I: pbuilder: network access will be disabled during build 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 I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spades_3.13.0+dfsg2-2.dsc] I: copying [./spades_3.13.0+dfsg2.orig.tar.xz] I: copying [./spades_3.13.0+dfsg2-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error 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 dpkg-source: info: extracting spades in spades-3.13.0+dfsg2 dpkg-source: info: unpacking spades_3.13.0+dfsg2.orig.tar.xz dpkg-source: info: unpacking spades_3.13.0+dfsg2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 0003_accept-system-bwa.patch dpkg-source: info: applying 0101_cmake_ignore_removed_python-yaml.patch dpkg-source: info: applying 0102_cmake_ignore_removed_python-joblib.patch dpkg-source: info: applying 0103_use-debian-packaged-bwa.patch dpkg-source: info: applying 0110_build_single_thread.patch dpkg-source: info: applying 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0115_enable_compiler_messages.patch dpkg-source: info: applying 0111_use_full_config_dirs.patch dpkg-source: info: applying 0116_stable_link_order.patch dpkg-source: info: applying 0117_build_with_debug.patch dpkg-source: info: applying 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying spelling dpkg-source: info: applying gcc7.patch I: using fakeroot in build. I: Installing the build-deps 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 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=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 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 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 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 Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, cmake, python-all-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, python-yaml, python-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on python-all-dev; however: Package python-all-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libhat-trie-dev; however: Package libhat-trie-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on python-yaml; however: Package python-yaml is not installed. pbuilder-satisfydepends-dummy depends on python-joblib; however: Package python-joblib is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor (>= 1.5.3); however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on lynx; however: Package lynx is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} bwa{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.1{a} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libbwa-dev{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libcurl4{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhat-trie-dev{a} libhat-trie0{a} libhts-dev{a} libhts2{a} libicu63{a} libidn11{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libpipeline1{a} libprocps7{a} libpsl5{a} libpython-all-dev{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librhash0{a} librtmp1{a} libruby2.5{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libssw-dev{a} libssw0{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libyaml-0-2{a} lsb-base{a} lynx{a} lynx-common{a} m4{a} man-db{a} mime-support{a} openssl{a} po-debconf{a} procps{a} python{a} python-all{a} python-all-dev{a} python-dev{a} python-joblib{a} python-minimal{a} python-yaml{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc fonts-lato krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libsasl2-modules psmisc publicsuffix python-lz4 python-numpy python-psutil python-pytest python-simplejson shared-mime-info xdg-user-dirs zip 0 packages upgraded, 136 newly installed, 0 to remove and 0 not upgraded. Need to get 93.9 MB of archives. After unpacking 380 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 42 http://deb.debian.org/debian buster/main amd64 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libruby2.5 amd64 2.5.5-3+deb10u3 [3438 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 ruby2.5 amd64 2.5.5-3+deb10u3 [400 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 ruby amd64 1:2.5.1 [11.3 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 asciidoctor all 1.5.8-1 [75.8 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 bwa amd64 0.7.17-3 [195 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libarchive13 amd64 3.3.3-4+deb10u1 [313 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libuv1 amd64 1.24.1-1+deb10u1 [110 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libbam-dev amd64 0.1.19-4 [125 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libbamtools-dev amd64 2.5.1+dfsg-3 [21.8 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 105 http://deb.debian.org/debian buster/main amd64 libbwa-dev amd64 0.7.17-3 [130 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libexpat1-dev amd64 2.2.6-2+deb10u1 [153 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libhat-trie-dev amd64 0.1.2-2 [19.9 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libnlopt0 amd64 2.4.2+dfsg-8+b1 [165 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libnlopt-dev amd64 2.4.2+dfsg-8+b1 [170 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libnlopt-cxx0 amd64 2.4.2+dfsg-8+b1 [174 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libnlopt-cxx-dev amd64 2.4.2+dfsg-8+b1 [188 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libpython2.7 amd64 2.7.16-2+deb10u1 [1036 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libpython2.7-dev amd64 2.7.16-2+deb10u1 [31.6 MB] Get: 123 http://deb.debian.org/debian buster/main amd64 libpython2-dev amd64 2.7.16-1 [20.9 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libpython-dev amd64 2.7.16-1 [20.9 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libpython-all-dev amd64 2.7.16-1 [1064 B] Get: 126 http://deb.debian.org/debian buster/main amd64 libssw0 amd64 1.1-2 [16.5 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libssw-dev amd64 1.1-2 [19.3 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 lynx-common all 2.8.9rel.1-3+deb10u1 [1212 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 lynx amd64 2.8.9rel.1-3+deb10u1 [642 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 python-all amd64 2.7.16-1 [1044 B] Get: 131 http://deb.debian.org/debian buster/main amd64 python2.7-dev amd64 2.7.16-2+deb10u1 [294 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 python2-dev amd64 2.7.16-1 [1212 B] Get: 133 http://deb.debian.org/debian buster/main amd64 python-dev amd64 2.7.16-1 [1192 B] 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 1s (64.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Setting up libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up lsb-base (10.2019051400) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up bwa (0.7.17-3) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libnlopt0:amd64 (2.4.2+dfsg-8+b1) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up ruby-minitest (5.11.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.24.1-1+deb10u1) ... Setting up libhat-trie0:amd64 (0.1.2-2) ... Setting up libexpat1-dev:amd64 (2.2.6-2+deb10u1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libbam-dev (0.1.19-4) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up lynx-common (2.8.9rel.1-3+deb10u1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libbwa-dev (0.7.17-3) ... Setting up libnlopt-cxx0:amd64 (2.4.2+dfsg-8+b1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libhat-trie-dev:amd64 (0.1.2-2) ... Setting up librhash0:amd64 (1.3.8-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libnlopt-dev:amd64 (2.4.2+dfsg-8+b1) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libssw0:amd64 (1.1-2) ... Setting up readline-common (7.0-5) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libssw-dev:amd64 (1.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libarchive13:amd64 (3.3.3-4+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libnlopt-cxx-dev:amd64 (2.4.2+dfsg-8+b1) ... Setting up libbamtools-dev:amd64 (2.5.1+dfsg-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u2) ... Setting up lynx (2.8.9rel.1-3+deb10u1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up libpython2.7:amd64 (2.7.16-2+deb10u1) ... Setting up libpython2.7-dev:amd64 (2.7.16-2+deb10u1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up rubygems-integration (1.11+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up cmake (3.13.4-1) ... Setting up libpython2-dev:amd64 (2.7.16-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python2-dev (2.7.16-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up python-all (2.7.16-1) ... Setting up libpython-dev:amd64 (2.7.16-1) ... Setting up python-joblib (0.13.0-2) ... Setting up python-yaml (3.13-2) ... Setting up python-dev (2.7.16-1) ... Setting up libpython-all-dev:amd64 (2.7.16-1) ... Setting up python-all-dev (2.7.16-1) ... Setting up dh-autoreconf (19) ... Setting up ruby2.5 (2.5.5-3+deb10u3) ... Setting up debhelper (12.1.1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up asciidoctor (1.5.8-1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libruby2.5:amd64 (2.5.5-3+deb10u3) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package 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 dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --sourcedirectory=src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/spades-3.13.0+dfsg2' dh_auto_clean rm -rf build_spades rm -rf install_spades rm -rf spades_test find . -name "*.pyc" -delete rm -rf /build/spades-3.13.0+dfsg2/debian/man_src/*.html /build/spades-3.13.0+dfsg2/debian/man_src/*.? rm -rf /build/spades-3.13.0+dfsg2/debian/man make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' dh_autoreconf_clean -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/spades-3.13.0+dfsg2' dh_clean -X.orig make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules build dh build --with python2 --sourcedirectory=src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/spades-3.13.0+dfsg2' echo "Simply use spades_compile.sh in auto_build" Simply use spades_compile.sh in auto_build make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules override_dh_auto_build make[1]: Entering directory '/build/spades-3.13.0+dfsg2' PREFIX=/build/spades-3.13.0+dfsg2/install_spades ./spades_compile.sh -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY) -- Boost version: 1.67.0 Making Release Configuration... Building SPAdes from N/A, sha: N/A -- Looking for include file features.h -- Looking for include file features.h - found -- Looking for include file sys/cdefs.h -- Looking for include file sys/cdefs.h - found -- Looking for atomic_fetchadd_long -- Looking for atomic_fetchadd_long - not found -- Looking for OSAtomicAdd64 -- Looking for OSAtomicAdd64 - not found -- Looking for OSSpinLockLock -- Looking for OSSpinLockLock - not found -- Looking for _malloc_thread_cleanup -- Looking for _malloc_thread_cleanup - not found -- Looking for _pthread_mutex_init_calloc_cb, -- Looking for _pthread_mutex_init_calloc_cb, - not found -- Looking for sbrk -- Looking for sbrk - found -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED - Success -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Performing Test JEMALLOC_TLS -- Performing Test JEMALLOC_TLS - Success -- Looking for memalign -- Looking for memalign - found -- Looking for valloc -- Looking for valloc - found -- Check size of int -- Check size of int - done -- Check size of long -- Check size of long - done -- Check size of intmax_t -- Check size of intmax_t - done -- Looking for open -- Looking for open - found -- Looking for include file execinfo.h -- Looking for include file execinfo.h - found -- Looking for include file signal.h -- Looking for include file signal.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file cxxabi.h -- Looking for include file cxxabi.h - not found -- Looking for include file dlfcn.h -- Looking for include file dlfcn.