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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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finished abnormally, OS return value: -6 #842

Closed Alteroldis closed 3 years ago

Alteroldis commented 3 years ago

Description of bug

spades-core: /var/calculate/tmp/portage/sci-biology/SPAdes-3.15.3/work/SPAdes-3.15.3/src/common/utils/kmer_mph/kmer_index_builder.hpp:297: size_t kmers::KMerDiskCounter<Seq, traits>::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = kmers::kmer_index_traits<RuntimeSeq<128> >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]: Assertion `std::is_sorted(beg, end, adt::array_less())' failed.

All internal tests passed. Inside the run script I extend limit of maximum number of open file descriptors, because otherwise the "OS return value: 24" error occured. It is strange that both errors occur in the same place, at the very beginning of the "Starting k-mer counting" stage. The 3.15.1 version is the same.

UPDATE1. The behavior of binaries version is the same

emerge --info Portage 3.0.20 (python 3.9.6-final-0, default/amd64/20/server, gcc-10.3.0, glibc-2.33-r1, 5.10.42-calculate x86_64) ================================================================= System uname: Linux-5.10.42-calculate-x86_64-AMD_Ryzen_Threadripper_2970WX_24-Core_Processor-with-glibc2.33 KiB Mem: 198033920 total, 931292 free KiB Swap: 396067836 total, 396043700 free Timestamp of repository science: Wed, 18 Aug 2021 10:52:55 +0000 Head commit of repository science: 158c816ab6e2495114cf1fb59257e31df82a4080 Timestamp of repository gentoo: Tue, 24 Aug 2021 15:30:01 +0000 sh bash 5.1_p8 ld GNU ld (Gentoo 2.36.1 p5) 2.36.1 app-shells/bash: 5.1_p8::gentoo dev-lang/perl: 5.34.0::gentoo dev-lang/python: 2.7.18_p11::gentoo, 3.9.6_p1::gentoo dev-util/cmake: 3.20.5::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.43.5::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.69-r5::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.35.2::gentoo, 2.36.1-r2::gentoo sys-devel/gcc: 10.3.0-r2::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.10::gentoo (virtual/os-headers) sys-libs/glibc: 2.33-r1::gentoo Repositories: custom location: /var/calculate/custom-overlay masters: calculate gentoo priority: 0 science location: /var/db/repos/science sync-type: git sync-uri: https://github.com/gentoo-mirror/science.git masters: gentoo calculate location: /var/db/repos/calculate sync-type: calculate sync-uri: git://github.com/calculatelinux/calculate.git masters: gentoo priority: 50 distros location: /var/db/repos/distros sync-type: calculate sync-uri: git://github.com/calculatelinux/distros.git masters: calculate gentoo priority: 50 gentoo location: /usr/portage sync-type: calculate sync-uri: git://github.com/calculatelinux/gentoo.git priority: 50 Installed sets: @autodeps, @custom ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=native -pipe" DISTDIR="/var/calculate/distfiles" EMERGE_DEFAULT_OPTS=" --autounmask --binpkg-changed-deps=n --binpkg-respect-use=y --jobs=4 --quiet-build=n --jobs=1" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync metadata-transfer multilib-strict network-sandbox parallel-fetch parallel-install pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles http://distfiles.gentoo.org" INSTALL_MASK="/etc/systemd /lib*/systemd /usr/lib*/systemd /etc/shorewall*/* -/etc/shorewall*/shorewall*.conf" LANG="ru_RU.utf8" LDFLAGS="-Wl,--as-needed" LINGUAS="en ru ru_RU" MAKEOPTS="-j49" PKGDIR="/var/calculate/packages/x86_64" PORTAGE_BINHOST="http://miroir.linuxtricks.fr/calculate/grp/x86_64" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/calculate/tmp" USE="3dnow 3dnowext a52 aac acl acpi aes amd64 amr audiofile avi avx avx2 bittorrent box bzip2 caps cdda cddb cdparanoia cgroups chm cli cpudetection cracklib css cue dav1d dftk djvu dri dv dvd dvdr dvdread ebook encode exif f16c faac fexif ffmpeg flac flash fma3 fma4 foomaticdb ftp gadu gd gphoto2 gpm gstreamer heif hunspell iconv id3tag idn ieee1394 imagemagick imap ios ipod irc jabber lame libglvnd libtirpc libwww lm-sensors logrotate lz4 mad matroska mikmod mimap mmx mmxext mp3 mpeg mpi-threads mplayer multilib musepack ncurses networkmanager nfs nfsv41 nls nptl ogg oggvorbis opencore-amr openmp opus oscar padlock pam pclmul pcre pgo popcnt ppp quicktime raw rdesktop rdrand readline real scanner seccomp semantic-desktop sha smp speex spell split-usr srt sse sse2 sse3 sse4_1 sse4_2 sse4a ssl ssse3 taglib tcpd tga theora threads truetype udev udisks unicode upnp upower usb userlocales v4l v4l2 vcd vhosts vnc vorbis vpx wavpack wayland webkit win32codecs wmf wxwindows x264 x265 xanim xattr xcomposite xmp xop xvid xvmc zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" CAMERAS="*" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 efi-32 pc" INPUT_DEVICES="libinput evdev mutouch synaptics" KERNEL="linux" L10N="en-GB en ru" LCD_DEVICES="* bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" OPENMPI_RM="slurm" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python2_7 python3_9" RUBY_TARGETS="ruby26" THEMES="CSS" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev i915 i965 intel nouveau nv nvidia r100 r200 r300 r600 radeon qxl radeonsi vesa virtualbox via" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.3

