.7967 bits per kmer). + 0:00:01.752 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.785 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.809 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:01.809 60M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 + 0:00:01.809 60M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 + 0:00:01.809 60M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 + 0:00:01.809 60M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model + 0:00:01.946 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 + 0:00:02.179 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 + 0:00:02.659 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 + 0:00:03.388 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 + 0:00:04.731 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 + 0:00:08.010 60M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 + 0:00:08.013 60M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 + 0:00:08.013 60M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 + 0:00:08.013 60M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 + 0:00:08.013 60M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 + 0:00:08.013 60M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 342.845 + 0:00:08.013 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171 + 0:00:08.013 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:08.013 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:08.013 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:08.013 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:08.013 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:08.024 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:08.024 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:08.044 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:08.044 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:08.060 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:08.060 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:08.076 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:08.076 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:08.076 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:08.076 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:08.076 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:08.076 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.092 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.092 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.108 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.108 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.124 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:08.124 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.139 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.140 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.156 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.156 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:08.172 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:08.172 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:08.172 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:08.172 60M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled + 0:00:08.172 60M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled + 0:00:08.172 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:08.172 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.188 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.188 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.204 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.204 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:08.220 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:08.220 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:08.232 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:08.232 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:08.232 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:08.248 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:08.248 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:08.248 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 + 0:00:08.248 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:08.248 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa + 0:00:08.248 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta + 0:00:08.248 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg + 0:00:08.248 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta + 0:00:08.248 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta + 0:00:08.248 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:08.248 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa + 0:00:08.248 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta + 0:00:08.248 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg + 0:00:08.248 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta + 0:00:08.248 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta + 0:00:08.248 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:08.249 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 8 seconds Max read length detected as 100 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K33/configs/config.info - 0:00:00.005 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb - 0:00:00.005 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from N/A, git revision N/A - 0:00:00.005 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 - 0:00:00.005 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.0+dfsg2/spades_test/dataset.info) with K=33 - 0:00:00.005 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.005 4M / 4M INFO General (launch.hpp : 51) SPAdes started - 0:00:00.005 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction - 0:00:00.005 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 - 0:00:00.005 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected - 0:00:00.006 4M / 4M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.006 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.006 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.006 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.006 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:03.392 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:03.785 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:03.785 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:04.192 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. - 0:00:04.192 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:04.225 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:04.225 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:04.225 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:04.225 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:04.225 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:04.225 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:06.484 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. - 0:00:06.950 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:07.340 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. - 0:00:07.340 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:07.363 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:07.824 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:07.825 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). - 0:00:07.825 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:07.886 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:07.886 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:07.886 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:07.886 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:07.969 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper - 0:00:07.969 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:07.969 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:07.994 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:08.018 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:08.058 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:08.110 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:08.110 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:08.110 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:08.480 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). - 0:00:08.480 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:08.520 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:08.537 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:08.537 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 - 0:00:08.537 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 - 0:00:08.537 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 - 0:00:08.537 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model - 0:00:08.636 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 - 0:00:08.762 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 - 0:00:08.978 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 - 0:00:09.263 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 - 0:00:09.773 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 - 0:00:10.677 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 - 0:00:12.633 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 - 0:00:15.122 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 - 0:00:15.123 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 - 0:00:15.123 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 - 0:00:15.123 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 - 0:00:15.123 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 - 0:00:15.123 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 108.181 - 0:00:15.123 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 3 - 0:00:15.123 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:15.123 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:15.123 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:15.123 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:15.123 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:15.132 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:15.132 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:15.164 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:15.164 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:15.192 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:15.192 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:15.212 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:15.212 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:15.212 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:15.212 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:15.212 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:15.212 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.240 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.240 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.264 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.264 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.280 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.280 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.280 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.280 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.280 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:15.280 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.281 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.281 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.281 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.281 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.281 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:15.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.308 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.308 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.328 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.328 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:15.356 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:15.356 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:15.356 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:15.356 64M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled - 0:00:15.356 64M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled - 0:00:15.356 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:15.356 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.376 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.376 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.400 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.400 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.428 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.428 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.448 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.448 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:15.448 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:15.476 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:15.476 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:15.476 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 - 0:00:15.476 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:15.476 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa - 0:00:15.476 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta - 0:00:15.476 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg - 0:00:15.477 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta - 0:00:15.477 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta - 0:00:15.477 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:15.477 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa - 0:00:15.477 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta - 0:00:15.477 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg - 0:00:15.477 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta - 0:00:15.477 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta - 0:00:15.477 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:15.477 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 15 seconds + 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb + 0:00:00.001 4M / 4M INFO General (main.cpp : 87) 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-3.13.0+dfsg2/spades_test/dataset.info) with K=33 + 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started + 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction + 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) 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 + 0:00:00.002 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 86.1526 + 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 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: 1.04436 Gb + 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.158 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.301 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.301 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.406 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. + 0:00:00.406 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.424 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:00.424 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.424 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.424 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.424 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:00.424 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:00.555 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. + 0:00:00.695 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.766 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. + 0:00:00.766 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.785 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.867 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.868 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). + 0:00:00.868 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:00.895 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:00.895 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:00.895 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:00.895 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:00.930 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper + 0:00:00.930 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:00.930 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:00.942 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:00.958 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:00.979 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:01.014 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:01.014 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.014 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.105 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (75.7202 bits per kmer). + 0:00:01.105 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.140 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.155 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:01.155 60M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 + 0:00:01.155 60M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 + 0:00:01.155 60M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 + 0:00:01.155 60M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model + 0:00:01.200 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 + 0:00:01.292 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 + 0:00:01.451 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 + 0:00:01.647 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 + 0:00:02.022 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 + 0:00:02.789 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 + 0:00:04.334 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 + 0:00:06.279 60M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 + 0:00:06.280 60M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 + 0:00:06.280 60M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 + 0:00:06.280 60M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 + 0:00:06.280 60M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 + 0:00:06.280 60M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 108.181 + 0:00:06.280 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 3 + 0:00:06.280 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:06.280 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:06.280 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:06.280 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:06.280 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:06.290 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:06.290 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:06.326 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:06.326 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:06.338 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:06.338 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:06.362 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:06.362 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:06.362 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:06.362 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:06.362 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:06.362 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.374 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.374 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.394 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.394 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.410 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:06.410 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.430 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.430 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.446 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.446 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:06.462 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:06.462 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:06.462 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:06.462 60M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled + 0:00:06.462 60M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled + 0:00:06.462 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:06.462 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.474 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.474 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.494 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.494 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:06.510 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:06.510 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:06.526 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:06.526 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:06.526 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:06.542 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:06.542 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:06.542 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 + 0:00:06.542 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:06.542 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa + 0:00:06.542 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta + 0:00:06.542 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg + 0:00:06.542 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta + 0:00:06.542 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta + 0:00:06.542 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:06.542 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa + 0:00:06.542 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta + 0:00:06.542 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg + 0:00:06.542 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta + 0:00:06.542 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta + 0:00:06.543 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:06.543 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 6 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/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 : 87) 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-3.13.0+dfsg2/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 : 51) SPAdes started - 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction - 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 + 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 : 87) 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-3.13.0+dfsg2/spades_test/dataset.info) with K=55 + 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 + 0:00:00.001 4M / 4M INFO General (launch.hpp : 51) SPAdes started + 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction + 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 76) 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 86.1526 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 (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 - 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.006 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:02.158 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:02.668 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:02.668 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:03.051 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:03.051 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:03.092 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:03.098 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:03.098 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:03.098 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:03.098 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:03.098 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:05.399 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. - 0:00:05.753 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:06.142 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. - 0:00:06.142 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:06.167 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:06.718 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:06.719 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). - 0:00:06.719 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:06.778 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:06.778 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:06.778 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:06.790 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted - 0:00:06.814 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:06.834 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:06.870 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:06.870 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:06.870 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:07.246 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:07.246 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:07.286 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:07.331 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:07.331 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 - 0:00:07.331 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 - 0:00:07.331 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 - 0:00:07.331 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model - 0:00:07.376 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 - 0:00:07.452 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 - 0:00:07.586 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 - 0:00:07.764 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 - 0:00:07.926 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 - 0:00:07.927 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 - 0:00:07.927 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 - 0:00:07.927 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 - 0:00:07.927 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 - 0:00:07.927 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 13.7375 - 0:00:07.927 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 1 - 0:00:07.927 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:07.927 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:07.927 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:07.927 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:07.927 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:07.927 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:07.927 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:07.927 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:10.218 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. - 0:00:10.595 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:10.962 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:10.962 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:11.001 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:11.426 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:11.427 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:11.427 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:11.467 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:11.467 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:11.467 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:11.510 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:11.510 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:11.510 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:11.510 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 4 candidates - 0:00:11.542 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:11.543 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:11.543 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:11.543 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:11.606 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:11.606 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:11.630 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:11.630 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:11.646 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times - 0:00:11.646 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:11.646 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:11.646 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:11.646 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:11.646 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times - 0:00:11.