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - not found -- Looking for include file link.h -- Looking for include file link.h - found -- Looking for backtrace -- Looking for backtrace - found -- Configuring done -- Generating done -- Build files have been written to: /build/spades-3.13.0+dfsg2/build_spades make[2]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' /usr/bin/cmake -S/build/spades-3.13.0+dfsg2/src -B/build/spades-3.13.0+dfsg2/build_spades --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/spades-3.13.0+dfsg2/build_spades/CMakeFiles /build/spades-3.13.0+dfsg2/build_spades/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/jemalloc /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/depend.internal". 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Scanning dependencies of target jemalloc make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/arena.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/arena.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/arena.c [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/base.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/base.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/base.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/chunk.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_mmap.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_mmap.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/chunk_mmap.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ctl.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ctl.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/ctl.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/hash.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/hash.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/hash.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/jemalloc.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/jemalloc.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/jemalloc.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mutex.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mutex.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/mutex.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/quarantine.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/quarantine.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/quarantine.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/stats.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/stats.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/stats.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tsd.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tsd.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/tsd.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/atomic.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/atomic.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/atomic.c [ 6%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/bitmap.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/bitmap.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/bitmap.c [ 6%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_dss.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_dss.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/chunk_dss.c [ 6%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ckh.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ckh.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/ckh.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/extent.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/extent.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/extent.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/huge.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/huge.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/huge.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mb.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mb.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/mb.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/prof.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/prof.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/prof.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/rtree.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/rtree.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/rtree.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tcache.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tcache.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/tcache.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/util.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc -I/build/spades-3.13.0+dfsg2/ext/src/jemalloc -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/util.c.o -c /build/spades-3.13.0+dfsg2/ext/src/jemalloc/util.c [ 10%] Linking C static library libjemalloc.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cmake -P CMakeFiles/jemalloc.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/jemalloc && /usr/bin/cmake -E cmake_link_script CMakeFiles/jemalloc.dir/link.txt --verbose=1 /usr/bin/ar qc libjemalloc.a CMakeFiles/jemalloc.dir/arena.c.o CMakeFiles/jemalloc.dir/base.c.o CMakeFiles/jemalloc.dir/chunk.c.o CMakeFiles/jemalloc.dir/chunk_mmap.c.o CMakeFiles/jemalloc.dir/ctl.c.o CMakeFiles/jemalloc.dir/hash.c.o CMakeFiles/jemalloc.dir/jemalloc.c.o CMakeFiles/jemalloc.dir/mutex.c.o CMakeFiles/jemalloc.dir/quarantine.c.o CMakeFiles/jemalloc.dir/stats.c.o CMakeFiles/jemalloc.dir/tsd.c.o CMakeFiles/jemalloc.dir/atomic.c.o CMakeFiles/jemalloc.dir/bitmap.c.o CMakeFiles/jemalloc.dir/chunk_dss.c.o CMakeFiles/jemalloc.dir/ckh.c.o CMakeFiles/jemalloc.dir/extent.c.o CMakeFiles/jemalloc.dir/huge.c.o CMakeFiles/jemalloc.dir/mb.c.o CMakeFiles/jemalloc.dir/prof.c.o CMakeFiles/jemalloc.dir/rtree.c.o CMakeFiles/jemalloc.dir/tcache.c.o CMakeFiles/jemalloc.dir/util.c.o /usr/bin/ranlib libjemalloc.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 10%] Built target jemalloc make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/ConsensusCore /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". 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/build/spades-3.13.0+dfsg2/ext/src/ConsensusCore/PairwiseAlignment.cpp [ 12%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore -I/build/spades-3.13.0+dfsg2/ext/src/ConsensusCore -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/ConsensusCore/Sequence.cpp [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore -I/build/spades-3.13.0+dfsg2/ext/src/ConsensusCore -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/ConsensusCore/Utils.cpp [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o cd 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-I/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore -I/build/spades-3.13.0+dfsg2/ext/src/ConsensusCore -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp [ 14%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore 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-I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/ConsensusCore/Poa/PoaConsensus.cpp [ 15%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore -I/build/spades-3.13.0+dfsg2/ext/src/ConsensusCore -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/ConsensusCore/Poa/PoaGraph.cpp [ 16%] Linking CXX static library libConsensusCore.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 /usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp [ 21%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 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/build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/bam/BamReader_p.cpp [ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp [ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/BamFile_p.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/ByteArray_p.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp [ 27%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:2: note: in expansion of macro '_bgzf_read' _bgzf_read(fp->fp, buf, 28); ^~~~~~~~~~ [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:2: note: in expansion of macro 'netwrite' netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:2: note: in expansion of macro 'netwrite' netwrite(fp->fd, buf, l); ^~~~~~~~ [ 28%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/block.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 28%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/consumer.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/queue.c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", ~~~^ %ld q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); ~~~~~ In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/queue.c: At top level: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/reader.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 30%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.c [ 30%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/writer.c In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 31%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp [ 31%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp [ 32%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp [ 32%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/api -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/ext/src/bamtools -I/build/spades-3.13.0+dfsg2/ext/src/bamtools/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/bamtools/api/internal/utils/BamException_p.cpp [ 32%] Linking CXX static library libBamTools.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib libBamTools.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 32%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/samtools /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/samtools /build/spades-3.13.0+dfsg2/build_spades/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/samtools/CMakeFiles/samtools.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/samtools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/samtools/CMakeFiles/samtools.dir/depend.internal". Scanning dependencies of target samtools make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 32%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/kstring.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/kstring.c [ 33%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_aux.c [ 33%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_import.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/sam.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/sam.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:355:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:358:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:362:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:366:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_index.c:380:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_pileup.c [ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_lpileup.c [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_md.c [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/razf.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c: In function 'razf_flush': /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c: In function '_razf_write': /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c: In function 'razf_close': /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:804:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:805:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:808:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c: In function 'save_zindex': /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/samtools/razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/faidx.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/faidx.c [ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bedidx.c [ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_sort.c [ 38%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/sam_header.c [ 38%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_reheader.c [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/kprobaln.c [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.0+dfsg2/build_spades/ext/samtools -I/build/spades-3.13.0+dfsg2/ext/src/samtools -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/spades-3.13.0+dfsg2/ext/src/samtools/bam_cat.c [ 39%] Linking CXX static library libsamtools.