I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 26 20:14:30 -12 2020 I: pbuilder-time-stamp: 1595837670 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 [subread_1.6.3+dfsg-1.dsc] I: copying [./subread_1.6.3+dfsg.orig.tar.xz] I: copying [./subread_1.6.3+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 30 07:52:42 2019 -12 gpgv: using RSA key B1A51EB2779DD01743CC19BA1CF792111B5228B0 gpgv: issuer "mestia@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./subread_1.6.3+dfsg-1.dsc dpkg-source: info: extracting subread in subread-1.6.3+dfsg dpkg-source: info: unpacking subread_1.6.3+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_1.6.3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying typo.patch dpkg-source: info: applying fix_ftbfs_kfreebsd.patch dpkg-source: info: applying arch_specific_flags.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26548/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='26548' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.m0OMDfe7yA/pbuilderrc_M8d0 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.m0OMDfe7yA/b1 --logfile b1/build.log subread_1.6.3+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled16-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 25 20:25 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/26548/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bc, debhelper (>= 12~), help2man, python, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 52 newly installed, 0 to remove and 0 not upgraded. Need to get 24.9 MB of archives. After unpacking 91.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 bc arm64 1.07.1-2+b1 [104 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 24.9 MB in 1s (17.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_arm64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_arm64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:arm64. Preparing to unpack .../14-libreadline7_7.0-5_arm64.deb ... Unpacking libreadline7:arm64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:arm64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:arm64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython2-stdlib:arm64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:arm64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython-stdlib:arm64 (2.7.16-1) ... Setting up libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... 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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20664 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_arm64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-3+b4_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... 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No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up bc (1.07.1-2+b1) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up help2man (1.47.8) ... 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 libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... 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 gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... 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:arm64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 I: Running cd /build/subread-1.6.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 1.6.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Mestiashvili dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/subread-1.6.3+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/build/subread-1.6.3+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o make[2]: Leaving directory '/build/subread-1.6.3+dfsg/src' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/subread.substvars debian/subread-data.substvars debian/files rm -fr -- debian/subread/ debian/tmp/ debian/subread-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/subread-1.6.3+dfsg' debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/subread-1.6.3+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/build/subread-1.6.3+dfsg/src' gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version rm -f longread-one/*.o cd longread-one && make make[3]: Entering directory '/build/subread-1.6.3+dfsg/src/longread-one' gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMsorted-hashtable.o LRMsorted-hashtable.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMbase-index.o LRMbase-index.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMchro-event.o LRMchro-event.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhelper.o LRMhelper.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMseek-zlib.o LRMseek-zlib.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMfile-io.o LRMfile-io.