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.706 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.706 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.730 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.731 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.731 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:11.731 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:11.754 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:11.754 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 - 0:00:11.778 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:11.814 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:11.814 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:11.814 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:11.814 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:11.814 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:11.814 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:11.814 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:11.814 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:14.163 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:14.522 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:14.922 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. - 0:00:14.922 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:14.948 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:15.462 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:15.463 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). - 0:00:15.463 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:15.483 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:15.483 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:15.483 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:15.502 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:15.502 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:15.502 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:15.502 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:15.522 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:15.522 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:15.522 64M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled - 0:00:15.522 64M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled - 0:00:15.522 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:15.522 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.530 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.530 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.548 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.554 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:15.566 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:15.566 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:15.582 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:15.582 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:15.582 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:15.606 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:15.606 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:15.606 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 - 0:00:15.606 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction - 0:00:15.606 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:15.606 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:15.622 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions - 0:00:15.622 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed - 0:00:15.622 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides - 0:00:15.623 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:15.623 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:15.623 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta - 0:00:15.623 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg - 0:00:15.623 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/simplified_contigs.fasta - 0:00:15.623 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/intermediate_contigs.fasta - 0:00:15.623 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting - 0:00:15.623 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:15.623 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:15.623 64M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 945 - 0:00:15.623 64M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 - 0:00:15.623 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:15.854 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:17.224 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:17.421 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:17.421 336M / 8G INFO General (pair_info_count.cpp : 213) 1636 paired reads (79.6495% of all) aligned to long edges - 0:00:17.424 64M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 - 0:00:17.543 256M / 8G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 - 0:00:17.544 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:17.551 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:17.552 256M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 - 0:00:17.552 256M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) - 0:00:17.552 256M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 2, rounding threshold 0 - 0:00:17.569 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:17.587 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:17.601 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation - 0:00:17.601 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:17.601 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:17.601 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:17.606 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:17.606 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:17.606 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:17.606 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:17.606 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:17.606 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:17.650 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:17.690 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:17.690 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index - 0:00:17.690 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator - 0:00:17.710 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:17.710 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:17.710 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:17.710 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index - 0:00:17.710 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving - 0:00:17.710 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:17.710 64M / 8G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 140.62 - 0:00:17.710 64M / 8G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 140.62 - 0:00:17.710 64M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library - 0:00:17.710 64M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library - 0:00:17.710 64M / 8G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:17.710 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:17.710 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths - 0:00:17.710 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:17.710 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:17.710 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:17.710 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:17.710 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:17.710 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:17.710 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:17.711 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:17.711 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:17.711 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:17.711 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths - 0:00:17.711 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:17.711 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:17.711 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:17.711 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:17.711 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:17.711 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:17.711 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:17.711 64M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished - 0:00:17.711 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:17.711 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:17.711 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta - 0:00:17.711 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg - 0:00:17.711 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.paths - 0:00:17.711 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/scaffolds.paths - 0:00:17.711 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:17.711 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 17 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 + 0:00:00.132 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.260 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.260 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.384 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:00.384 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.401 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:00.401 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.401 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.401 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.401 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:00.401 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:00.533 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. + 0:00:00.655 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.717 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. + 0:00:00.717 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.736 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.874 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.875 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). + 0:00:00.875 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:00.912 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:00.913 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:00.913 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:00.928 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted + 0:00:00.944 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:00.960 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:00.996 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:00.996 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.996 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.099 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9168 bytes occupied (77.2856 bits per kmer). + 0:00:01.099 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.124 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.141 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:01.141 60M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 + 0:00:01.141 60M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 + 0:00:01.141 60M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 + 0:00:01.141 60M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model + 0:00:01.167 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 + 0:00:01.214 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 + 0:00:01.347 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 + 0:00:01.523 60M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 + 0:00:01.685 60M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 + 0:00:01.685 60M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 + 0:00:01.685 60M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 + 0:00:01.685 60M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 + 0:00:01.685 60M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 + 0:00:01.685 60M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 13.7375 + 0:00:01.685 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 1 + 0:00:01.685 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:01.685 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:01.685 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:01.685 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.685 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.686 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.686 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.686 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.792 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. + 0:00:01.925 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.984 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:01.984 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.009 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:02.080 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:02.082 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). + 0:00:02.082 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:02.097 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:02.097 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:02.097 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:02.121 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:02.121 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:02.121 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:02.122 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 4 candidates + 0:00:02.140 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:02.141 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:02.141 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:02.141 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:02.156 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:02.156 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:02.176 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:02.176 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:02.200 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:02.200 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:02.212 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times + 0:00:02.212 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:02.212 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:02.212 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.212 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:02.212 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.230 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times + 0:00:02.230 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.244 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.244 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.260 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.260 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.260 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.260 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.261 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:02.261 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.276 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.276 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.300 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.300 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.312 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.313 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:02.313 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:02.313 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:02.313 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:02.313 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:02.313 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:02.313 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:02.449 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:02.583 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.649 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. + 0:00:02.649 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.670 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:02.756 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:02.766 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). + 0:00:02.766 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:02.776 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:02.777 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:02.777 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:02.789 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:02.789 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:02.789 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:02.789 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:02.816 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:02.816 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:02.816 60M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled + 0:00:02.816 60M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled + 0:00:02.816 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.816 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.828 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.828 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.844 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.845 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.856 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.856 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.872 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.872 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:02.872 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:02.884 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:02.884 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:02.884 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 + 0:00:02.884 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction + 0:00:02.884 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:02.884 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:02.898 60M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions + 0:00:02.898 60M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed + 0:00:02.898 60M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides + 0:00:02.899 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:02.899 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:02.899 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta + 0:00:02.899 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg + 0:00:02.899 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/simplified_contigs.fasta + 0:00:02.899 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/intermediate_contigs.fasta + 0:00:02.899 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting + 0:00:02.899 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:02.899 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:02.899 60M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 945 + 0:00:02.899 60M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 + 0:00:02.899 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:03.157 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:03.933 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:04.092 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:04.092 316M / 8G INFO General (pair_info_count.cpp : 213) 1636 paired reads (79.6495% of all) aligned to long edges + 0:00:04.129 60M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 + 0:00:04.307 252M / 8G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 + 0:00:04.307 252M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:04.317 252M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:04.317 252M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 + 0:00:04.317 252M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) + 0:00:04.317 252M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 2, rounding threshold 0 + 0:00:04.334 264M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:04.358 264M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:04.399 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation + 0:00:04.399 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:04.399 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:04.399 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:04.408 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:04.408 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:04.408 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:04.408 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:04.408 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:04.408 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:04.444 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:04.472 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:04.472 60M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index + 0:00:04.472 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator + 0:00:04.488 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:04.488 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:04.488 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:04.488 60M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index + 0:00:04.488 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving + 0:00:04.488 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:04.488 60M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started + 0:00:04.488 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:04.488 60M / 8G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 140.62 + 0:00:04.488 60M / 8G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 140.62 + 0:00:04.489 60M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library + 0:00:04.489 60M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library + 0:00:04.489 60M / 8G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:04.489 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:04.489 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:04.489 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:04.489 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:04.489 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:04.489 60M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished + 0:00:04.489 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:04.489 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:04.489 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta + 0:00:04.489 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg + 0:00:04.489 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.paths + 0:00:04.489 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/scaffolds.paths + 0:00:04.489 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:04.490 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 4 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 @@ -3542,7 +3577,7 @@ System information: SPAdes version: 3.13.0 Python version: 2.7.16 - OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-debian-10.11 + OS: Linux-5.10.0-9-amd64-x86_64-with-debian-10.11 Output dir: /build/spades-3.13.0+dfsg2/spades_test Mode: read error correction and assembling @@ -3583,71 +3618,71 @@ == Running read error correction tool: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-hammer /build/spades-3.13.0+dfsg2/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 - 0:00:00.001 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.0+dfsg2/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 + 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.0+dfsg2/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 - 0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] - 0:00:00.002 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes + 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 === - 0:00:00.002 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count - 0:00:00.170 260M / 260M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:00.252 320M / 320M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:00.292 320M / 320M INFO K-mer Counting (kmer_data.cpp : 299) Total 4108 reads processed - 0:00:01.511 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 + 0:00:00.213 244M / 244M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:00.247 300M / 300M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:00.303 300M / 300M INFO K-mer Counting (kmer_data.cpp : 299) Total 4108 reads processed + 0:00:01.370 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 - 0:00:01.511 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:01.746 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:01.916 1G / 1G INFO K-mer Counting (kmer_data.cpp : 331) Total 4108 reads processed - 0:00:01.917 1G / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:01.917 1G / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:01.917 1G / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:01.917 1G / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.951416 Gb - 0:00:01.917 1G / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:04.304 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:04.373 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:04.438 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed - 0:00:05.048 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.486 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. - 0:00:05.486 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.500 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:05.884 1G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:05.885 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). - 0:00:05.919 64M / 10G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order - 0:00:05.933 64M / 10G INFO