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 /usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o /usr/bin/ranlib libsamtools.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 39%] Built target samtools make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/cppformat /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/cppformat /build/spades-3.13.0+dfsg2/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/cppformat/CMakeFiles/format.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/cppformat/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/cppformat/CMakeFiles/format.dir/depend.internal". Scanning dependencies of target format make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 40%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/cppformat -I/build/spades-3.13.0+dfsg2/ext/src/cppformat -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g3 -O2 -o CMakeFiles/format.dir/format.cc.o -c /build/spades-3.13.0+dfsg2/ext/src/cppformat/format.cc [ 40%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/cppformat -I/build/spades-3.13.0+dfsg2/ext/src/cppformat -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g3 -O2 -o CMakeFiles/format.dir/posix.cc.o -c /build/spades-3.13.0+dfsg2/ext/src/cppformat/posix.cc [ 41%] Linking CXX static library libformat.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 /usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o /usr/bin/ranlib libformat.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 41%] Built target format make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/cityhash /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/cityhash /build/spades-3.13.0+dfsg2/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/depend.internal". 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Scanning dependencies of target cityhash make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 41%] Building CXX object ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/cityhash && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/cityhash -I/build/spades-3.13.0+dfsg2/ext/src/cityhash -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/cityhash.dir/city.cc.o -c /build/spades-3.13.0+dfsg2/ext/src/cityhash/city.cc [ 42%] Linking CXX static library libcityhash.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/cityhash && /usr/bin/cmake -P CMakeFiles/cityhash.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/cityhash && /usr/bin/cmake -E cmake_link_script CMakeFiles/cityhash.dir/link.txt --verbose=1 /usr/bin/ar qc libcityhash.a CMakeFiles/cityhash.dir/city.cc.o /usr/bin/ranlib libcityhash.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 42%] Built target cityhash make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/getopt_pp /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp /build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend.internal". Scanning dependencies of target getopt_pp make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 42%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp -I/build/spades-3.13.0+dfsg2/ext/src/getopt_pp -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/getopt_pp/getopt_pp.cpp [ 42%] Linking CXX static library libgetopt_pp.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 /usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o /usr/bin/ranlib libgetopt_pp.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 42%] Built target getopt_pp make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/llvm /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/llvm /build/spades-3.13.0+dfsg2/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/llvm/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/depend.internal". Scanning dependencies of target llvm-support make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 42%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Atomic.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/ErrorHandling.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Hashing.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/LineIterator.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/MemoryBuffer.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Mutex.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Mutex.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Mutex.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Path.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Regex.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Signals.cpp [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/SmallVector.cpp [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/SourceMgr.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/StringMap.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/StringRef.cpp [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/Twine.cpp [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/YAMLParser.cpp [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/YAMLTraits.cpp [ 49%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/raw_ostream.cpp [ 49%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/regcomp.c [ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/regerror.c [ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/regexec.c [ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/regfree.c [ 51%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.0+dfsg2/build_spades/ext/llvm -I/build/spades-3.13.0+dfsg2/ext/src/llvm -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/spades-3.13.0+dfsg2/ext/src/llvm/regstrlcpy.c [ 51%] Linking CXX static library libllvm-support.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 /usr/bin/ar qc libllvm-support.a CMakeFiles/llvm-support.dir/Atomic.cpp.o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o CMakeFiles/llvm-support.dir/Hashing.cpp.o CMakeFiles/llvm-support.dir/LineIterator.cpp.o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o CMakeFiles/llvm-support.dir/Mutex.cpp.o CMakeFiles/llvm-support.dir/Path.cpp.o CMakeFiles/llvm-support.dir/Regex.cpp.o CMakeFiles/llvm-support.dir/Signals.cpp.o CMakeFiles/llvm-support.dir/SmallVector.cpp.o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o CMakeFiles/llvm-support.dir/StringMap.cpp.o CMakeFiles/llvm-support.dir/StringRef.cpp.o CMakeFiles/llvm-support.dir/Twine.cpp.o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o CMakeFiles/llvm-support.dir/regcomp.c.o CMakeFiles/llvm-support.dir/regerror.c.o CMakeFiles/llvm-support.dir/regexec.c.o CMakeFiles/llvm-support.dir/regfree.c.o CMakeFiles/llvm-support.dir/regstrlcpy.c.o /usr/bin/ranlib libllvm-support.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 51%] Built target llvm-support make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/gqf /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/gqf /build/spades-3.13.0+dfsg2/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/gqf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Scanning dependencies of target gqf make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 52%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/gqf && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/gqf -I/build/spades-3.13.0+dfsg2/ext/src/gqf -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/gqf.dir/gqf.c.o -c /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:614:16: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%02llx ", j); ~~~~~^ ~ %02lx /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c: In function 'qf_dump': /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:645:13: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%llu %llu %llu\n", ~~~^ %lu qf->metadata->nblocks, ~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:645:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%llu %llu %llu\n", ~~~^ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:647:6: qf->metadata->ndistinct_elts, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:645:23: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%llu %llu %llu\n", ~~~^ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:648:6: qf->metadata->nelts); ~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c: In function 'qf_init': /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1451:22: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); ~~~^ ~~~~~~~~ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1451:27: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); ~~~^ ~~~~~~~~~~~~~~~~~~ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1451:32: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); ~~~^ ~~~~~~~~~~ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1477:31: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "nslots: %llu\n", qf->metadata->range); ~~~^ ~~~~~~~~~~~~~~~~~~~ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1479:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "bits per slot: %llu range: %016llx\n", qf->metadata->bits_per_slot, (uint64_t)qf->metadata->range); ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ %lu /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1479:59: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr, "bits per slot: %llu range: %016llx\n", qf->metadata->bits_per_slot, (uint64_t)qf->metadata->range); ~~~~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %016lx /build/spades-3.13.0+dfsg2/ext/include/gqf/gqf.h: In function 'qf_deserialize': /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1610:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qf->metadata, sizeof(qfmetadata), 1, fin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/ext/src/gqf/gqf.c:1619:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qf->blocks, qf->metadata->size, 1, fin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Linking C static library libgqf.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 52%] Built target gqf make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/edlib /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/edlib /build/spades-3.13.0+dfsg2/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/edlib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Scanning dependencies of target edlib make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 53%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/edlib && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/edlib -I/build/spades-3.13.0+dfsg2/ext/src/edlib -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/spades-3.13.0+dfsg2/ext/src/edlib/edlib.cpp [ 53%] Linking CXX static library libedlib.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o /usr/bin/ranlib libedlib.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 53%] Built target edlib make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/ext/src/gfa1 /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/ext/gfa1 /build/spades-3.13.0+dfsg2/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/ext/gfa1/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Scanning dependencies of target gfa1 make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o cd /build/spades-3.13.0+dfsg2/build_spades/ext/gfa1 && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/ext/gfa1 -I/build/spades-3.13.0+dfsg2/ext/src/gfa1 -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/gfa1.dir/gfa.c.o -c /build/spades-3.13.0+dfsg2/ext/src/gfa1/gfa.c [ 54%] Linking C static library libgfa1.a cd /build/spades-3.13.0+dfsg2/build_spades/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 /usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o /usr/bin/ranlib libgfa1.