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhashtable.o LRMhashtable.c gcc -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.3"\" -fmessage-length=0 -ggdb -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE make[3]: Leaving directory '/build/subread-1.6.3+dfsg/src/longread-one' gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SNPCalling.c: In function 'main': SNPCalling.c:1460:32: warning: '/temp-snps-' directive writing 11 bytes into a region of size between 1 and 300 [-Wformat-overflow=] sprintf(temp_file_prefix, "%s/temp-snps-%06u-%s-", temp_location, getpid(), mac_rand); ^~~~~~~~~~~ SNPCalling.c:1460:29: note: using the range [0, 4294967295] for directive argument sprintf(temp_file_prefix, "%s/temp-snps-%06u-%s-", temp_location, getpid(), mac_rand); ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from SNPCalling.c:26: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 20 and 335 bytes into a destination of size 300 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:66:24: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 300 [-Wformat-overflow=] sprintf(tmp_fname, "%s.reads", context->config.index_prefix); ^~~~~~ In file included from /usr/include/stdio.h:873, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 306 bytes into a destination of size 300 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:77:25: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=] sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:75:25: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=] sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:87:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=] sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); ^~~~ In file included from /usr/include/stdio.h:873, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 318 bytes into a destination of size 300 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_indexes_forindel': SUBindel.c:110:26: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=] sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); ^~~~ SUBindel.c:110:22: note: directive argument in the range [0, 2147483647] sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 319 bytes into a destination of size 300 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.3"\" -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/subread-1.6.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv detectionCall repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities ########################################################### # # # Installation successfully completed. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/build/subread-1.6.3+dfsg/src' dh_auto_build -- CC=aarch64-linux-gnu-gcc make[1]: Leaving directory '/build/subread-1.6.3+dfsg' rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/subread-1.6.3+dfsg' debian/tests/subread-tests /build/subread-1.6.3+dfsg  ************************************************** ************************************************** *** *** *** This script will test the major functions *** *** in our package, including the index build- *** *** er, subread-align, subjunc, featureCounts *** *** and exactSNP. *** *** *** *** Test will start in seconds. *** *** *** ************************************************** ************************************************** 9876543210[0,0H ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //=========================== indexBuilder setting ===========================\\ || || || Index name : small1 || || Index space : base-space || || One block index : yes || || Repeat threshold : 100 repeats || || Distance to next subread : 1 || || || || Input files : 1 file in total || || o chr901.fa || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 8%, 0 mins elapsed, rate=537.5k bps/s, total=0m || || 16%, 0 mins elapsed, rate=688.6k bps/s, total=0m || || 24%, 0 mins elapsed, rate=824.9k bps/s, total=0m || || 33%, 0 mins elapsed, rate=925.7k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1018.5k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1098.7k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1161.8k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1232.0k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1292.8k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1346.0k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1405.7k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1442.7k bps/s, total=0m || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=991.9k bps/s, total=0m || || 16%, 0 mins elapsed, rate=986.0k bps/s, total=0m || || 24%, 0 mins elapsed, rate=995.8k bps/s, total=0m || || 33%, 0 mins elapsed, rate=994.8k bps/s, total=0m || || 41%, 0 mins elapsed, rate=994.2k bps/s, total=0m || || 49%, 0 mins elapsed, rate=993.8k bps/s, total=0m || || 58%, 0 mins elapsed, rate=993.6k bps/s, total=0m || || 66%, 0 mins elapsed, rate=996.3k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1006.5k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1007.5k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1027.5k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1026.5k bps/s, total=0m || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.2 minutes. || || Index ../small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:27, pid=29616) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [9,9] || || Load the 1-th index block... || || 33% completed, 0.0 mins elapsed, rate=33.5k reads per second || || 39% completed, 0.0 mins elapsed, rate=33.1k reads per second || || 46% completed, 0.0 mins elapsed, rate=32.9k reads per second || || 53% completed, 0.0 mins elapsed, rate=32.7k reads per second || || 60% completed, 0.0 mins elapsed, rate=32.7k reads per second || || 74% completed, 0.0 mins elapsed, rate=9.0k reads per second || || 83% completed, 0.0 mins elapsed, rate=9.3k reads per second || || 91% completed, 0.0 mins elapsed, rate=9.6k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total