General (main.cpp : 148) Clustering Hamming graph. - 0:00:05.980 64M / 10G INFO General (main.cpp : 155) Extracting clusters - 0:00:06.025 64M / 10G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 - 0:00:06.025 64M / 10G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. - 0:00:06.025 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:06.096 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:06.164 64M / 10G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. - 0:00:06.165 64M / 10G INFO K-mer Counting (kmer_data.cpp : 403) There are 1974 kmers in total. Among them 0 (0%) are singletons. - 0:00:06.165 64M / 10G INFO General (main.cpp : 173) Subclustering Hamming graph - 0:00:06.192 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 - 0:00:06.193 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 - 0:00:06.193 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)) - 0:00:06.193 64M / 10G INFO General (main.cpp : 178) Finished clustering. - 0:00:06.193 64M / 10G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. - 0:00:06.268 64M / 10G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. - 0:00:06.269 64M / 10G INFO General (main.cpp : 222) Solid k-mers finalized - 0:00:06.269 64M / 10G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. - 0:00:06.269 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 - 0:00:06.508 408M / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. - 0:00:06.552 408M / 10G INFO General (hammer_tools.cpp : 175) Processed batch 0 - 0:00:06.566 408M / 10G INFO General (hammer_tools.cpp : 185) Written batch 0 - 0:00:06.669 64M / 10G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. - 0:00:06.669 64M / 10G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. - 0:00:06.669 64M / 10G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml - 0:00:06.669 64M / 10G INFO General (main.cpp : 262) All done. Exiting. + 0:00:01.370 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:01.547 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:01.731 1G / 1G INFO K-mer Counting (kmer_data.cpp : 331) Total 4108 reads processed + 0:00:01.731 1G / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.731 1G / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.731 1G / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.731 1G / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.01493 Gb + 0:00:01.731 1G / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:01.820 9G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:01.853 9G / 9G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:01.892 9G / 9G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed + 0:00:02.021 1G / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.083 1G / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. + 0:00:02.083 1G / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.095 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:02.191 1G / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:02.192 1G / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). + 0:00:02.208 60M / 9G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order + 0:00:02.219 60M / 9G INFO General (main.cpp : 148) Clustering Hamming graph. + 0:00:02.255 60M / 9G INFO General (main.cpp : 155) Extracting clusters + 0:00:02.287 60M / 9G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 + 0:00:02.287 60M / 9G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. + 0:00:02.287 60M / 9G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:02.355 60M / 9G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:02.399 60M / 9G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. + 0:00:02.399 60M / 9G INFO K-mer Counting (kmer_data.cpp : 403) There are 1974 kmers in total. Among them 0 (0%) are singletons. + 0:00:02.399 60M / 9G INFO General (main.cpp : 173) Subclustering Hamming graph + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 + 0:00:02.422 60M / 9G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 + 0:00:02.422 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)) + 0:00:02.422 60M / 9G INFO General (main.cpp : 178) Finished clustering. + 0:00:02.422 60M / 9G INFO General (main.cpp : 197) Starting solid k-mers expansion in 15 threads. + 0:00:02.467 60M / 9G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. + 0:00:02.467 60M / 9G INFO General (main.cpp : 222) Solid k-mers finalized + 0:00:02.467 60M / 9G INFO General (hammer_tools.cpp : 220) Starting read correction in 15 threads. + 0:00:02.467 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 + 0:00:02.767 388M / 9G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. + 0:00:02.800 388M / 9G INFO General (hammer_tools.cpp : 175) Processed batch 0 + 0:00:02.805 388M / 9G INFO General (hammer_tools.cpp : 185) Written batch 0 + 0:00:02.928 60M / 9G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. + 0:00:02.928 60M / 9G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. + 0:00:02.928 60M / 9G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml + 0:00:02.928 60M / 9G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) @@ -3663,163 +3698,163 @@ == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K21/configs/config.info - 0:00:00.001 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K21/configs/mda_mode.info - 0:00:00.001 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K21/configs/meta_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 : 87) 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-3.13.0+dfsg2/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 : 51) SPAdes started - 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction - 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) 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 - 0:00:00.178 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written - 0:00:00.180 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:00.474 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.476 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:00.730 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.733 4M / 140M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.733 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.733 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.733 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.734 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.734 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.734 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:02.728 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:03.149 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:03.149 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:03.586 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. - 0:00:03.586 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:03.623 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:03.623 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:03.623 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:03.624 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:03.624 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:03.624 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 - 0:00:05.971 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. - 0:00:06.431 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:06.842 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. - 0:00:06.842 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:06.864 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:07.326 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:07.327 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). - 0:00:07.327 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:07.398 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:07.399 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:07.399 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:07.399 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:07.458 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper - 0:00:07.458 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:07.459 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:07.478 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:07.518 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:07.534 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:07.590 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:07.590 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:07.590 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:08.091 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). - 0:00:08.091 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:08.140 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:08.171 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:08.171 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:08.172 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:08.172 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:08.206 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:08.206 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:08.226 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:08.226 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:08.246 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:08.246 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:08.271 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:08.271 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:08.271 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:08.271 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:08.271 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:08.271 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.294 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.294 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.327 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.328 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.347 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.347 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.347 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:08.347 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.374 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.374 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.394 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.394 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.418 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.418 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:08.418 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:08.418 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:08.419 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:08.446 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:08.446 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:08.466 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:08.466 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:08.490 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:08.490 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:08.510 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:08.510 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.534 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.534 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:08.558 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:08.558 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.582 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.582 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:08.602 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:08.602 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:08.630 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:08.630 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:08.644 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:08.644 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:08.663 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:08.663 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:08.678 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:08.678 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.706 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.706 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:08.730 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:08.730 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.750 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.750 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:08.762 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:08.762 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) - 0:00:08.783 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:08.783 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:08.815 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:08.815 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:08.815 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 - 0:00:08.815 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:08.815 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa - 0:00:08.815 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta - 0:00:08.816 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg - 0:00:08.816 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta - 0:00:08.816 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta - 0:00:08.816 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:08.816 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa - 0:00:08.816 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta - 0:00:08.816 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg - 0:00:08.816 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta - 0:00:08.816 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta - 0:00:08.816 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:08.816 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 8 seconds + 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K21/configs/mda_mode.info + 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K21/configs/meta_mode.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 : 87) 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-3.13.0+dfsg2/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 : 51) SPAdes started + 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction + 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) 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 + 0:00:00.158 124M / 132M INFO General (binary_converter.hpp : 117) 2054 reads written + 0:00:00.169 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:00.401 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:00.422 4M / 196M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:00.660 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:00.681 4M / 196M INFO General (construction.cpp : 111) Max read length 100 + 0:00:00.681 4M / 196M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:00.681 4M / 196M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:00.681 4M / 196M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:00.682 4M / 196M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.682 4M / 196M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.682 4M / 196M INFO General (kmer_splitters.hpp : 97) Using cell size of 298261 + 0:00:00.822 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.957 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.957 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.068 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. + 0:00:01.068 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.083 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.083 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.083 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.083 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.084 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.084 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 279620 + 0:00:01.200 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. + 0:00:01.349 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.421 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. + 0:00:01.421 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.451 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.594 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:01.595 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). + 0:00:01.595 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:01.630 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:01.630 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:01.630 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:01.630 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:01.662 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper + 0:00:01.662 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:01.662 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:01.690 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:01.702 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:01.714 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:01.742 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:01.742 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.742 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.827 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (74.7967 bits per kmer). + 0:00:01.827 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.859 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.880 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:01.880 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:01.880 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:01.880 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:01.895 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:01.895 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:01.910 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:01.910 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:01.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:01.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:01.939 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:01.939 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:01.939 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:01.939 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:01.939 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:01.939 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.955 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.955 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.971 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.971 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.987 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.987 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.987 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:01.987 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.002 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.003 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.019 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.019 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.035 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.035 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:02.035 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:02.035 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.035 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.050 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.050 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:02.066 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:02.066 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:02.082 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:02.082 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:02.098 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:02.098 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.115 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.115 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:02.131 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:02.131 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.146 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.146 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:02.162 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:02.162 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.178 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.178 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:02.194 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:02.194 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:02.210 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:02.210 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:02.226 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:02.226 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.243 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.243 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:02.258 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:02.259 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.275 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.275 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:02.291 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:02.291 60M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) + 0:00:02.307 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:02.307 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:02.323 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:02.323 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:02.323 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 + 0:00:02.323 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:02.323 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa + 0:00:02.323 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta + 0:00:02.323 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg + 0:00:02.323 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta + 0:00:02.323 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta + 0:00:02.323 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:02.323 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph_with_scaffolds.gfa + 0:00:02.323 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/before_rr.fasta + 0:00:02.323 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K21/assembly_graph.fastg + 0:00:02.323 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/simplified_contigs.fasta + 0:00:02.323 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K21/final_contigs.fasta + 0:00:02.323 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:02.324 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 2 seconds Max read length detected as 100 == Running assembler: K33 @@ -3831,566 +3866,566 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 87) 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-3.13.0+dfsg2/spades_test/dataset.info) with K=33 - 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 : 51) SPAdes started - 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction - 0:00:00.001 4M / 4M INFO General (launch.hpp : 65) 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 - 0:00:00.010 4M / 4M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.010 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.010 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.010 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.010 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.010 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.010 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:02.799 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:03.161 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:03.161 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:03.581 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. - 0:00:03.581 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:03.612 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:03.612 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:03.612 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:03.612 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:03.612 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:03.612 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:05.957 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. - 0:00:06.329 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:06.730 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. - 0:00:06.730 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:06.748 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:07.309 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:07.310 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). - 0:00:07.310 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:07.385 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:07.386 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:07.386 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:07.386 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:07.446 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper - 0:00:07.446 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:07.446 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:07.477 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:07.505 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:07.517 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:07.577 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:07.577 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:07.577 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:07.937 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). - 0:00:07.937 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:07.990 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:08.018 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:08.018 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:08.018 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:08.018 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:08.037 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:08.037 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:08.061 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:08.061 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:08.085 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:08.085 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:08.105 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times - 0:00:08.105 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:08.105 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:08.105 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:08.106 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:08.106 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.133 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.133 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.146 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.146 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.157 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.157 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:08.157 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.157 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.157 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.157 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.157 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.158 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.158 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:08.158 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.177 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.177 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.189 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.189 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:08.213 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:08.214 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:08.214 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:08.214 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:08.214 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:08.229 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:08.229 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:08.246 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:08.246 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:08.269 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:08.269 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:08.