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Built target gfa1 make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/modules/coverage_model /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model /build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Scanning dependencies of target coverage_model make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model -I/build/spades-3.13.0+dfsg2/src/common/modules/coverage_model -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/coverage_model/kmer_coverage_model.cpp /build/spades-3.13.0+dfsg2/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/spades-3.13.0+dfsg2/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] if (converged_ && Valley_ > x[2] && x[2] > 2) { ^~~~~~~ /build/spades-3.13.0+dfsg2/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] ErrorThreshold_ = (Valley_ < mean_coverage_ ? ^~~~~~~ [ 54%] Linking CXX static library libcoverage_model.a cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 /usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o /usr/bin/ranlib libcoverage_model.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Built target coverage_model make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/io /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/io /build/spades-3.13.0+dfsg2/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Scanning dependencies of target input make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/io -I/build/spades-3.13.0+dfsg2/src/common/io -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/io/reads/parser.cpp [ 54%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/io -I/build/spades-3.13.0+dfsg2/src/common/io -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/io/sam/read.cpp [ 55%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/io -I/build/spades-3.13.0+dfsg2/src/common/io -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/io/sam/sam_reader.cpp [ 55%] Linking CXX static library libinput.a cd /build/spades-3.13.0+dfsg2/build_spades/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 55%] Built target input make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/pipeline /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/pipeline /build/spades-3.13.0+dfsg2/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/pipeline/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Scanning dependencies of target pipeline make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 55%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/pipeline -I/build/spades-3.13.0+dfsg2/src/common/pipeline -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/pipeline/stage.cpp [ 56%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/pipeline -I/build/spades-3.13.0+dfsg2/src/common/pipeline -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/pipeline/config_struct.cpp [ 56%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/pipeline -I/build/spades-3.13.0+dfsg2/src/common/pipeline -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/pipeline/genomic_info_filler.cpp [ 57%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/pipeline -I/build/spades-3.13.0+dfsg2/src/common/pipeline -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/pipeline/library.cpp [ 57%] Linking CXX static library libpipeline.a cd /build/spades-3.13.0+dfsg2/build_spades/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 /usr/bin/ar qc libpipeline.a CMakeFiles/pipeline.dir/stage.cpp.o CMakeFiles/pipeline.dir/config_struct.cpp.o CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o CMakeFiles/pipeline.dir/library.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 57%] Built target pipeline make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/sequence /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/sequence /build/spades-3.13.0+dfsg2/build_spades/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/sequence/CMakeFiles/sequence.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/sequence/CMakeFiles/sequence.dir/depend.internal". Scanning dependencies of target sequence make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 58%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/sequence && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/sequence -I/build/spades-3.13.0+dfsg2/src/common/sequence -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/sequence/sequence_tools.cpp [ 58%] Linking CXX static library libsequence.a cd /build/spades-3.13.0+dfsg2/build_spades/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o /usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 58%] Built target sequence make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/assembly_graph /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/depend.internal". Scanning dependencies of target assembly_graph make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 58%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/assembly_graph/components/connected_component.cpp [ 59%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/assembly_graph/paths/bidirectional_path.cpp [ 59%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp [ 59%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp [ 60%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/assembly_graph/graph_support/scaff_supplementary.cpp /build/spades-3.13.0+dfsg2/src/common/assembly_graph/graph_support/scaff_supplementary.cpp: In member function 'bool path_extend::ScaffoldingUniqueEdgeAnalyzer::ConservativeByPaths(path_extend::EdgeId, const path_extend::GraphCoverageMap&, const path_extend::pe_config::LongReads&, int) const': /build/spades-3.13.0+dfsg2/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:130:63: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] if (maxx < lr_config.unique_edge_priority * double(alt)) { ^ [ 60%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/alignment/edge_index_refiller.cpp [ 61%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/common/assembly_graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp [ 61%] Linking CXX static library libassembly_graph.a cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 /usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 61%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/modules/path_extend /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/depend.internal". Scanning dependencies of target path_extend make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 62%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/pe_config_struct.cpp [ 62%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/pipeline/launch_support.cpp [ 63%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/pipeline/launcher.cpp [ 63%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/pipeline/extenders_logic.cpp [ 63%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] if (sum < absolute_weight_threshold_) { ^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp [ 64%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp [ 65%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp [ 65%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual std::map >, double> path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:102:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] if (iter->second < min_read_count_){ ^~~~~~~~~~~~~~~ [ 65%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/common/modules/path_extend -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp [ 66%] Linking CXX static library libpath_extend.a cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 66%] Built target path_extend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/modules /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/modules /build/spades-3.13.0+dfsg2/build_spades/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/modules/CMakeFiles/modules.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/modules/CMakeFiles/modules.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/modules/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/modules/CMakeFiles/modules.dir/depend.internal". Scanning dependencies of target modules make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 67%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules -I/build/spades-3.13.0+dfsg2/src/common/modules -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/genome_consistance_checker.cpp [ 67%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules -I/build/spades-3.13.0+dfsg2/src/common/modules -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/alignment/gap_info.cpp [ 67%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/modules -I/build/spades-3.13.0+dfsg2/src/common/modules -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/modules/alignment/bwa_index.cpp [ 68%] Linking CXX static library libmodules.a cd /build/spades-3.13.0+dfsg2/build_spades/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 68%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/paired_info /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/paired_info /build/spades-3.13.0+dfsg2/build_spades/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/paired_info/CMakeFiles/paired_info.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/paired_info/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/paired_info/CMakeFiles/paired_info.dir/depend.internal". Scanning dependencies of target paired_info make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 68%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/paired_info -I/build/spades-3.13.0+dfsg2/src/common/paired_info -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/paired_info/distance_estimation.cpp [ 69%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/paired_info -I/build/spades-3.13.0+dfsg2/src/common/paired_info -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/paired_info/weighted_distance_estimation.cpp [ 69%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/paired_info -I/build/spades-3.13.0+dfsg2/src/common/paired_info -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/paired_info/smoothing_distance_estimation.cpp [ 69%] Linking CXX static library libpaired_info.a cd /build/spades-3.13.0+dfsg2/build_spades/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o /usr/bin/ranlib libpaired_info.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 69%] Built target paired_info make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/stages /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/stages /build/spades-3.13.0+dfsg2/build_spades/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/stages/CMakeFiles/stages.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/stages/CMakeFiles/stages.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/stages/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/stages/CMakeFiles/stages.dir/depend.internal". Scanning dependencies of target stages make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 69%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/stages -I/build/spades-3.13.0+dfsg2/src/common/stages -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/construction.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/stages/construction.cpp [ 70%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/stages -I/build/spades-3.13.0+dfsg2/src/common/stages -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/stages/simplification.cpp [ 70%] Linking CXX static library libstages.a cd /build/spades-3.13.0+dfsg2/build_spades/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/stages && /usr/bin/cmake -E cmake_link_script CMakeFiles/stages.dir/link.txt --verbose=1 /usr/bin/ar qc libstages.a CMakeFiles/stages.dir/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o /usr/bin/ranlib libstages.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 70%] Built target stages make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/utils /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/utils /build/spades-3.13.0+dfsg2/build_spades/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/utils/CMakeFiles/utils.