reads : 19998 || || Mapped : 18757 (93.8%) || || Uniquely mapped : 18757 || || Multi-mapping : 0 || || || || Unmapped : 1241 || || || || Indels : 3 || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:30, pid=29620) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [9,9] || || Load the 1-th index block... || || 33% completed, 0.0 mins elapsed, rate=34.5k reads per second || || 39% completed, 0.0 mins elapsed, rate=34.5k reads per second || || 46% completed, 0.0 mins elapsed, rate=34.5k reads per second || || 53% completed, 0.0 mins elapsed, rate=34.4k reads per second || || 60% completed, 0.0 mins elapsed, rate=34.5k reads per second || || 74% completed, 0.0 mins elapsed, rate=9.1k reads per second || || 83% completed, 0.0 mins elapsed, rate=9.5k reads per second || || 91% completed, 0.0 mins elapsed, rate=9.8k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total reads : 19998 || || Mapped : 18757 (93.8%) || || Uniquely mapped : 18757 || || Multi-mapping : 0 || || || || Unmapped : 1241 || || || || Indels : 3 || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:32, pid=29624) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [9,9] || || Load the 1-th index block... || || 33% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 39% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 46% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 53% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 60% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 74% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || 83% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || 91% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total fragments : 19998 || || Mapped : 19216 (96.1%) || || Uniquely mapped : 19216 || || Multi-mapping : 0 || || || || Unmapped : 782 || || || || Correctly paired : 18827 || || Not mapped in pairs : 389 || || Only one end mapped : 4 || || Multi-chromosomes : 0 || || Different strands : 0 || || Not in PE distance : 385 || || Abnormal order : 0 || || || || Indels : 14 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:36, pid=29628) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [9,9] || || Load the 1-th index block... || || 33% completed, 0.0 mins elapsed, rate=16.3k fragments per second || || 39% completed, 0.0 mins elapsed, rate=16.3k fragments per second || || 46% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 53% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 60% completed, 0.0 mins elapsed, rate=16.2k fragments per second || || 74% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || 83% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || 91% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total fragments : 19998 || || Mapped : 19216 (96.1%) || || Uniquely mapped : 19216 || || Multi-mapping : 0 || || || || Unmapped : 782 || || || || Correctly paired : 18827 || || Not mapped in pairs : 389 || || Only one end mapped : 4 || || Multi-chromosomes : 0 || || Different strands : 0 || || Not in PE distance : 385 || || Abnormal order : 0 || || || || Indels : 14 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-error-r1.fq || || Input file 2 : test-error-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:40, pid=29663) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [-14,-14] || || Load the 1-th index block... || || 33% completed, 0.0 mins elapsed, rate=17.6k fragments per second || || 39% completed, 0.0 mins elapsed, rate=17.5k fragments per second || || 46% completed, 0.0 mins elapsed, rate=17.5k fragments per second || || 53% completed, 0.0 mins elapsed, rate=17.5k fragments per second || || 60% completed, 0.0 mins elapsed, rate=17.5k fragments per second || || 74% completed, 0.0 mins elapsed, rate=7.0k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.0k fragments per second || || 91% completed, 0.0 mins elapsed, rate=7.0k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total fragments : 20000 || || Mapped : 18697 (93.5%) || || Uniquely mapped : 18697 || || Multi-mapping : 0 || || || || Unmapped : 1303 || || || || Correctly paired : 13917 || || Not mapped in pairs : 4780 || || Only one end mapped : 4502 || || Multi-chromosomes : 0 || || Different strands : 0 || || Not in PE distance : 273 || || Abnormal order : 5 || || || || Indels : 31 || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-err-mut-r1.fq.gz || || Input file 2 : test-err-mut-r2.fq.gz || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || Read group name : MyTestGroup || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:43, pid=29667) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [-14,-14] || || Load the 1-th index block... || || 34% completed, 0.0 mins elapsed, rate=16.8k fragments per second || || 40% completed, 0.0 mins elapsed, rate=17.2k fragments per second || || 48% completed, 0.0 mins elapsed, rate=17.4k fragments per second || || 53% completed, 0.0 mins elapsed, rate=17.6k fragments per second || || 59% completed, 0.0 mins elapsed, rate=17.7k fragments per second || || 67% completed, 0.0 mins elapsed, rate=17.8k fragments per second || || 75% completed, 0.0 mins elapsed, rate=6.9k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.3k fragments per second || || 92% completed, 0.0 mins elapsed, rate=7.7k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total