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:08.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.305 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.305 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:08.317 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:08.317 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.329 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.329 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:08.345 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:08.345 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:08.361 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:08.361 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:08.377 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:08.377 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:08.401 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:08.401 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:08.413 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:08.413 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:08.426 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:08.426 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:08.443 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:08.443 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:08.457 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:08.457 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:08.473 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:08.473 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) - 0:00:08.497 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:08.497 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:08.509 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:08.509 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:08.509 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 - 0:00:08.509 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:08.509 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa - 0:00:08.510 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta - 0:00:08.510 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg - 0:00:08.510 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta - 0:00:08.510 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta - 0:00:08.510 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:08.510 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa - 0:00:08.510 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta - 0:00:08.510 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg - 0:00:08.510 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta - 0:00:08.510 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta - 0:00:08.510 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:08.510 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 8 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 : 51) SPAdes started + 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction + 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) 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 : 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 + 0:00:00.140 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.290 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.290 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.403 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. + 0:00:00.404 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.425 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:00.425 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.425 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.426 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.426 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:00.426 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:00.528 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. + 0:00:00.656 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.716 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. + 0:00:00.716 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.739 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.836 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.837 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). + 0:00:00.837 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:00.878 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:00.879 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:00.879 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:00.879 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:00.902 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper + 0:00:00.902 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:00.903 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:00.926 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:00.938 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:00.950 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:00.966 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:00.966 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.966 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.033 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (75.7202 bits per kmer). + 0:00:01.033 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.054 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.063 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:01.063 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:01.063 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:01.063 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:01.078 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:01.078 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:01.087 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:01.087 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:01.095 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:01.095 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:01.114 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times + 0:00:01.114 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:01.114 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:01.114 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:01.114 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:01.114 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.125 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.125 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.139 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.139 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.146 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.146 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:01.146 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.146 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.147 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.147 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:01.147 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.163 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.163 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.169 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.169 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.178 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.179 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:01.179 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:01.179 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:01.179 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:01.195 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:01.195 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:01.210 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:01.210 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:01.226 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:01.226 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:01.242 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:01.242 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.258 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.258 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:01.274 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:01.274 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.290 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.291 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:01.306 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:01.306 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:01.321 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:01.321 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:01.330 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:01.330 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:01.338 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:01.338 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:01.354 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:01.354 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.362 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.362 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:01.378 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:01.378 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.386 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.386 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:01.395 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:01.395 60M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) + 0:00:01.402 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:01.402 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:01.418 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:01.418 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:01.419 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 + 0:00:01.419 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:01.419 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa + 0:00:01.419 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta + 0:00:01.419 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg + 0:00:01.419 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta + 0:00:01.419 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta + 0:00:01.419 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:01.419 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa + 0:00:01.419 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta + 0:00:01.419 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg + 0:00:01.419 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta + 0:00:01.419 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta + 0:00:01.419 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:01.419 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 1 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K55/configs/config.info - 0:00:00.001 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K55/configs/mda_mode.info - 0:00:00.001 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K55/configs/meta_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 : 87) Starting SPAdes, built from N/A, git revision N/A - 0:00:00.002 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 - 0:00:00.002 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.0+dfsg2/spades_test/dataset.info) with K=55 - 0:00:00.002 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 - 0:00:00.002 4M / 4M INFO General (launch.hpp : 51) SPAdes started - 0:00:00.002 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction - 0:00:00.002 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 1 - 0:00:00.002 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached - 0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction - 0:00:00.002 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected - 0:00:00.003 4M / 4M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.003 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.003 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.003 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.003 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.003 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.003 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:02.149 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:02.627 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:02.627 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:02.977 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:02.977 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:03.014 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:03.014 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:03.014 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:03.014 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:03.014 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:03.014 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:05.200 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. - 0:00:05.581 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.849 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. - 0:00:05.849 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.874 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:06.050 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:06.051 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). - 0:00:06.051 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:06.085 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:06.085 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:06.085 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:06.105 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted - 0:00:06.125 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:06.137 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:06.169 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:06.169 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:06.169 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:06.353 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:06.353 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:06.375 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:06.395 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:06.395 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:06.395 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:06.395 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:06.395 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:06.395 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:06.395 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:08.453 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. - 0:00:08.790 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:08.990 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. - 0:00:08.990 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.007 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:09.081 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:09.082 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). - 0:00:09.082 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:09.097 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:09.097 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:09.097 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:09.106 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:09.106 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:09.106 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:09.106 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 4 candidates - 0:00:09.117 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:09.117 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:09.117 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:09.133 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:09.133 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper - 0:00:09.149 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times - 0:00:09.149 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover - 0:00:09.165 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times - 0:00:09.165 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage - 0:00:09.181 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 0 times - 0:00:09.181 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover - 0:00:09.197 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times - 0:00:09.197 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification - 0:00:09.197 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:09.197 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:09.197 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:09.197 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.215 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times - 0:00:09.215 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.229 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.229 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.245 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.245 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.245 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:09.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.261 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:09.261 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.277 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.277 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.293 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.293 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:09.293 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:09.293 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:09.293 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:09.293 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:09.293 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:09.293 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:11.301 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:11.701 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:11.929 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. - 0:00:11.929 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:11.953 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:12.046 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:12.047 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). - 0:00:12.047 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:12.069 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:12.070 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:12.070 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:12.097 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:12.097 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:12.097 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:12.097 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:12.109 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting - 0:00:12.109 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:12.109 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:12.109 64M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900 - 0:00:12.109 64M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 - 0:00:12.109 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:12.271 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:13.294 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:13.453 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:13.453 336M / 8G INFO General (pair_info_count.cpp : 213) 1636 paired reads (79.6495% of all) aligned to long edges - 0:00:13.455 64M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 - 0:00:13.553 256M / 8G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 - 0:00:13.554 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:13.561 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:13.562 256M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 - 0:00:13.562 256M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) - 0:00:13.562 256M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 - 0:00:13.576 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:13.594 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:13.605 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation - 0:00:13.605 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:13.605 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:13.605 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:13.613 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:13.613 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:13.613 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:13.613 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:13.613 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:13.613 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:13.649 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:13.685 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:13.685 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index - 0:00:13.685 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator - 0:00:13.709 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:13.709 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:13.709 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:13.709 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index - 0:00:13.709 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving - 0:00:13.709 64M / 8G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings - 0:00:13.709 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:13.709 64M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library - 0:00:13.709 64M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library - 0:00:13.709 64M / 8G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:13.709 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:13.710 64M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished - 0:00:13.710 64M / 8G INFO General (repeat_resolving.cpp : 75) Restoring initial path extend settings - 0:00:13.710 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:13.710 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:13.710 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta - 0:00:13.710 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg - 0:00:13.710 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.paths - 0:00:13.710 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/scaffolds.paths - 0:00:13.710 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Second Phase Setup - 0:00:13.710 64M / 8G INFO General (second_phase_setup.cpp : 20) Preparing second phase - 0:00:13.710 64M / 8G INFO General (second_phase_setup.cpp : 28) Moving preliminary contigs from /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.fasta to /build/spades-3.13.0+dfsg2/spades_test//K55/first_pe_contigs.fasta - 0:00:13.710 64M / 8G INFO General (second_phase_setup.cpp : 40) Ready to run second phase - 0:00:13.710 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:13.710 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:13.710 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:13.710 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:13.710 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:13.724 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:13.724 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:13.737 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:13.737 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:13.753 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:13.753 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:13.753 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:13.