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/utils/CMakeFiles/utils.dir/depend.internal". Scanning dependencies of target utils make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 70%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/utils -I/build/spades-3.13.0+dfsg2/src/common/utils -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/utils/memory_limit.cpp [ 71%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/utils -I/build/spades-3.13.0+dfsg2/src/common/utils -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/utils/filesystem/copy_file.cpp [ 71%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/utils -I/build/spades-3.13.0+dfsg2/src/common/utils -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/utils/filesystem/path_helper.cpp [ 72%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/utils -I/build/spades-3.13.0+dfsg2/src/common/utils -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/utils/filesystem/temporary.cpp [ 72%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/utils -I/build/spades-3.13.0+dfsg2/src/common/utils -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/utils/logger/logger_impl.cpp [ 73%] Linking CXX static library libutils.a cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 73%] Built target utils make -f common/utils/kmer_mph/CMakeFiles/mph_index.dir/build.make common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/utils/kmer_mph /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph /build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend.internal". Scanning dependencies of target mph_index make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/utils/kmer_mph/CMakeFiles/mph_index.dir/build.make common/utils/kmer_mph/CMakeFiles/mph_index.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 73%] Building CXX object common/utils/kmer_mph/CMakeFiles/mph_index.dir/1.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph -I/build/spades-3.13.0+dfsg2/src/common/utils/kmer_mph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/mph_index.dir/1.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/utils/kmer_mph/1.cpp [ 74%] Linking CXX static library libmph_index.a cd /build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph && /usr/bin/cmake -P CMakeFiles/mph_index.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/utils/kmer_mph && /usr/bin/cmake -E cmake_link_script CMakeFiles/mph_index.dir/link.txt --verbose=1 /usr/bin/ar qc libmph_index.a CMakeFiles/mph_index.dir/1.cpp.o /usr/bin/ranlib libmph_index.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 74%] Built target mph_index make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common /build/spades-3.13.0+dfsg2/build_spades/common/CMakeFiles/common_modules.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/CMakeFiles/common_modules.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/CMakeFiles/common_modules.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/CMakeFiles/common_modules.dir/depend.internal". Scanning dependencies of target common_modules make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 74%] Building CXX object common/CMakeFiles/common_modules.dir/empty.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common -I/build/spades-3.13.0+dfsg2/src/common -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/common_modules.dir/empty.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/empty.cpp [ 75%] Linking CXX static library libcommon_modules.a cd /build/spades-3.13.0+dfsg2/build_spades/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common && /usr/bin/cmake -E cmake_link_script CMakeFiles/common_modules.dir/link.txt --verbose=1 /usr/bin/ar qc libcommon_modules.a CMakeFiles/common_modules.dir/empty.cpp.o /usr/bin/ranlib libcommon_modules.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 75%] Built target common_modules make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/common/io/graph /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/common/io/graph /build/spades-3.13.0+dfsg2/build_spades/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/io/graph/CMakeFiles/graphio.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/common/io/graph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/common/io/graph/CMakeFiles/graphio.dir/depend.internal". Scanning dependencies of target graphio make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 75%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/io/graph -I/build/spades-3.13.0+dfsg2/src/common/io/graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/io/graph/gfa_reader.cpp [ 76%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/io/graph -I/build/spades-3.13.0+dfsg2/src/common/io/graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/io/graph/gfa_writer.cpp [ 76%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/common/io/graph -I/build/spades-3.13.0+dfsg2/src/common/io/graph -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/spades-3.13.0+dfsg2/src/common/io/graph/fastg_writer.cpp [ 77%] Linking CXX static library libgraphio.a cd /build/spades-3.13.0+dfsg2/build_spades/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o /usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 77%] Built target graphio make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/spades /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/spades /build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-stages.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-stages.dir/depend.internal". Scanning dependencies of target spades-stages make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 77%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/gap_closer.cpp [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/mismatch_correction.cpp [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/pair_info_count.cpp /build/spades-3.13.0+dfsg2/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::CollectLibInformation(const conj_graph_pack&, size_t&, size_t, size_t)': /build/spades-3.13.0+dfsg2/src/projects/spades/pair_info_count.cpp:224:46: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] if (data.median_insert_size < gp.k_value + 2) ~~~~~~~~~~~^~~ In file included from /build/spades-3.13.0+dfsg2/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.0+dfsg2/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.0+dfsg2/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.0+dfsg2/src/common/assembly_graph/stats/picture_dump.hpp: In instantiation of 'size_t debruijn_graph::stats::Nx(Graph&, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]': /build/spades-3.13.0+dfsg2/src/projects/spades/pair_info_count.cpp:319:109: required from here /build/spades-3.13.0+dfsg2/src/common/assembly_graph/stats/picture_dump.hpp:457:24: warning: conversion from '__gnu_cxx::__alloc_traits, long unsigned int>::value_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] if (lengths[i] >= len_perc) In file included from /build/spades-3.13.0+dfsg2/src/common/utils/standard_base.hpp:135, from /build/spades-3.13.0+dfsg2/src/common/paired_info/insert_size_refiner.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.0+dfsg2/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.0+dfsg2/src/common/math/xmath.h: In instantiation of 'bool math::ls(T, U) [with T = int; U = omnigraph::de::DEWeight]': /build/spades-3.13.0+dfsg2/src/common/math/xmath.h:314:34: required from 'bool math::gr(T, U) [with T = omnigraph::de::DEWeight; U = int]' /build/spades-3.13.0+dfsg2/src/common/paired_info/pair_info_filler.hpp:75:39: required from here /build/spades-3.13.0+dfsg2/src/common/math/xmath.h:303:21: warning: conversion from 'int' to 'float' may change value [-Wconversion] return (lhs < rhs); ~~~~~^~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/second_phase_setup.cpp [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/distance_estimation.cpp [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/repeat_resolving.cpp [ 80%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/contig_output_stage.cpp [ 80%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp In file included from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.0+dfsg2/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.0+dfsg2/src/common/sequence/sequence.hpp: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /build/spades-3.13.0+dfsg2/src/common/sequence/sequence.hpp:176:20: warning: '*((void*)& __tmp +80)' may be used uninitialized in this function [-Wmaybe-uninitialized] rtl_ = rhs.rtl_; ~~~~^~~~ In file included from /usr/include/c++/8/bits/stl_pair.h:59, from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/vector:60, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/8/bits/move.h:193:11: note: '*((void*)& __tmp +80)' was declared here _Tp __tmp = _GLIBCXX_MOVE(__a); ^~~~~ In file included from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.0+dfsg2/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.0+dfsg2/src/common/sequence/sequence.hpp:175:15: warning: '*((void*)(& __tmp)+64).Sequence::size_' may be used uninitialized in this function [-Wmaybe-uninitialized] size_ = rhs.size_; ~~~~~~^~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_pair.h:59, from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/vector:60, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/8/bits/move.h:193:11: note: '*((void*)(& __tmp)+64).Sequence::size_' was declared here _Tp __tmp = _GLIBCXX_MOVE(__a); ^~~~~ In file included from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.0+dfsg2/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.0+dfsg2/src/common/sequence/sequence.hpp:174:15: warning: '*((void*)(& __tmp)+64).Sequence::from_' may be used uninitialized in this function [-Wmaybe-uninitialized] from_ = rhs.from_; ~~~~~~^~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_pair.h:59, from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/vector:60, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.0+dfsg2/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.0+dfsg2/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/8/bits/move.h:193:11: note: '*((void*)(& __tmp)+64).Sequence::from_' was declared here _Tp __tmp = _GLIBCXX_MOVE(__a); ^~~~~ [ 81%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/chromosome_removal.cpp [ 81%] Linking CXX static library libspades-stages.a cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 /usr/bin/ar qc libspades-stages.a CMakeFiles/spades-stages.dir/gap_closer.cpp.o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 81%] Built target spades-stages make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/spades /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/spades /build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-core.