fragments : 20001 || || Mapped : 18660 (93.3%) || || Uniquely mapped : 18660 || || Multi-mapping : 0 || || || || Unmapped : 1341 || || || || Correctly paired : 13560 || || Not mapped in pairs : 5100 || || Only one end mapped : 4786 || || Multi-chromosomes : 0 || || Different strands : 0 || || Not in PE distance : 309 || || Abnormal order : 5 || || || || Indels : 161 || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// 76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array 25531897eb452b012b95ae4b1ca08fd7 ../small1.00.b.tab ************************************************* *** SINGLE-END READS NO ERROR ****** ************************************************* unmatched= 0 ; matched= 18757 ; unmapped= 1241 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.937943794379 paired_match= 0 ; paired= 0.0 ************************************************* *** SINGLE-END READS NO ERROR NO DUP ****** ************************************************* unmatched= 0 ; matched= 18757 ; unmapped= 1241 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.937943794379 paired_match= 0 ; paired= 0.0 ************************************************* *** READS WITH NO ERROR ****** ************************************************* unmatched= 0 ; matched= 38428 ; unmapped= 1568 ; reads= 39996 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.960796079608 paired_match= 38424 ; paired= 0.999895909233 ************************************************* *** READS NO ERROR, NO DUPLICATED REPORT ****** ************************************************* unmatched= 0 ; matched= 38428 ; unmapped= 1568 ; reads= 39996 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.960796079608 paired_match= 38424 ; paired= 0.999895909233 ************************************************* *** READS WITH ONLY SEQUENCING ERROR ****** ************************************************* unmatched= 10 ; matched= 32882 ; unmapped= 7108 ; reads= 40000 ;NN= 0 accuracy= 0.999695974705 ; sensitivity= 0.8223 paired_match= 28380 ; paired= 0.863086186972 ************************************************* *** READS WITH SEQUENCING ERROR AND MUTATION *** *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** ************************************************* unmatched= 13 ; matched= 32519 ; unmapped= 7468 ; reads= 40002 ;NN= 0 accuracy= 0.999600393459 ; sensitivity= 0.813259337033 paired_match= 27736 ; paired= 0.852916756358 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //=========================== indexBuilder setting ===========================\\ || || || Index name : small1 || || Index space : base-space || || Memory : 8000 Mbytes || || Repeat threshold : 100 repeats || || Distance to next subread : 3 || || || || Input files : 1 file in total || || o chr901.fa || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 8%, 0 mins elapsed, rate=1190.2k bps/s, total=0m || || 16%, 0 mins elapsed, rate=1461.7k bps/s, total=0m || || 24%, 0 mins elapsed, rate=1677.5k bps/s, total=0m || || 33%, 0 mins elapsed, rate=1841.3k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1983.7k bps/s, total=0m || || 49%, 0 mins elapsed, rate=2109.3k bps/s, total=0m || || 58%, 0 mins elapsed, rate=2209.2k bps/s, total=0m || || 66%, 0 mins elapsed, rate=2314.4k bps/s, total=0m || || 74%, 0 mins elapsed, rate=2411.1k bps/s, total=0m || || 83%, 0 mins elapsed, rate=2494.5k bps/s, total=0m || || 91%, 0 mins elapsed, rate=2581.7k bps/s, total=0m || || 99%, 0 mins elapsed, rate=2638.0k bps/s, total=0m || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=2975.6k bps/s, total=0m || || 16%, 0 mins elapsed, rate=2923.4k bps/s, total=0m || || 24%, 0 mins elapsed, rate=2940.6k bps/s, total=0m || || 33%, 0 mins elapsed, rate=2949.3k bps/s, total=0m || || 41%, 0 mins elapsed, rate=2933.7k bps/s, total=0m || || 49%, 0 mins elapsed, rate=2940.6k bps/s, total=0m || || 58%, 0 mins elapsed, rate=2945.6k bps/s, total=0m || || 66%, 0 mins elapsed, rate=2949.3k bps/s, total=0m || || 74%, 0 mins elapsed, rate=2975.6k bps/s, total=0m || || 83%, 0 mins elapsed, rate=2986.3k bps/s, total=0m || || 91%, 0 mins elapsed, rate=3014.8k bps/s, total=0m || || 99%, 0 mins elapsed, rate=3020.6k bps/s, total=0m || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.1 minutes. || || Index ../small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //============================= subjunc setting ==============================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctions.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 14 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:50, pid=29870) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [2,41] || || Load the 1-th index block... || || 41% completed, 0.0 mins elapsed, rate=8.9k fragments per second || || 48% completed, 0.0 mins elapsed, rate=8.9k fragments per second || || 54% completed, 0.0 mins elapsed, rate=8.9k fragments per second || || 61% completed, 0.0 mins elapsed, rate=8.9k fragments per second || || 77% completed, 0.0 mins elapsed, rate=5.4k fragments per second || || 87% completed, 0.0 mins elapsed, rate=5.5k fragments per second || || 97% completed, 0.0 mins elapsed, rate=5.5k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total fragments : 16052 || || Mapped : 15251 (95.0%) || || Uniquely mapped : 15251 || || Multi-mapping : 0 || || || || Unmapped : 801 || || || || Correctly paired : 13854 || || Not mapped in pairs : 1397 || || Only one end mapped : 966 || || Multi-chromosomes : 0 || || Different strands : 37 || || Not in PE distance : 332 || || Abnormal order : 62 || || || || Junctions : 416 || || Indels : 182 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //============================= subjunc setting ==============================\\ || || || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctionsNfusions.bam (BAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 28 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (26-Jul-2020 20:16:53, pid=29872) =================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [2,41] || || Load the 1-th index block... || || 41% completed, 0.0 mins elapsed, rate=4.6k fragments per second || || 48% completed, 0.0 mins elapsed, rate=4.7k fragments per second || || 54% completed, 0.0 mins elapsed, rate=4.7k fragments per second || || 61% completed, 0.0 mins elapsed, rate=4.7k fragments per second || || 77% completed, 0.1 mins elapsed, rate=3.6k fragments per second || || 87% completed, 0.1 mins elapsed, rate=3.7k fragments per second || || 97% completed, 0.1 mins elapsed, rate=3.7k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Total fragments : 16052 || || Mapped : 15241 (94.9%) || || Uniquely mapped : 15241 || || Multi-mapping : 0 || || || || Unmapped : 811 || || || || Correctly paired : 13759 || || Not mapped in pairs : 1482 || || Only one end mapped : 1017 || || Multi-chromosomes : 0 || || Different strands : 37 || || Not in PE distance : 366 || || Abnormal order : 62 || || || || Junctions : 434 || || Fusions : 32 || || Indels : 182 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || P test-minimum.sam || || || || Output file : test-minimum.FC || || Summary : test-minimum.FC.summary || || Annotation : test-minimum.GTF (GTF) || || Dir for temp files : result || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file test-minimum.sam... || || Paired-end reads are included. || || Assign alignments to features... || || Total alignments : 998 || || Successfully assigned alignments : 389 (39.0%) || || Running time : 0.00 minutes || || || || || || Summary of counting results can be found in file "result/test-minimum.FC. || || summary" || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ Basic Test finished. The results are in result/test-minimum.FC ================================================================================ ================================================================================ FeatureCounts Chromosome Name Aliases Tests http://subread.sourceforge.net/ ================================================================================ Testing chromosome aliases ... [PASS] ================================================================================ FeatureCounts Chromosome Name Inference Tests http://subread.sourceforge.net/ ================================================================================ Testing automatic inference of chromosome names ... [PASS] ================================================================================ FeatureCounts Corner Case Tests http://subread.sourceforge.net/ ================================================================================ Testing indel reads ... [PASS] Testing junction reads ... [PASS] Testing paired-end reads (fragment counting) ... [PASS] Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] Testing multi-overlapping reads ... [PASS] Testing feature-level summarization ... [PASS] Testing gene-level summarization ... [PASS] Testing multi-mapping reads ... [PASS] Testing multi-mapping reads (primary only) ... [PASS] Testing both ends mapped ... [PASS] Testing disallowing chimeric fragments ... [PASS] Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] Testing Read to position (3' end) ... [PASS] Testing Read extension to the 3' end ... [PASS] Testing Read extension to the 5' end ... [PASS] Testing Low maxOPs value ... [PASS] Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] Testing SAF format annotations ... [PASS] Testing SAM format input ... [PASS] Testing BAM format input ... [PASS] Testing unstranded read summarization ... [PASS] Testing stranded read summarization ... [PASS] Testing reversely stranded read summarization ... [PASS] Testing Ignoring duplicate fragments ... [PASS] Testing Junction reads only ... [PASS] Testing Exonic reads only ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //============================= exactSNP setting =============================\\ || || || Input file : test-in.BAM (BAM) || || Output file : test-out.VCF || || Reference genome : chr901.fa || || || || Threads : 1 || || Min supporting reads : 1 || || Min pct. of supporting reads : 0.0% || || Min base quality score : 13 || || Number of trimmed bases : 3 || || || || Q value cutoff : 10E-12.0 || || P value upper bound : 0.00500 || || Flanking windows size : 5 || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (26-Jul-2020 20:16:59) ======================\\ || || || Split BAM file into result/temp-snps-030565-ED2798000CC6-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed reads : 50204 || || Reported SNPs : 415 || || Reported indels : 21 || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================//  ************************************************** ************************************************** *** *** *** Test finished. *** *** *** *** Should there be any error, please visit *** *** http://subread.sourceforge.net/ for more *** *** information. *** *** *** ************************************************** **************************************************  make[1]: Leaving directory '/build/subread-1.6.3+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/subread.substvars debian/subread-data.substvars rm -fr -- debian/.debhelper/generated/subread/ debian/subread/ debian/tmp/ debian/.debhelper/generated/subread-data/ debian/subread-data/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/subread-1.6.3+dfsg' find /build/subread-1.6.3+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1 help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \ /build/subread-1.6.3+dfsg/bin/subread-align | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/subread-align.1; help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \ /build/subread-1.6.3+dfsg/bin/subread-buildindex | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1; help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \ /build/subread-1.6.3+dfsg/bin/subjunc | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/subjunc.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \ /build/subread-1.6.3+dfsg/bin/featureCounts | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/featureCounts.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \ /build/subread-1.6.3+dfsg/bin/exactSNP | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /build/subread-1.6.3+dfsg/bin/subindel | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/subindel.1; help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \ /build/subread-1.6.3+dfsg/bin/sublong| debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/sublong.1; help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \ /build/subread-1.6.3+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1; help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \ /build/subread-1.6.3+dfsg/bin/utilities/propmapped | debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/propmapped.1; help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \ /build/subread-1.6.3+dfsg/bin/utilities/qualityScores| debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/qualityScores.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \ to each other in the output. A dummy read is added for each singleton read that does not have a pair. \ The output file is compatible with featureCounts program' \ /build/subread-1.6.3+dfsg/bin/utilities/repair| debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/repair.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \ /build/subread-1.6.3+dfsg/bin/utilities/removeDup| debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/removeDup.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Flatten features included in a GTF annotation and save the modified annotation \ to a SAF format file.' \ /build/subread-1.6.3+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /build/subread-1.6.3+dfsg/debian/subread/usr/share/man/man1/flattenGTF.1; dh_auto_install install -d /build/subread-1.6.3\+dfsg/debian/tmp make[1]: Leaving directory '/build/subread-1.6.3+dfsg' dh_install install -d debian/subread/usr/bin cp --reflink=auto -a ./bin/exactSNP ./bin/featureCounts ./bin/subindel ./bin/subjunc ./bin/sublong ./bin/subread-align ./bin/subread-buildindex debian/subread/usr/bin/ install -d debian/subread/usr/lib/subread cp --reflink=auto -a ./bin/utilities/flattenGTF ./bin/utilities/propmapped ./bin/utilities/qualityScores ./bin/utilities/removeDup ./bin/utilities/repair ./bin/utilities/subread-fullscan ./bin/utilities/txUnique debian/subread/usr/lib/subread/ install -d debian/.debhelper/generated/subread install -d debian/subread-data/usr/share/doc/subread/examples cp --reflink=auto -a ./annotation debian/subread-data/usr/share/doc/subread/examples/ install -d debian/.debhelper/generated/subread-data dh_installdocs install -d debian/subread/usr/share/doc/subread cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread chown -R 0:0 debian/subread/usr/share/doc chmod -R u\+rw,go=rX debian/subread/usr/share/doc install -p -m0644 debian/README.Debian debian/subread/usr/share/doc/subread/README.Debian install -p -m0644 debian/copyright debian/subread/usr/share/doc/subread/copyright install -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs install -p -m0644 debian/changelog debian/subread-data/usr/share/doc/subread-data/changelog.Debian install -p -m0644 debian/changelog debian/subread/usr/share/doc/subread/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/subread-1.6.3+dfsg' tar --sort=name \ --mtime="@1548875987" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ -cJf /build/subread-1.6.3+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ make[1]: Leaving directory '/build/subread-1.6.3+dfsg' dh_installman man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/flattenGTF.1 > debian/subread/usr/share/man/man1/flattenGTF.1.dh-new man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/repair.1 > debian/subread/usr/share/man/man1/repair.1.dh-new man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/propmapped.1 > debian/subread/usr/share/man/man1/propmapped.1.dh-new man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/sublong.1 > debian/subread/usr/share/man/man1/sublong.1.dh-new man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/exactSNP.1 > debian/subread/usr/share/man/man1/exactSNP.1.dh-new man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subjunc.1 > debian/subread/usr/share/man/man1/subjunc.1.dh-new man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subread-align.1 > debian/subread/usr/share/man/man1/subread-align.1.dh-new mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/qualityScores.1 > debian/subread/usr/share/man/man1/qualityScores.1.dh-new mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/removeDup.1 > debian/subread/usr/share/man/man1/removeDup.1.dh-new mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subread-fullscan.1 > debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/featureCounts.1 > debian/subread/usr/share/man/man1/featureCounts.1.dh-new mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subindel.1 > debian/subread/usr/share/man/man1/subindel.1.dh-new mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subread-buildindex.1 > debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/removeDup.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 debian/subread/usr/share/man/man1/subread-buildindex.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/subread cd debian/subread-data chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 cd '/build/subread-1.6.3+dfsg' cd '/build/subread-1.6.3+dfsg' dh_fixperms find debian/subread -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/subread-data -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz install -d debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -q -mdebian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug dh_strip install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ea objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ea/a8b93de0d04661cb09dcca6f4bb2ed427ed280.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ea/a8b93de0d04661cb09dcca6f4bb2ed427ed280.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ea/a8b93de0d04661cb09dcca6f4bb2ed427ed280.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ea/a8b93de0d04661cb09dcca6f4bb2ed427ed280.debug debian/subread/usr/lib/subread/txUnique install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/62a5a9f8171c666e6efa07e5f31134a19cd191.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/62a5a9f8171c666e6efa07e5f31134a19cd191.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/62a5a9f8171c666e6efa07e5f31134a19cd191.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/62a5a9f8171c666e6efa07e5f31134a19cd191.debug debian/subread/usr/lib/subread/subread-fullscan install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5a objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5a/3b1828cbcbb9af6b738672e6fd8a251835560c.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5a/3b1828cbcbb9af6b738672e6fd8a251835560c.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5a/3b1828cbcbb9af6b738672e6fd8a251835560c.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5a/3b1828cbcbb9af6b738672e6fd8a251835560c.debug debian/subread/usr/lib/subread/repair install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95/d696a6a61fd477ba0a4b157eed6504457802ea.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95/d696a6a61fd477ba0a4b157eed6504457802ea.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95/d696a6a61fd477ba0a4b157eed6504457802ea.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95/d696a6a61fd477ba0a4b157eed6504457802ea.debug debian/subread/usr/lib/subread/removeDup install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7/008eddbe9a2e33b86fb6ab37e41e660acdfc54.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7/008eddbe9a2e33b86fb6ab37e41e660acdfc54.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7/008eddbe9a2e33b86fb6ab37e41e660acdfc54.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e7/008eddbe9a2e33b86fb6ab37e41e660acdfc54.debug debian/subread/usr/lib/subread/qualityScores install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/49/ad154c62c69f3c07406f7b30f2f63b46cb8e48.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/49/ad154c62c69f3c07406f7b30f2f63b46cb8e48.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/49/ad154c62c69f3c07406f7b30f2f63b46cb8e48.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/49/ad154c62c69f3c07406f7b30f2f63b46cb8e48.debug debian/subread/usr/lib/subread/propmapped install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/dd objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/dd/c1e0ddc7f7ffa9ec2ae6335c5304bb61187b98.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/dd/c1e0ddc7f7ffa9ec2ae6335c5304bb61187b98.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/dd/c1e0ddc7f7ffa9ec2ae6335c5304bb61187b98.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/dd/c1e0ddc7f7ffa9ec2ae6335c5304bb61187b98.debug debian/subread/usr/lib/subread/flattenGTF install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/0f852b4ce656017be2bed1b227885f3187e574.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/0f852b4ce656017be2bed1b227885f3187e574.