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:13.769 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:13.769 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:13.785 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:13.785 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:13.797 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:13.797 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:13.797 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:13.797 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:13.797 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:13.797 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:13.797 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:13.797 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:15.709 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:16.006 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:16.217 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. - 0:00:16.217 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:16.231 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:16.307 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:16.308 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). - 0:00:16.308 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:16.325 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:16.325 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:16.325 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:16.337 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:16.337 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:16.337 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:16.337 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:16.349 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:16.349 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:16.349 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:16.349 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:16.349 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:16.369 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:16.369 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:16.384 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:16.385 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:16.401 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:16.401 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:16.416 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:16.417 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:16.437 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:16.437 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:16.453 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:16.453 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:16.484 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:16.485 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:16.500 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:16.501 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:16.516 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:16.517 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage - 0:00:16.532 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times - 0:00:16.533 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper - 0:00:16.548 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times - 0:00:16.549 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:16.564 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:16.565 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 - 0:00:16.581 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:16.596 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:16.597 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:16.613 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:16.613 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:16.629 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:16.629 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) - 0:00:16.645 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times - 0:00:16.645 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) - 0:00:16.661 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:16.661 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges - 0:00:16.676 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times - 0:00:16.677 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:16.677 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 - 0:00:16.677 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction - 0:00:16.677 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:16.677 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:16.692 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions - 0:00:16.693 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed - 0:00:16.693 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides - 0:00:16.693 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:16.693 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:16.693 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta - 0:00:16.693 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg - 0:00:16.693 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/simplified_contigs.fasta - 0:00:16.693 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/intermediate_contigs.fasta - 0:00:16.693 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting - 0:00:16.693 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:16.693 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:16.693 64M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900 - 0:00:16.693 64M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 - 0:00:16.693 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:16.844 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:17.770 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:17.926 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:17.926 336M / 8G INFO General (pair_info_count.cpp : 213) 1636 paired reads (79.6495% of all) aligned to long edges - 0:00:17.929 64M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 - 0:00:18.024 256M / 8G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 - 0:00:18.024 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:18.037 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:18.037 256M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 - 0:00:18.037 256M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) - 0:00:18.037 256M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 - 0:00:18.057 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:18.070 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:18.080 64M / 8G INFO General (pair_info_count.cpp : 327) Mapping contigs library #1 - 0:00:18.080 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:18.080 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 1 reads processed - 0:00:18.080 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation - 0:00:18.080 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:18.080 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:18.080 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:18.089 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:18.089 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:18.089 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:18.089 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:18.089 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:18.089 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:18.113 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:18.137 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:18.137 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index - 0:00:18.137 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator - 0:00:18.153 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:18.153 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:18.153 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:18.153 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index - 0:00:18.153 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving - 0:00:18.153 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:18.153 64M / 8G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 - 0:00:18.153 64M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library - 0:00:18.153 64M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library - 0:00:18.153 64M / 8G INFO General (extenders_logic.cpp : 474) Using 1 single read library - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 359) Filling backbone edges for long reads scaffolding... - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 361) with long reads paths - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 370) Removing fake unique with paired-end libs - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 381) 0 unique edges - 0:00:18.153 64M / 8G INFO General (extenders_logic.cpp : 386) Using 0 long reads scaffolding libraries - 0:00:18.153 64M / 8G INFO General (extenders_logic.cpp : 396) Using additional coordinated coverage extender - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:18.153 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:18.153 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:18.153 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:18.153 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:18.153 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:18.153 64M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished - 0:00:18.153 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:18.153 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa - 0:00:18.153 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta - 0:00:18.153 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg - 0:00:18.153 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.paths - 0:00:18.154 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/scaffolds.paths - 0:00:18.154 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:18.154 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 18 seconds + 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K55/configs/mda_mode.info + 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K55/configs/meta_mode.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 : 87) 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-3.13.0+dfsg2/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): 15 + 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started + 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction + 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 1 + 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) 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 86.1526 + 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 + 0:00:00.118 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.257 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.258 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.354 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:00.354 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.374 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:00.375 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.375 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.375 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.375 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:00.375 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:00.483 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. + 0:00:00.601 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.662 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. + 0:00:00.662 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.682 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.759 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.760 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). + 0:00:00.760 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:00.791 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:00.791 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:00.791 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:00.806 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted + 0:00:00.823 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:00.843 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:00.874 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:00.875 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.875 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.953 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9168 bytes occupied (77.2856 bits per kmer). + 0:00:00.953 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:00.971 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:00.995 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:00.995 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:00.995 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.995 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.995 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.996 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:00.996 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.108 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. + 0:00:01.224 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.290 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. + 0:00:01.290 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.311 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.386 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:01.388 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). + 0:00:01.388 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:01.399 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:01.399 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:01.399 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:01.427 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:01.427 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:01.427 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:01.427 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 4 candidates + 0:00:01.446 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:01.447 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:01.447 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:01.463 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:01.463 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper + 0:00:01.478 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times + 0:00:01.478 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover + 0:00:01.494 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times + 0:00:01.494 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage + 0:00:01.510 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 0 times + 0:00:01.510 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover + 0:00:01.530 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times + 0:00:01.530 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification + 0:00:01.530 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:01.531 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:01.531 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:01.531 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.542 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times + 0:00:01.542 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.563 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.563 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.578 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.578 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:01.578 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.578 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.578 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.579 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.579 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:01.579 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.590 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.590 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.600 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.600 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.614 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.614 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:01.614 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:01.615 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.615 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.615 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.615 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.615 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.724 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:01.840 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.898 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. + 0:00:01.898 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.919 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.986 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:01.987 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). + 0:00:01.987 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:01.999 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:01.999 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:01.999 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:02.015 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:02.015 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:02.015 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:02.016 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:02.027 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting + 0:00:02.027 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:02.027 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:02.027 60M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900 + 0:00:02.027 60M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 + 0:00:02.027 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:02.252 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:03.199 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:03.391 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:03.391 316M / 8G INFO General (pair_info_count.cpp : 213) 1636 paired reads (79.6495% of all) aligned to long edges + 0:00:03.436 60M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 + 0:00:03.639 252M / 8G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 + 0:00:03.639 252M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:03.647 252M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:03.648 252M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 + 0:00:03.648 252M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) + 0:00:03.648 252M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 + 0:00:03.667 264M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:03.683 264M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:03.728 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation + 0:00:03.728 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:03.728 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:03.728 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:03.738 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:03.738 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:03.738 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:03.738 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:03.739 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:03.739 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:03.778 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:03.810 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:03.810 60M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index + 0:00:03.811 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator + 0:00:03.824 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:03.824 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:03.824 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:03.824 60M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index + 0:00:03.824 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving + 0:00:03.825 60M / 8G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings + 0:00:03.825 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:03.825 60M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library + 0:00:03.825 60M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library + 0:00:03.825 60M / 8G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:03.825 60M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished + 0:00:03.825 60M / 8G INFO General (repeat_resolving.cpp : 75) Restoring initial path extend settings + 0:00:03.825 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:03.825 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:03.825 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta + 0:00:03.825 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg + 0:00:03.825 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.paths + 0:00:03.825 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/scaffolds.paths + 0:00:03.826 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Second Phase Setup + 0:00:03.826 60M / 8G INFO General (second_phase_setup.cpp : 20) Preparing second phase + 0:00:03.826 60M / 8G INFO General (second_phase_setup.cpp : 28) Moving preliminary contigs from /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.fasta to /build/spades-3.13.0+dfsg2/spades_test//K55/first_pe_contigs.fasta + 0:00:03.826 60M / 8G INFO General (second_phase_setup.cpp : 40) Ready to run second phase + 0:00:03.826 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:03.826 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:03.830 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:03.831 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:03.831 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:03.854 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:03.854 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:03.899 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:03.899 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:03.922 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:03.922 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:03.923 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:03.923 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:03.923 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:03.942 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:03.942 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:03.950 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:03.950 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:03.966 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:03.967 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:03.967 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:03.967 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:03.967 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:03.967 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:03.967 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:03.967 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:04.095 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:04.237 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:04.314 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. + 0:00:04.314 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:04.337 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:04.421 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:04.422 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). + 0:00:04.422 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:04.440 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:04.440 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:04.440 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:04.454 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:04.454 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:04.455 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:04.455 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:04.474 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:04.475 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:04.475 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:04.475 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:04.475 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:04.486 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:04.486 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:04.506 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:04.506 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:04.518 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:04.518 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:04.530 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:04.531 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:04.543 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:04.543 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:04.562 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:04.562 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:04.575 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:04.575 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:04.594 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:04.594 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:04.602 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:04.602 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:04.618 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:04.618 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage + 0:00:04.631 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times + 0:00:04.631 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper + 0:00:04.650 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times + 0:00:04.650 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:04.662 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:04.662 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:04.678 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:04.678 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:04.690 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:04.690 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:04.706 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:04.706 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:04.722 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:04.722 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) + 0:00:04.734 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times + 0:00:04.734 60M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) + 0:00:04.750 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:04.751 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges + 0:00:04.762 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times + 0:00:04.763 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:04.763 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 + 0:00:04.763 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction + 0:00:04.763 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:04.763 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:04.781 60M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions + 0:00:04.781 60M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed + 0:00:04.781 60M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides + 0:00:04.782 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:04.782 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:04.782 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta + 0:00:04.782 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg + 0:00:04.782 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/simplified_contigs.fasta + 0:00:04.782 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/intermediate_contigs.fasta + 0:00:04.782 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting + 0:00:04.782 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:04.782 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:04.782 60M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900 + 0:00:04.782 60M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 + 0:00:04.782 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:05.019 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:05.958 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:06.155 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:06.155 316M / 8G INFO General (pair_info_count.cpp : 213) 1636 paired reads (79.6495% of all) aligned to long edges + 0:00:06.192 60M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 + 0:00:06.376 252M / 8G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 + 0:00:06.376 252M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:06.387 252M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:06.387 252M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 + 0:00:06.387 252M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) + 