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/spades/CMakeFiles/spades-core.dir/depend.internal". Scanning dependencies of target spades-core make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 82%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/main.cpp [ 82%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/spades/series_analysis.cpp [ 82%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/spades -I/build/spades-3.13.0+dfsg2/src/projects/spades -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/mts/contig_abundance.cpp [ 83%] Linking CXX executable ../../bin/spades-core cd /build/spades-3.13.0+dfsg2/build_spades/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-core.dir/main.cpp.o CMakeFiles/spades-core.dir/series_analysis.cpp.o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a -lnlopt ../../ext/bamtools/api/libBamTools.a -lssw ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/assembly_graph/libassembly_graph.a -lhat-trie ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 83%] Built target spades-core make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/hammer /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/hammer /build/spades-3.13.0+dfsg2/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/hammer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/depend.internal". Scanning dependencies of target spades-hammer make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 84%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/hammer -I/build/spades-3.13.0+dfsg2/src/projects/hammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/hammer/main.cpp [ 84%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/hammer -I/build/spades-3.13.0+dfsg2/src/projects/hammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/hammer/hammer_tools.cpp [ 85%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/hammer -I/build/spades-3.13.0+dfsg2/src/projects/hammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/hammer/hamcluster.cpp [ 85%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/hammer -I/build/spades-3.13.0+dfsg2/src/projects/hammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/hammer/kmer_cluster.cpp /build/spades-3.13.0+dfsg2/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/spades-3.13.0+dfsg2/src/projects/hammer/kmer_cluster.cpp:356:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (uint32_t j=0; j::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) ~~~~~~~~~~~~~~~~~~~~~^~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] num_flows = measurements.size(); ~~~~~~~~~~~~~~~~~^~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] unsigned int prefix_size = master_read.sequence.size(); ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::__cxx11::string&)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] int backward_idx = seq.size()-1; ~~~~~~~~~~^~ [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:86:63: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] transition_flow_[nuc][flow] = (1-nuc_avaliability[nuc]) + nuc_avaliability[nuc] * (1-droop_rate) * incomplete_extension_rate; ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:97:45: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] int num_flows = read.raw_measurements.size(); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:127:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] float delta = (next_normalizer - normalizer) / window_size; ^~~~~~~~~~~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:166:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] float delta = (next_normalizer - normalizer) / window_size; ^~~~~~~~~~~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:350:38: warning: conversion from 'double' to 'float' changes value from '1.0e+20' to '1.00000002e+20f' [-Wfloat-conversion] float sum_of_squares_upper_bound = 1e20; //max_flows; // Squared distance of solution to measurements ^~~~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:409:36: warning: conversion from 'double' to 'float' changes value from '-1.0000000000000001e-1' to '-1.00000001e-1f' [-Wfloat-conversion] float max_per_flow_metric = -0.1; ^~~ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/seqeval/TreephaserLite.cpp:514:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/main.cpp In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/penalty_estimator.hpp:43, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/main.cpp:26: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.hpp:147:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] idx = std::min(idx, (const int)(alphas_.size() - 1)); ^ In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/penalty_estimator.hpp:44, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/main.cpp:26: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h: In member function 'std::vector hammer::correction::HRunSizeSearcher::TryFindAllDeletions(char, bool)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h:383:79: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] const char start = (const char)std::max(1, observed_size_ - max_error_size); ^ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h: In member function 'hammer::correction::IonEvent hammer::correction::HRunSizeSearcher::TryFindInsertion(char)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h:408:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] (const char)(found ? hkmer_[K - 1].len : observed_size_ + 1), ^ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h: In member function 'hammer::correction::IonEvent hammer::correction::HRunSizeSearcher::TryFindDeletion(char)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h:416:79: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] const char start = (const char)std::max(1, observed_size_ - max_error_size); ^ /build/spades-3.13.0+dfsg2/src/projects/ionhammer/read_corrector_structs_new.h:426:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] (const char)(found ? hkmer_[K - 1].len : observed_size_ - 1), ^ In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/main.cpp:26: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/penalty_estimator.hpp: In member function 'void hammer::correction::GammaPoissonLikelihoodCalcer::Update(hammer::correction::GammaPoissonLikelihoodCalcer::PenaltyState&, const hammer::correction::IonEvent&, const hammer::KMerStat*) const': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/penalty_estimator.hpp:160:76: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] min((const uint)std::abs(event.fixed_size_ - event.overserved_size_), ^ In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/main.cpp:28: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.hpp:131:56: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] bin = std::min(bin, (const int)(borders_.size() - 1)); ^ [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/reference.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/quality_metrics.cpp In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/subcluster.hpp:18, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/quality_metrics.h:10, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/quality_metrics.cpp:5: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.hpp:147:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] idx = std::min(idx, (const int)(alphas_.size() - 1)); ^ In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/quality_metrics.h:10, from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/quality_metrics.cpp:5: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.hpp:131:56: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] bin = std::min(bin, (const int)(borders_.size() - 1)); ^ [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/quality_thresholds_estimator.cpp [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/hamcluster_1.cpp [ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.cpp In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.cpp:5: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/gamma_poisson_model.hpp:147:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] idx = std::min(idx, (const int)(alphas_.size() - 1)); ^ [ 93%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/projects/ionhammer -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.cpp:5: /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.0+dfsg2/src/projects/ionhammer/normal_quality_model.hpp:131:56: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] bin = std::min(bin, (const int)(borders_.size() - 1)); ^ [ 93%] Linking CXX executable ../../bin/spades-ionhammer cd /build/spades-3.13.0+dfsg2/build_spades/projects/ionhammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-ionhammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o CMakeFiles/spades-ionhammer.dir/main.cpp.o CMakeFiles/spades-ionhammer.dir/reference.cpp.o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -o ../../bin/spades-ionhammer ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/bamtools/api/libBamTools.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../ext/cityhash/libcityhash.a make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 93%] Built target spades-ionhammer make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/corrector /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/corrector /build/spades-3.13.0+dfsg2/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/corrector/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/depend.internal". Scanning dependencies of target spades-corrector-core make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/corrector -I/build/spades-3.13.0+dfsg2/src/projects/corrector -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/corrector/positional_read.cpp [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/corrector -I/build/spades-3.13.0+dfsg2/src/projects/corrector -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/corrector/interesting_pos_processor.cpp [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/corrector -I/build/spades-3.13.0+dfsg2/src/projects/corrector -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/corrector/contig_processor.cpp /build/spades-3.13.0+dfsg2/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/spades-3.13.0+dfsg2/src/projects/corrector/contig_processor.cpp:165:94: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { ^ /build/spades-3.13.0+dfsg2/src/projects/corrector/contig_processor.cpp:165:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { ~~~~~~~~~~~~~~^~ [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/corrector -I/build/spades-3.13.0+dfsg2/src/projects/corrector -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/corrector/dataset_processor.cpp [ 95%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/corrector -I/build/spades-3.13.0+dfsg2/src/projects/corrector -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/corrector/config_struct.cpp [ 95%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/corrector -I/build/spades-3.13.0+dfsg2/src/projects/corrector -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/corrector/main.cpp [ 96%] Linking CXX executable ../../bin/spades-corrector-core cd /build/spades-3.13.0+dfsg2/build_spades/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o CMakeFiles/spades-corrector-core.dir/main.cpp.o -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 96%] Built target spades-corrector-core make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/scaffold_correction /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction /build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend.internal". Scanning dependencies of target spades-truseq-scfcorrection make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 96%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction -I/build/spades-3.13.0+dfsg2/src/projects/scaffold_correction -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/scaffold_correction/main.cpp [ 97%] Linking CXX executable ../../bin/spades-truseq-scfcorrection cd /build/spades-3.13.0+dfsg2/build_spades/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 97%] Built target spades-truseq-scfcorrection make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/kmercount /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/depend.internal". Scanning dependencies of target spades-read-filter make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 97%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount -I/build/spades-3.13.0+dfsg2/src/projects/kmercount -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/kmercount/read_filter.cpp [ 98%] Linking CXX executable ../../bin/spades-read-filter cd /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 98%] Built target spades-read-filter make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/kmercount /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/depend.internal". Scanning dependencies of target spades-kmercount make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 99%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/kmercount -I/build/spades-3.13.0+dfsg2/src/projects/kmercount -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/kmercount/main.cpp [ 99%] Linking CXX executable ../../bin/spades-kmercount cd /build/spades-3.13.0+dfsg2/build_spades/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-kmercount.dir/main.cpp.o -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 99%] Built target spades-kmercount make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/gbuilder /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder /build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend.internal". Scanning dependencies of target spades-gbuilder make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [ 99%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder -I/build/spades-3.13.0+dfsg2/src/projects/gbuilder -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/gbuilder/main.cpp [100%] Linking CXX executable ../../bin/spades-gbuilder cd /build/spades-3.13.0+dfsg2/build_spades/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-gbuilder.dir/main.cpp.o -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/gfa1/libgfa1.