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/0f852b4ce656017be2bed1b227885f3187e574.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/21/0f852b4ce656017be2bed1b227885f3187e574.debug debian/subread/usr/bin/subread-buildindex install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/818fae1480dc5472b429a1f15c5bee93a85c04.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/818fae1480dc5472b429a1f15c5bee93a85c04.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/818fae1480dc5472b429a1f15c5bee93a85c04.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/818fae1480dc5472b429a1f15c5bee93a85c04.debug debian/subread/usr/bin/subread-align install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/93de45a6a67ddc3ff29ee935abffb076ab5378.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/93de45a6a67ddc3ff29ee935abffb076ab5378.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/93de45a6a67ddc3ff29ee935abffb076ab5378.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/93de45a6a67ddc3ff29ee935abffb076ab5378.debug debian/subread/usr/bin/sublong install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a0 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a0/fb908a359259c6b07c1129372244ebef43c3cc.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a0/fb908a359259c6b07c1129372244ebef43c3cc.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a0/fb908a359259c6b07c1129372244ebef43c3cc.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a0/fb908a359259c6b07c1129372244ebef43c3cc.debug debian/subread/usr/bin/subjunc install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/46f7081c31e5b975e8a7190ee8fb0c22f887f5.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/46f7081c31e5b975e8a7190ee8fb0c22f887f5.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/46f7081c31e5b975e8a7190ee8fb0c22f887f5.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/46f7081c31e5b975e8a7190ee8fb0c22f887f5.debug debian/subread/usr/bin/subindel install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6a objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6a/916b7c9f63ef7db926984b9ad71f2560cb828d.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6a/916b7c9f63ef7db926984b9ad71f2560cb828d.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6a/916b7c9f63ef7db926984b9ad71f2560cb828d.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6a/916b7c9f63ef7db926984b9ad71f2560cb828d.debug debian/subread/usr/bin/featureCounts objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/fbd3d517aa6b0deef43a65f327d60470fea915.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/fbd3d517aa6b0deef43a65f327d60470fea915.debug chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/fbd3d517aa6b0deef43a65f327d60470fea915.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/31/fbd3d517aa6b0deef43a65f327d60470fea915.debug debian/subread/usr/bin/exactSNP install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/subread/usr/lib/debug install -d debian/.debhelper/subread/dbgsym-root/usr/share/doc ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym dh_makeshlibs rm -f debian/subread/DEBIAN/shlibs rm -f debian/subread-data/DEBIAN/shlibs dh_shlibdeps install -d debian/subread/DEBIAN dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex dh_installdeb install -d debian/subread-data/DEBIAN dh_gencontrol echo misc:Depends= >> debian/subread-data.substvars echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -Pdebian/subread-data -UMulti-Arch echo misc:Depends= >> debian/subread.substvars echo misc:Pre-Depends= >> debian/subread.substvars install -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=210f852b4ce656017be2bed1b227885f3187e574 2c62a5a9f8171c666e6efa07e5f31134a19cd191 31818fae1480dc5472b429a1f15c5bee93a85c04 31fbd3d517aa6b0deef43a65f327d60470fea915 49ad154c62c69f3c07406f7b30f2f63b46cb8e48 5a3b1828cbcbb9af6b738672e6fd8a251835560c 6a916b7c9f63ef7db926984b9ad71f2560cb828d 95d696a6a61fd477ba0a4b157eed6504457802ea a0fb908a359259c6b07c1129372244ebef43c3cc ddc1e0ddc7f7ffa9ec2ae6335c5304bb61187b98 e193de45a6a67ddc3ff29ee935abffb076ab5378 e7008eddbe9a2e33b86fb6ab37e41e660acdfc54 eaa8b93de0d04661cb09dcca6f4bb2ed427ed280 f746f7081c31e5b975e8a7190ee8fb0c22f887f5" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/subread -UMulti-Arch chmod 0644 -- debian/subread-data/DEBIAN/control chown 0:0 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/subread/DEBIAN/control chown 0:0 -- debian/subread/DEBIAN/control dh_md5sums cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums chown 0:0 -- debian/subread/DEBIAN/md5sums cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/subread-data/DEBIAN/md5sums chown 0:0 -- debian/subread-data/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/subread .. dpkg-deb --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --build debian/subread-data .. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.6.3+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_1.6.3+dfsg-1_all.deb'. dpkg-deb: building package 'subread' in '../subread_1.6.3+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../subread_1.6.3+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: 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/26548 and its subdirectories I: Current time: Sun Jul 26 20:18:42 -12 2020 I: pbuilder-time-stamp: 1595837922