0:00:06.387 252M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 + 0:00:06.405 264M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:06.423 264M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:06.464 60M / 8G INFO General (pair_info_count.cpp : 327) Mapping contigs library #1 + 0:00:06.464 60M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:06.465 60M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 1 reads processed + 0:00:06.465 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation + 0:00:06.465 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:06.465 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:06.465 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:06.478 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:06.478 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:06.479 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:06.479 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:06.479 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:06.479 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:06.506 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:06.535 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:06.535 60M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index + 0:00:06.535 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator + 0:00:06.542 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:06.542 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:06.542 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:06.542 60M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index + 0:00:06.543 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving + 0:00:06.543 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:06.543 60M / 8G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 + 0:00:06.543 60M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library + 0:00:06.543 60M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library + 0:00:06.543 60M / 8G INFO General (extenders_logic.cpp : 474) Using 1 single read library + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 359) Filling backbone edges for long reads scaffolding... + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 361) with long reads paths + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 370) Removing fake unique with paired-end libs + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 381) 0 unique edges + 0:00:06.543 60M / 8G INFO General (extenders_logic.cpp : 386) Using 0 long reads scaffolding libraries + 0:00:06.543 60M / 8G INFO General (extenders_logic.cpp : 396) Using additional coordinated coverage extender + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:06.543 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:06.543 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:06.543 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:06.543 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:06.543 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:06.543 60M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished + 0:00:06.543 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:06.543 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph_with_scaffolds.gfa + 0:00:06.543 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K55/before_rr.fasta + 0:00:06.544 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K55/assembly_graph.fastg + 0:00:06.544 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/final_contigs.paths + 0:00:06.544 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K55/scaffolds.paths + 0:00:06.544 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:06.545 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 6 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 @@ -4415,7 +4450,7 @@ System information: SPAdes version: 3.13.0 Python version: 2.7.16 - OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-debian-10.11 + OS: Linux-5.10.0-9-amd64-x86_64-with-debian-10.11 Output dir: /build/spades-3.13.0+dfsg2/spades_test Mode: read error correction and assembling @@ -4463,59 +4498,59 @@ 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-3.13.0+dfsg2/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 + 0:00:00.000 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 === 0:00:00.001 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 (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 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 262144 - 0:00:01.666 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:01.723 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:01.761 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed - 0:00:02.065 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:02.291 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. - 0:00:02.291 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:02.320 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:02.414 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:02.416 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). - 0:00:02.416 64M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order - 0:00:02.427 64M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. - 0:00:02.466 64M / 8G INFO General (main.cpp : 155) Extracting clusters - 0:00:02.495 64M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 - 0:00:02.495 64M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. - 0:00:02.495 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz - 0:00:02.534 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz - 0:00:02.575 64M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. - 0:00:02.575 64M / 8G INFO K-mer Counting (kmer_data.cpp : 403) There are 1974 kmers in total. Among them 0 (0%) are singletons. - 0:00:02.575 64M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 - 0:00:02.591 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 - 0:00:02.591 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)) - 0:00:02.591 64M / 8G INFO General (main.cpp : 178) Finished clustering. - 0:00:02.591 64M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. - 0:00:02.646 64M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. - 0:00:02.646 64M / 8G INFO General (main.cpp : 222) Solid k-mers finalized - 0:00:02.647 64M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. - 0:00:02.647 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 - 0:00:02.816 408M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. - 0:00:02.840 408M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 - 0:00:02.845 408M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 - 0:00:02.914 64M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. - 0:00:02.914 64M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. - 0:00:02.915 64M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml - 0:00:02.915 64M / 8G INFO General (main.cpp : 262) All done. Exiting. + 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 279620 + 0:00:00.067 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:00.126 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:00.166 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed + 0:00:00.299 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.366 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. + 0:00:00.366 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.378 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.462 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.463 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). + 0:00:00.463 60M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order + 0:00:00.474 60M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. + 0:00:00.513 60M / 8G INFO General (main.cpp : 155) Extracting clusters + 0:00:00.541 60M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 + 0:00:00.542 60M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. + 0:00:00.542 60M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz + 0:00:00.585 60M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz + 0:00:00.647 60M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. + 0:00:00.647 60M / 8G INFO K-mer Counting (kmer_data.cpp : 403) There are 1974 kmers in total. Among them 0 (0%) are singletons. + 0:00:00.647 60M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 + 0:00:00.662 60M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 + 0:00:00.662 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)) + 0:00:00.662 60M / 8G INFO General (main.cpp : 178) Finished clustering. + 0:00:00.662 60M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 15 threads. + 0:00:00.733 60M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. + 0:00:00.733 60M / 8G INFO General (main.cpp : 222) Solid k-mers finalized + 0:00:00.733 60M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 15 threads. + 0:00:00.733 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 + 0:00:01.046 388M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. + 0:00:01.070 388M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 + 0:00:01.076 388M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 + 0:00:01.202 60M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. + 0:00:01.202 60M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. + 0:00:01.202 60M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml + 0:00:01.202 60M / 8G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) @@ -4537,239 +4572,239 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 87) 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-3.13.0+dfsg2/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 : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) 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) - 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads - 0:00:00.122 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written - 0:00:00.124 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads - 0:00:00.319 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.320 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads - 0:00:00.517 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written - 0:00:00.519 4M / 140M INFO General (construction.cpp : 111) Max read length 100 - 0:00:00.519 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 - 0:00:00.519 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting - 0:00:00.520 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:00.520 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:00.520 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb - 0:00:00.520 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:02.360 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:02.698 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:02.698 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:02.957 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. - 0:00:02.957 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:02.971 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:02.971 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:02.971 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:02.971 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:02.971 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:02.971 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:04.718 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. - 0:00:05.045 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.262 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. - 0:00:05.262 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.275 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:05.367 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:05.368 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). - 0:00:05.368 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:05.398 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:05.398 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping - 0:00:05.398 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) - 0:00:05.398 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping - 0:00:05.429 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper - 0:00:05.429 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:05.429 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:05.445 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted - 0:00:05.457 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:05.473 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:05.505 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:05.505 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:05.505 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:05.587 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). - 0:00:05.587 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:05.611 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:05.627 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:05.627 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 72 - 0:00:05.627 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage - 0:00:05.627 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 225.839 - 0:00:05.627 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 22.5839 - 0:00:05.627 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 22.5839 - 0:00:05.627 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:05.627 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:05.627 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:05.627 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:05.627 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:05.641 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:05.641 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges - 0:00:05.641 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT - 0:00:05.673 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times - 0:00:05.673 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges - 0:00:05.689 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times - 0:00:05.689 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:05.705 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:05.705 64M / 8G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections - 0:00:05.705 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:05.705 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:05.705 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:05.705 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:05.705 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:05.705 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:05.705 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:05.729 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:05.729 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:05.745 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:05.745 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:05.761 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:05.761 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:05.777 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:05.777 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:05.777 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:05.793 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:05.793 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:05.809 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:05.809 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:05.825 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:05.825 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:05.841 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:05.841 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:05.841 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:05.857 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:05.857 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:05.873 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:05.873 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:05.889 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:05.889 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:05.897 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:05.897 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:05.897 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:05.913 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:05.913 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:05.929 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:05.929 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:05.945 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:05.945 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:05.961 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:05.961 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:05.961 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:05.977 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:05.977 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:05.993 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:05.993 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.009 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.009 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.025 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.025 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:06.025 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.041 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.041 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:06.057 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:06.057 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.073 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.073 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.089 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.089 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:06.089 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.105 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.105 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:06.121 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:06.121 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.137 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.137 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.153 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.153 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:06.153 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.169 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.169 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:06.185 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:06.185 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.201 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.201 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.217 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.217 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:06.217 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.233 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.233 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:06.249 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:06.249 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.265 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.265 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.281 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:06.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.297 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.297 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:06.313 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:06.313 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.329 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.329 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.345 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.345 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:06.345 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.361 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.361 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:06.377 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:06.377 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.393 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.393 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:06.405 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:06.405 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:06.405 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:06.405 64M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled - 0:00:06.405 64M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled - 0:00:06.405 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:06.405 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:06.405 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:06.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:06.412 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:06.412 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:06.412 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:06.412 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 - 0:00:06.412 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:06.412 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa - 0:00:06.412 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta - 0:00:06.412 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg - 0:00:06.412 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta - 0:00:06.412 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta - 0:00:06.412 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:06.412 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa - 0:00:06.412 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta - 0:00:06.412 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg - 0:00:06.412 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta - 0:00:06.412 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta - 0:00:06.412 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:06.412 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 6 seconds + 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads + 0:00:00.152 124M / 132M INFO General (binary_converter.hpp : 117) 2054 reads written + 0:00:00.163 4M / 132M INFO General (read_converter.hpp : 87) Converting single reads + 0:00:00.401 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:00.422 4M / 196M INFO General (read_converter.hpp : 95) Converting merged reads + 0:00:00.650 184M / 196M INFO General (binary_converter.hpp : 117) 0 reads written + 0:00:00.670 4M / 196M INFO General (construction.cpp : 111) Max read length 100 + 0:00:00.670 4M / 196M INFO General (construction.cpp : 117) Average read length 86.1526 + 0:00:00.670 4M / 196M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting + 0:00:00.670 4M / 196M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 225 files using 15 threads. This might take a while. + 0:00:00.670 4M / 196M INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.670 4M / 196M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04436 Gb + 0:00:00.670 4M / 196M INFO General (kmer_splitters.hpp : 97) Using cell size of 149130 + 0:00:00.822 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.941 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.941 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.054 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. + 0:00:01.054 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.080 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:01.080 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.080 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.080 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.080 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.080 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.175 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. + 0:00:01.305 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.366 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. + 0:00:01.367 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.378 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.472 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:01.473 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). + 0:00:01.473 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:01.514 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:01.515 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping + 0:00:01.515 60M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) + 0:00:01.515 60M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping + 0:00:01.554 60M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper + 0:00:01.554 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:01.554 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:01.570 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted + 0:00:01.586 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:01.602 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:01.634 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:01.634 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.634 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.723 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9200 bytes occupied (75.7202 bits per kmer). + 0:00:01.723 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.747 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.764 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:01.764 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 72 + 0:00:01.764 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage + 0:00:01.765 60M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 225.839 + 0:00:01.765 60M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 22.5839 + 0:00:01.765 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 22.5839 + 0:00:01.765 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:01.765 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:01.765 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:01.765 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:01.765 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:01.786 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:01.786 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges + 0:00:01.786 60M / 8G INFO General (simplification.cpp : 76) Removing short polyAT + 0:00:01.822 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times + 0:00:01.822 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges + 0:00:01.838 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times + 0:00:01.838 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:01.854 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:01.854 60M / 8G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections + 0:00:01.854 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:01.854 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:01.854 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:01.854 