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [100%] Built target spades-gbuilder make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' cd /build/spades-3.13.0+dfsg2/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.0+dfsg2/src /build/spades-3.13.0+dfsg2/src/projects/gmapper /build/spades-3.13.0+dfsg2/build_spades /build/spades-3.13.0+dfsg2/build_spades/projects/gmapper /build/spades-3.13.0+dfsg2/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/depend.internal". Dependee "/build/spades-3.13.0+dfsg2/build_spades/projects/gmapper/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.0+dfsg2/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/depend.internal". Scanning dependencies of target spades-gmapper make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' [100%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o cd /build/spades-3.13.0+dfsg2/build_spades/projects/gmapper && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.0+dfsg2/build_spades/projects/gmapper -I/build/spades-3.13.0+dfsg2/src/projects/gmapper -I/build/spades-3.13.0+dfsg2/src/include -I/build/spades-3.13.0+dfsg2/build_spades/include -I/build/spades-3.13.0+dfsg2/src -I/build/spades-3.13.0+dfsg2/src/common -isystem /build/spades-3.13.0+dfsg2/src/../ext/include -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/spades-3.13.0+dfsg2/src/projects/gmapper/main.cpp [100%] Linking CXX executable ../../bin/spades-gmapper cd /build/spades-3.13.0+dfsg2/build_spades/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.13.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-gmapper.dir/main.cpp.o -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [100%] Built target spades-gmapper make[3]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' /usr/bin/cmake -E cmake_progress_start /build/spades-3.13.0+dfsg2/build_spades/CMakeFiles 0 make[2]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' make[2]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[3]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 10%] Built target jemalloc make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 16%] Built target ConsensusCore make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 32%] Built target BamTools make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 39%] Built target samtools make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 41%] Built target format make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 42%] Built target cityhash make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 42%] Built target getopt_pp make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 51%] Built target llvm-support make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 52%] Built target gqf make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 53%] Built target edlib make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Built target gfa1 make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 54%] Built target coverage_model make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 55%] Built target input make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 57%] Built target pipeline make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 58%] Built target sequence make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 61%] Built target assembly_graph make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 66%] Built target path_extend make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 68%] Built target modules make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 69%] Built target paired_info make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 70%] Built target stages make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 73%] Built target utils make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 74%] Built target mph_index make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 75%] Built target common_modules make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 77%] Built target graphio make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 81%] Built target spades-stages make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 83%] Built target spades-core make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 87%] Built target spades-hammer make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 93%] Built target spades-ionhammer make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 96%] Built target spades-corrector-core make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 97%] Built target spades-truseq-scfcorrection make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 98%] Built target spades-read-filter make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [ 99%] Built target spades-kmercount make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [100%] Built target spades-gbuilder make[4]: Entering directory '/build/spades-3.13.0+dfsg2/build_spades' make[4]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' [100%] Built target spades-gmapper make[3]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' Install the project... -- Install configuration: "RelWithDebInfo" -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/metaspades.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/plasmidspades.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/rnaspades.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/truspades.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades_init.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/VERSION -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/operons_1K.txt -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/operons_1K.gff -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/genes_1K.txt -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/genes_1K.gff -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_plasmid -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/manual.html -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/README.md -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/truspades_manual.html -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/rnaspades_manual.html -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/LICENSE -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/GPLv2.txt -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-core -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/tsa.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/toy.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/rna_fast_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/construction.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/config.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/simplification.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/pe_params.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-hammer -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/hammer -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/hammer/config.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-ionhammer -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/ionhammer -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/ionhammer/ionhammer.cfg -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-corrector-core -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/corrector -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/corrector/corrector.info -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-truseq-scfcorrection -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-kmercount -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-gbuilder -- Installing: /build/spades-3.13.0+dfsg2/install_spades/bin/spades-gmapper -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/hammer_logic.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/spades_logic.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/corrector_logic.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/support.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/options_storage.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/id_generation.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/launch_options.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/alignment.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/sam_parser.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/SeqIO.py -- Installing: /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/__init__.py make[2]: Leaving directory '/build/spades-3.13.0+dfsg2/build_spades' find /build/spades-3.13.0+dfsg2/install_spades \ -type f \ -print0 \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + /build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/__init__.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/SeqIO.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/sam_parser.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/common/alignment.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/launch_options.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/id_generation.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/options_storage.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/support.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/corrector_logic.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/spades_logic.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/process_cfg.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/spades_pipeline/hammer_logic.py/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/corrector/corrector.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/ionhammer/ionhammer.cfg/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/hammer/config.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/mda_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/moleculo_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/pe_params.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/rna_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/simplification.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/careful_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/config.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/large_genome_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/meta_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/careful_mda_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/construction.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/distance_estimation.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/rna_fast_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/toy.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/detail_info_printer.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/plasmid_mode.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/configs/debruijn/tsa.info/build/spades-3.13.0+dfsg2/install_spades/share/spades/GPLv2.txt/build/spades-3.13.0+dfsg2/install_spades/share/spades/LICENSE/build/spades-3.13.0+dfsg2/install_spades/share/spades/rnaspades_manual.html/build/spades-3.13.0+dfsg2/install_spades/share/spades/truspades_manual.html/build/spades-3.13.0+dfsg2/install_spades/share/spades/README.md/build/spades-3.13.0+dfsg2/install_spades/share/spades/manual.html/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_plasmid/pl1.fq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_plasmid/pl2.fq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/reference_1K.fa.