Operating System

Calculate Linux

Python Version

3.9.6

Method of SPAdes installation

sources

No errors reported in spades.log

Alteroldis commented 3 years ago

Problem overcomed. I dont know about cause of problem, but if to install with cmake functions of ebuild, then all work. Perhaps the reason is that the cmake functions in the ebuild set the compilation flags necessary for the system.

Attached the my ebuild. # Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 PYTHON_COMPAT=( python{2_7,3_{6,7,8,9}} ) inherit cmake-utils eutils toolchain-funcs DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" HOMEPAGE="http://cab.spbu.ru/software/spades" SRC_URI=" https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz" # DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid genomes # (still present in the release but no longer supported) LICENSE="GPL-2" SLOT="0" KEYWORDS="" IUSE="test" CMAKE_USE_DIR="${S}/src" DEPEND=" sys-libs/zlib app-arch/bzip2 dev-python/regex" RDEPEND="${DEPEND}" # BUG: # SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, # not *.so or *.a are even used) # # BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their # existing packages # nlopt # llvm # python_libs # bamtools # ConsensusCore # ssw # jemalloc # htrie # getopt_pp # cppformat # cityhash # samtools # bwa # BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? # bwa-0.7.12 # bwa-0.6.2 #src_unpack() { # unpack ${A} # mv ${WORKDIR}/* ${S} #} #src_prepare() { # cmake-utils_src_prepare #} src_configure() { #local mycmakeargs=( # -DCMAKE_INSTALL_PREFIX="${ED}/usr" #) cmake-utils_src_configure } src_compile() { cd ${BUILD_DIR} #emake VERBOSE=2 emake } src_install() { cd ${BUILD_DIR} default if [ "$(usex test)" = yes ]; then cd "${ED}"/usr; ./bin/spades.py --test || die else einfo "To running test of installation, turn on test-use" fi rm -rf "${ED}"/usr/share/spades/test_dataset* rm -rf "${ED}"/usr/spades_test rm -f "${ED}"/usr/share/spades/*.html # BUG: move *.py files to standard site-packages/ subdirectories #insinto /usr/share/"${PN}" #dodoc "${DISTDIR}"/${P}_*manual.html }