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:01.855 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:01.855 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:01.855 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.870 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.870 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.886 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.886 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.902 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.902 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.918 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.918 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:01.918 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.934 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.934 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.950 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.951 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.966 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.966 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.982 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.982 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:01.983 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.998 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.998 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.014 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.014 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.030 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.030 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.046 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.046 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:02.046 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.063 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.063 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.078 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.078 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.094 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.094 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.110 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.110 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:02.110 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.126 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.126 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.142 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.142 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.158 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.158 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.174 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.174 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:02.174 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.190 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.190 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.208 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.208 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.222 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.222 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.238 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.238 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:02.238 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.254 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.254 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.270 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.270 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.286 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.286 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.302 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.302 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:02.302 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.318 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.318 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.334 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.334 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.350 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.351 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.366 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.366 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:02.366 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.382 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.382 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.398 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.398 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.414 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.414 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.430 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.430 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:02.430 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.446 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.446 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.462 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.462 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.478 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.478 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.494 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.494 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:02.494 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.510 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.510 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.526 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.526 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.542 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.542 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.558 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.558 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:02.558 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:02.559 60M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled + 0:00:02.559 60M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled + 0:00:02.559 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.559 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.559 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.574 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.574 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.590 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.590 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:02.606 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:02.606 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.628 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.628 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:02.642 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:02.642 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.658 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.658 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:02.666 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:02.666 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:02.682 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:02.682 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.690 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.690 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.706 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.706 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:02.723 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:02.723 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.738 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.738 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:02.754 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:02.754 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.770 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.770 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:02.786 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:02.786 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:02.802 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:02.802 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:02.803 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:02.803 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 + 0:00:02.803 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:02.803 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa + 0:00:02.803 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta + 0:00:02.803 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg + 0:00:02.803 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta + 0:00:02.803 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta + 0:00:02.803 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:02.803 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph_with_scaffolds.gfa + 0:00:02.803 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/before_rr.fasta + 0:00:02.803 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K33/assembly_graph.fastg + 0:00:02.803 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/simplified_contigs.fasta + 0:00:02.803 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K33/final_contigs.fasta + 0:00:02.803 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:02.803 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 2 seconds Max read length detected as 100 == Running assembler: K49 @@ -4781,7 +4816,7 @@ 0:00:00.000 4M / 4M INFO General (main.cpp : 87) 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-3.13.0+dfsg2/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): 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 : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 @@ -4791,365 +4826,365 @@ 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 - 0:00:01.941 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K - 0:00:02.303 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads - 0:00:02.303 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:02.561 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 956 kmers in total. - 0:00:02.561 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:02.581 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction - 0:00:02.581 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:02.581 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:02.581 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:02.581 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:02.581 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:04.577 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 956 kmers. - 0:00:04.945 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:05.293 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 957 kmers in total. - 0:00:05.293 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:05.330 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:05.709 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:05.710 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (81.6552 bits per kmer). - 0:00:05.710 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers - 0:00:05.793 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. - 0:00:05.793 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph - 0:00:05.793 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths - 0:00:05.813 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5 sequences extracted - 0:00:05.821 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops - 0:00:05.837 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected - 0:00:05.869 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) - 0:00:05.869 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:05.869 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:06.153 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.6736 bits per kmer). - 0:00:06.153 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. - 0:00:06.189 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM - 0:00:06.214 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding - 0:00:06.214 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 53 - 0:00:06.214 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage - 0:00:06.214 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 162.527 - 0:00:06.214 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 16.2527 - 0:00:06.214 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 16.2527 - 0:00:06.214 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 - 0:00:06.214 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:06.214 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:06.214 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:06.214 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:06.214 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:06.214 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:06.214 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:08.341 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 10 sequences. - 0:00:08.845 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:09.233 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 956 kmers in total. - 0:00:09.233 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:09.262 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:09.505 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:09.506 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.6736 bits per kmer). - 0:00:09.506 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:09.537 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:09.537 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:09.538 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:09.573 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:09.573 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:09.573 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:09.573 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:09.589 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification - 0:00:09.589 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning - 0:00:09.589 64M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled - 0:00:09.589 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover - 0:00:09.617 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times - 0:00:09.617 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges - 0:00:09.617 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT - 0:00:09.661 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times - 0:00:09.661 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges - 0:00:09.685 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times - 0:00:09.685 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:09.713 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 2 times - 0:00:09.713 64M / 8G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections - 0:00:09.713 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:09.713 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/0/0 - 0:00:09.713 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification - 0:00:09.713 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started - 0:00:09.713 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:09.713 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 - 0:00:09.713 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.733 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:09.733 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:09.757 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:09.757 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.781 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.781 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.805 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.805 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 - 0:00:09.805 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.833 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:09.833 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:09.849 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:09.849 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.877 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.877 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.897 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.897 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 - 0:00:09.897 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:09.925 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:09.925 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:09.949 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:09.949 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:09.977 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:09.977 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:09.989 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:09.989 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 - 0:00:09.989 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.017 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.017 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.033 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.033 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.045 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.045 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.057 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.057 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 - 0:00:10.057 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.077 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.077 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.089 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.089 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.109 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.109 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.121 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.121 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 - 0:00:10.121 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.141 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.141 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.157 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.157 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.169 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.169 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.189 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.189 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 - 0:00:10.189 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.209 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.209 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.221 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.221 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.233 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.233 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.253 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.253 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 - 0:00:10.253 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.265 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.265 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.285 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.285 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.297 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.297 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.317 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.317 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 - 0:00:10.317 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.329 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.329 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.345 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.345 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.365 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.365 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.377 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.377 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 - 0:00:10.377 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.397 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.397 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.409 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.409 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.429 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.429 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.441 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 - 0:00:10.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:10.461 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:10.461 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper - 0:00:10.477 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times - 0:00:10.477 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:10.489 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:10.489 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover - 0:00:10.509 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times - 0:00:10.509 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer - 0:00:10.509 64M / 8G INFO General (graph_pack.hpp : 101) Index refill - 0:00:10.509 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index - 0:00:10.509 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. - 0:00:10.509 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 - 0:00:10.509 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb - 0:00:10.509 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 - 0:00:12.718 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. - 0:00:13.091 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. - 0:00:13.293 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. - 0:00:13.293 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. - 0:00:13.321 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices - 0:00:13.397 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. - 0:00:13.398 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (82.103 bits per kmer). - 0:00:13.398 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. - 0:00:13.413 64M / 8G INFO General (edge_index.hpp : 92) Index refilled - 0:00:13.413 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps - 0:00:13.413 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) - 0:00:13.429 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads - 0:00:13.429 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices - 0:00:13.429 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps - 0:00:13.429 64M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates - 0:00:13.441 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup - 0:00:13.441 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification - 0:00:13.441 64M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled - 0:00:13.441 64M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled - 0:00:13.441 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:13.441 64M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance - 0:00:13.