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/genes_1K.gff/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/genes_1K.txt/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/operons_1K.gff/build/spades-3.13.0+dfsg2/install_spades/share/spades/test_dataset/operons_1K.txt/build/spades-3.13.0+dfsg2/install_spades/share/spades/VERSION/build/spades-3.13.0+dfsg2/install_spades/bin/spades-gmapper/build/spades-3.13.0+dfsg2/install_spades/bin/spades-gbuilder/build/spades-3.13.0+dfsg2/install_spades/bin/spades-kmercount/build/spades-3.13.0+dfsg2/install_spades/bin/spades-truseq-scfcorrection/build/spades-3.13.0+dfsg2/install_spades/bin/spades-corrector-core/build/spades-3.13.0+dfsg2/install_spades/bin/spades-ionhammer/build/spades-3.13.0+dfsg2/install_spades/bin/spades-hammer/build/spades-3.13.0+dfsg2/install_spades/bin/spades-core/build/spades-3.13.0+dfsg2/install_spades/bin/spades_init.py/build/spades-3.13.0+dfsg2/install_spades/bin/truspades.py/build/spades-3.13.0+dfsg2/install_spades/bin/rnaspades.py/build/spades-3.13.0+dfsg2/install_spades/bin/plasmidspades.py/build/spades-3.13.0+dfsg2/install_spades/bin/metaspades.py/build/spades-3.13.0+dfsg2/install_spades/bin/spades.pymake[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/spades-3.13.0+dfsg2' # Ugly hack to make files available for dh_aut_test and autopkgtest mkdir -p /build/spades-3.13.0+dfsg2/../share/ ln -s /build/spades-3.13.0+dfsg2/install_spades/share/spades /build/spades-3.13.0+dfsg2/../share/ ln -s /usr/bin/bwa /build/spades-3.13.0+dfsg2/install_spades/bin/spades-bwa /build/spades-3.13.0+dfsg2/install_spades/bin/spades.py --test Command line: /build/spades-3.13.0+dfsg2/install_spades/bin/spades.py --test System information: SPAdes version: 3.13.0 Python version: 2.7.16 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 Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/spades-3.13.0+dfsg2/spades_test/tmp Threads: 16 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/spades-3.13.0+dfsg2/spades_test/spades.log ===== Read error correction started. == 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 0:00:00.000 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 === 0:00:00.001 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) == Dataset description file was created: /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == 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 0:00:00.002 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 0:00:00.002 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 0:00:00.000 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 0:00:00.001 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 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 0:00:00.132 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 * Corrected reads are in /build/spades-3.13.0+dfsg2/spades_test/corrected/ * Assembled contigs are in /build/spades-3.13.0+dfsg2/spades_test/contigs.fasta * Assembled scaffolds are in /build/spades-3.13.0+dfsg2/spades_test/scaffolds.fasta * Assembly graph is in /build/spades-3.13.0+dfsg2/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-3.13.0+dfsg2/spades_test/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /build/spades-3.13.0+dfsg2/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /build/spades-3.13.0+dfsg2/spades_test/scaffolds.paths ======= SPAdes pipeline finished. ========= TEST PASSED CORRECTLY. SPAdes log can be found here: /build/spades-3.13.0+dfsg2/spades_test/spades.log Thank you for using SPAdes! /build/spades-3.13.0+dfsg2/install_spades/bin/metaspades.py --test Command line: /build/spades-3.13.0+dfsg2/install_spades/bin/metaspades.py --test System information: SPAdes version: 3.13.0 Python version: 2.7.16 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 Debug mode is turned OFF Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 33, 55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/spades-3.13.0+dfsg2/spades_test/tmp Threads: 16 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/spades-3.13.0+dfsg2/spades_test/spades.log ===== Read error correction started. == 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 0:00:00.000 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 0:00:00.001 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 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 0:00:01.370 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) == Dataset description file was created: /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == 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 0:00:00.000 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 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 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K33/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/K33/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=33 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 0:00:00.000 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 * Corrected reads are in /build/spades-3.13.0+dfsg2/spades_test/corrected/ * Assembled contigs are in /build/spades-3.13.0+dfsg2/spades_test/contigs.fasta * Assembled scaffolds are in /build/spades-3.13.0+dfsg2/spades_test/scaffolds.fasta * Assembly graph is in /build/spades-3.13.0+dfsg2/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-3.13.0+dfsg2/spades_test/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /build/spades-3.13.0+dfsg2/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /build/spades-3.13.0+dfsg2/spades_test/scaffolds.paths ======= SPAdes pipeline finished. ========= TEST PASSED CORRECTLY. SPAdes log can be found here: /build/spades-3.13.0+dfsg2/spades_test/spades.log Thank you for using SPAdes! /build/spades-3.13.0+dfsg2/install_spades/bin/rnaspades.py --test Command line: /build/spades-3.13.0+dfsg2/install_spades/bin/rnaspades.py --test System information: SPAdes version: 3.13.0 Python version: 2.7.16 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 Debug mode is turned OFF Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: auto Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/spades-3.13.0+dfsg2/spades_test/tmp Threads: 16 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/spades-3.13.0+dfsg2/spades_test/spades.log /build/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100 /build/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 Reads length: 100 K values to be used: [33, 49] ===== Read error correction started. == 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 0:00:00.000 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 0:00:00.001 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 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 0:00:00.067 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) == Dataset description file was created: /build/spades-3.13.0+dfsg2/spades_test/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == 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 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K33/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/K33/configs/rna_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=33 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 0:00:00.152 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 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K49/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K49/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.0+dfsg2/spades_test/K49/configs/rna_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=49 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 15 0:00:00.000 4M / 4M INFO General (launch.hpp : 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 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 0:00:00.119 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 * Corrected reads are in /build/spades-3.13.0+dfsg2/spades_test/corrected/ * Assembled transcripts are in /build/spades-3.13.0+dfsg2/spades_test/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /build/spades-3.13.0+dfsg2/spades_test/transcripts.paths * Hard filtered transcripts are in /build/spades-3.13.0+dfsg2/spades_test/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /build/spades-3.13.0+dfsg2/spades_test/soft_filtered_transcripts.fasta ======= SPAdes pipeline finished. ========= TEST PASSED CORRECTLY. SPAdes log can be found here: /build/spades-3.13.0+dfsg2/spades_test/spades.log Thank you for using SPAdes! # Difficult to test truSPAdes before installing because bwa-spades # is still not in the right place. Let's do this later in an # autopkgtest. # /build/spades-3.13.0+dfsg2/install_spades/bin/truspades.py --test # Cleunup symlinks rm -rf /build/spades-3.13.0+dfsg2/../share/ unlink /build/spades-3.13.0+dfsg2/install_spades/bin/spades-bwa make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2 --sourcedirectory=src --buildsystem=cmake dh_testroot -O--sourcedirectory=src -O--buildsystem=cmake dh_prep -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_install make[1]: Entering directory '/build/spades-3.13.0+dfsg2' echo "Nothing to install" Nothing to install find /build/spades-3.13.0+dfsg2 -name *.pyc -delete make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules override_dh_install make[1]: Entering directory '/build/spades-3.13.0+dfsg2' dh_install mkdir -p debian/spades/usr/lib/spades mv debian/spades/usr/bin debian/spades/usr/lib/spades mkdir -p debian/spades/usr/bin install debian/bin/spades debian/spades/usr/bin/ chmod +x debian/spades/usr/bin/spades rm -f debian/spades/usr/share/spades/GPLv2.txt rm -f debian/spades/usr/share/spades/README.md rm -f debian/spades/usr/share/spades/LICENSE ln -s ../../../share/spades/VERSION debian/spades/usr/lib/spades/bin/VERSION make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules override_dh_installdocs make[1]: Entering directory '/build/spades-3.13.0+dfsg2' dh_installdocs rm -f debian/spades/usr/share/spades/*.html rm -f debian/spades/usr/share/spades/manual.md make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/spades-3.13.0+dfsg2' LANG="C" LANGUAGE="en_US:en" LC_ALL=C.UTF-8 lynx -dump changelog.html > changelog dh_installchangelogs changelog rm changelog make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' debian/rules override_dh_installman make[1]: Entering directory '/build/spades-3.13.0+dfsg2' mkdir -p /build/spades-3.13.0+dfsg2/debian/man asciidoctor -a docdate='' -b manpage /build/spades-3.13.0+dfsg2/debian/man_src/*.adoc cp /build/spades-3.13.0+dfsg2/debian/man_src/*.? /build/spades-3.13.0+dfsg2/debian/man dh_installman -- make[1]: Leaving directory '/build/spades-3.13.0+dfsg2' dh_python2 -O--sourcedirectory=src -O--buildsystem=cmake E: dh_python2 dh_python2:408: no package to act on (python-foo or one with ${python:Depends} in Depends) dh_installinit -O--sourcedirectory=src -O--buildsystem=cmake dh_perl -O--sourcedirectory=src -O--buildsystem=cmake dh_link -O--sourcedirectory=src -O--buildsystem=cmake dh_link: skipping link from usr/bin/spades to self dh_strip_nondeterminism -O--sourcedirectory=src -O--buildsystem=cmake dh_compress -O--sourcedirectory=src -O--buildsystem=cmake dh_fixperms -O--sourcedirectory=src -O--buildsystem=cmake dh_missing -O--sourcedirectory=src -O--buildsystem=cmake dh_strip -O--sourcedirectory=src -O--buildsystem=cmake dh_makeshlibs -O--sourcedirectory=src -O--buildsystem=cmake dh_shlibdeps -O--sourcedirectory=src -O--buildsystem=cmake dh_installdeb -O--sourcedirectory=src -O--buildsystem=cmake 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-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) dpkg-source --after-build . 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/2692573 and its subdirectories I: Current time: Wed Dec 15 23:42:45 +14 2021 I: pbuilder-time-stamp: 1639561365