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:13.457 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:13.457 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:13.473 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:13.473 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:13.485 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:13.485 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:13.501 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:13.501 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:13.517 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:13.517 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:13.533 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:13.533 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:13.549 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:13.549 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:13.565 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:13.565 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:13.581 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:13.581 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover - 0:00:13.597 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times - 0:00:13.597 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover - 0:00:13.613 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times - 0:00:13.613 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper - 0:00:13.629 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times - 0:00:13.629 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper - 0:00:13.645 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times - 0:00:13.645 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover - 0:00:13.661 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times - 0:00:13.661 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover - 0:00:13.677 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times - 0:00:13.677 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips - 0:00:13.693 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times - 0:00:13.693 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges - 0:00:13.693 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage - 0:00:13.693 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 163.349 - 0:00:13.693 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction - 0:00:13.693 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:13.693 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:13.711 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions - 0:00:13.711 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed - 0:00:13.711 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides - 0:00:13.712 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:13.712 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph_with_scaffolds.gfa - 0:00:13.712 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/before_rr.fasta - 0:00:13.712 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph.fastg - 0:00:13.712 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/simplified_contigs.fasta - 0:00:13.712 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/intermediate_contigs.fasta - 0:00:13.712 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting - 0:00:13.712 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process - 0:00:13.712 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done - 0:00:13.712 64M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 951 - 0:00:13.712 64M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 - 0:00:13.712 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) - 0:00:13.841 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:15.398 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:15.733 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) - 0:00:15.733 336M / 8G INFO General (pair_info_count.cpp : 213) 1750 paired reads (85.1996% of all) aligned to long edges - 0:00:15.736 64M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.706, deviation = 10.4968, left quantile = 201, right quantile = 228, read length = 100 - 0:00:15.736 64M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 - 0:00:15.736 64M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) - 0:00:15.736 64M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0 - 0:00:15.754 76M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:15.769 76M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed - 0:00:15.787 64M / 8G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #0 - 0:00:15.787 64M / 8G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well - 0:00:15.787 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper - 0:00:15.805 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 4108 reads processed - 0:00:15.806 64M / 8G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0 - 0:00:15.806 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation - 0:00:15.806 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 - 0:00:15.806 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done - 0:00:15.806 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator - 0:00:15.818 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info - 0:00:15.818 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 - 0:00:15.818 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering - 0:00:15.818 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information - 0:00:15.818 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished - 0:00:15.818 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information - 0:00:15.870 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:15.917 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 - 0:00:15.917 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving - 0:00:15.917 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving - 0:00:15.917 64M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started - 0:00:15.917 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 - 0:00:15.917 64M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library - 0:00:15.917 64M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library - 0:00:15.917 64M / 8G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries - 0:00:15.917 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:15.918 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps - 0:00:15.918 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths - 0:00:15.918 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 257) Paths finalized - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 462) Finalizing main paths - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 81 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 111 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 467) Finalizing paths - hard - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 467) Finalizing paths - soft - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 56 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 71 - 0:00:15.918 64M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished - 0:00:15.918 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output - 0:00:15.918 64M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph_with_scaffolds.gfa - 0:00:15.918 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/before_rr.fasta - 0:00:15.918 64M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph.fastg - 0:00:15.919 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K49/transcripts.paths - 0:00:15.919 64M / 8G INFO General (launch.hpp : 149) SPAdes finished - 0:00:15.919 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 15 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 + 0:00:00.119 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K + 0:00:00.254 60M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads + 0:00:00.254 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.346 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 956 kmers in total. + 0:00:00.347 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.365 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction + 0:00:00.365 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.365 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:00.366 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:00.366 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:00.366 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:00.475 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 956 kmers. + 0:00:00.602 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:00.652 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 957 kmers in total. + 0:00:00.652 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:00.674 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:00.810 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:00.811 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (81.6552 bits per kmer). + 0:00:00.811 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers + 0:00:00.826 60M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. + 0:00:00.827 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph + 0:00:00.827 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths + 0:00:00.842 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5 sequences extracted + 0:00:00.859 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops + 0:00:00.875 60M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected + 0:00:00.911 60M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) + 0:00:00.911 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:00.911 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.058 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9176 bytes occupied (76.7866 bits per kmer). + 0:00:01.058 60M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. + 0:00:01.078 60M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM + 0:00:01.115 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding + 0:00:01.116 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 53 + 0:00:01.116 60M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage + 0:00:01.116 60M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 162.527 + 0:00:01.116 60M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 16.2527 + 0:00:01.116 60M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 16.2527 + 0:00:01.116 60M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 + 0:00:01.116 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:01.116 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:01.116 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:01.116 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:01.116 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:01.116 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:01.116 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:01.223 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 10 sequences. + 0:00:01.355 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:01.418 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 956 kmers in total. + 0:00:01.418 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:01.439 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:01.512 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:01.513 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.6736 bits per kmer). + 0:00:01.513 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:01.531 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:01.531 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:01.531 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:01.540 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:01.541 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:01.541 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:01.541 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:01.555 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification + 0:00:01.555 60M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning + 0:00:01.555 60M / 8G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled + 0:00:01.555 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover + 0:00:01.566 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times + 0:00:01.566 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges + 0:00:01.566 60M / 8G INFO General (simplification.cpp : 76) Removing short polyAT + 0:00:01.587 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times + 0:00:01.587 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges + 0:00:01.598 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times + 0:00:01.598 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:01.610 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 2 times + 0:00:01.610 60M / 8G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections + 0:00:01.610 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:01.610 60M / 8G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/0/0 + 0:00:01.610 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification + 0:00:01.610 60M / 8G INFO General (simplification.cpp : 357) Graph simplification started + 0:00:01.611 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:01.611 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 + 0:00:01.611 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.618 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.618 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.630 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.630 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.643 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.643 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.656 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.656 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 + 0:00:01.656 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.666 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.666 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.682 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.682 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.694 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.694 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.702 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.702 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 + 0:00:01.702 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.714 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.714 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.727 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.727 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.742 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.742 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.758 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.758 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 + 0:00:01.758 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.770 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.770 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.778 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.778 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.794 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.794 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.806 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.806 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 + 0:00:01.806 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.814 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.814 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.830 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.830 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.842 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.842 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.850 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.850 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 + 0:00:01.850 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.863 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.863 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.878 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.878 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.894 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.894 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.906 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.906 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 + 0:00:01.906 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.922 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.922 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.938 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.938 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.946 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.946 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:01.958 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:01.958 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 + 0:00:01.958 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:01.966 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:01.966 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:01.979 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:01.979 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:01.994 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:01.994 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.010 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.010 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 + 0:00:02.010 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.022 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.022 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.038 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.038 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.050 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.050 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.058 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.058 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 + 0:00:02.058 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.071 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.071 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.086 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.086 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.102 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.102 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.115 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.115 60M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 + 0:00:02.115 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.122 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.122 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper + 0:00:02.134 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times + 0:00:02.134 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.142 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.142 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover + 0:00:02.158 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times + 0:00:02.158 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer + 0:00:02.158 60M / 8G INFO General (graph_pack.hpp : 101) Index refill + 0:00:02.158 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index + 0:00:02.158 60M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 240 files using 15 threads. This might take a while. + 0:00:02.159 60M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 + 0:00:02.159 60M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.04314 Gb + 0:00:02.159 60M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 + 0:00:02.272 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. + 0:00:02.399 60M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. + 0:00:02.460 60M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. + 0:00:02.460 60M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. + 0:00:02.472 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices + 0:00:02.558 60M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. + 0:00:02.559 60M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (82.103 bits per kmer). + 0:00:02.560 60M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. + 0:00:02.575 60M / 8G INFO General (edge_index.hpp : 92) Index refilled + 0:00:02.575 60M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps + 0:00:02.575 60M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) + 0:00:02.603 60M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads + 0:00:02.603 60M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices + 0:00:02.603 60M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps + 0:00:02.603 60M / 8G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 0 gaps after checking 0 candidates + 0:00:02.631 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup + 0:00:02.631 60M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification + 0:00:02.631 60M / 8G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled + 0:00:02.631 60M / 8G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled + 0:00:02.631 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.631 60M / 8G INFO General (graph_simplification.hpp : 634) Creating parallel br instance + 0:00:02.631 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.658 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.658 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.678 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.678 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:02.706 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:02.706 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.731 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.731 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:02.746 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:02.746 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.771 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.771 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:02.794 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:02.794 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:02.818 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:02.818 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.842 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.842 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover + 0:00:02.854 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times + 0:00:02.855 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover + 0:00:02.878 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times + 0:00:02.878 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper + 0:00:02.886 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times + 0:00:02.886 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper + 0:00:02.902 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times + 0:00:02.902 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover + 0:00:02.918 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times + 0:00:02.918 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover + 0:00:02.934 60M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times + 0:00:02.934 60M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips + 0:00:02.950 60M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times + 0:00:02.950 60M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges + 0:00:02.950 60M / 8G INFO General (simplification.cpp : 470) Counting average coverage + 0:00:02.950 60M / 8G INFO General (simplification.cpp : 476) Average coverage = 163.349 + 0:00:02.950 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction + 0:00:02.950 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:02.950 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:02.969 60M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions + 0:00:02.969 60M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed + 0:00:02.969 60M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides + 0:00:02.969 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:02.969 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph_with_scaffolds.gfa + 0:00:02.969 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/before_rr.fasta + 0:00:02.969 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph.fastg + 0:00:02.969 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/simplified_contigs.fasta + 0:00:02.969 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/intermediate_contigs.fasta + 0:00:02.970 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting + 0:00:02.970 60M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process + 0:00:02.970 60M / 8G INFO General (graph_pack.hpp : 111) Normalizing done + 0:00:02.970 60M / 8G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 951 + 0:00:02.970 60M / 8G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 + 0:00:02.970 60M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) + 0:00:03.189 316M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:04.065 316M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:04.246 316M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) + 0:00:04.246 316M / 8G INFO General (pair_info_count.cpp : 213) 1750 paired reads (85.1996% of all) aligned to long edges + 0:00:04.275 60M / 8G INFO General (pair_info_count.cpp : 354) Insert size = 214.706, deviation = 10.4968, left quantile = 201, right quantile = 228, read length = 100 + 0:00:04.275 60M / 8G INFO General (pair_info_count.cpp : 383) Mapping library #0 + 0:00:04.275 60M / 8G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) + 0:00:04.275 60M / 8G INFO General (pair_info_count.cpp : 289) Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0 + 0:00:04.294 72M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:04.308 72M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed + 0:00:04.321 60M / 8G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #0 + 0:00:04.321 60M / 8G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well + 0:00:04.321 60M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper + 0:00:04.338 60M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 4108 reads processed + 0:00:04.339 60M / 8G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0 + 0:00:04.339 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation + 0:00:04.339 60M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 + 0:00:04.339 60M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done + 0:00:04.339 60M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator + 0:00:04.358 60M / 8G INFO General (distance_estimation.cpp : 34) Filtering info + 0:00:04.358 60M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 + 0:00:04.358 60M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering + 0:00:04.358 60M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information + 0:00:04.358 60M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished + 0:00:04.358 60M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information + 0:00:04.386 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:04.418 60M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 + 0:00:04.418 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving + 0:00:04.418 60M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving + 0:00:04.418 60M / 8G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started + 0:00:04.418 60M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 + 0:00:04.419 60M / 8G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library + 0:00:04.419 60M / 8G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library + 0:00:04.419 60M / 8G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:04.419 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 455) Gap closing completed + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 234) Finalizing paths + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 236) Deduplicating paths + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 240) Paths deduplicated + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps + 0:00:04.419 60M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths + 0:00:04.419 60M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 257) Paths finalized + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 462) Finalizing main paths + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 81 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 111 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 467) Finalizing paths - hard + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 467) Finalizing paths - soft + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 56 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 + 0:00:04.419 60M / 8G INFO General (launcher.cpp : 281) Length cutoff: 71 + 0:00:04.420 60M / 8G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished + 0:00:04.420 60M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output + 0:00:04.420 60M / 8G INFO General (contig_output_stage.cpp : 40) Writing GFA to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph_with_scaffolds.gfa + 0:00:04.420 60M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.0+dfsg2/spades_test//K49/before_rr.fasta + 0:00:04.420 60M / 8G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /build/spades-3.13.0+dfsg2/spades_test//K49/assembly_graph.fastg + 0:00:04.420 60M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.0+dfsg2/spades_test//K49/transcripts.paths + 0:00:04.420 60M / 8G INFO General (launch.hpp : 149) SPAdes finished + 0:00:04.420 60M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 4 seconds ===== Assembling finished. Used k-mer sizes: 33, 49 @@ -5234,8 +5269,8 @@ dh_gencontrol -O--sourcedirectory=src -O--buildsystem=cmake dh_md5sums -O--sourcedirectory=src -O--buildsystem=cmake dh_builddeb -O--sourcedirectory=src -O--buildsystem=cmake -dpkg-deb: building package 'spades' in '../spades_3.13.0+dfsg2-2_amd64.deb'. dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_3.13.0+dfsg2-2_amd64.deb'. +dpkg-deb: building package 'spades' in '../spades_3.13.0+dfsg2-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../spades_3.13.0+dfsg2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5243,12 +5278,14 @@ 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/2692573/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2692573/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/3267546 and its subdirectories -I: Current time: Tue Jan 17 03:31:19 -12 2023 -I: pbuilder-time-stamp: 1673969479 +I: removing directory /srv/workspace/pbuilder/2692573 and its subdirectories +I: Current time: Wed Dec 15 23:42:45 +14 2021 +I: pbuilder-time-stamp: 1639561365