RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-24 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 Buildd toolchain package versions: launchpad-buildd_134 python-lpbuildd_134 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.1 dpkg-dev_1.17.5ubuntu5.4 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 29 Oct 09:59:09 ntpdate[1651]: adjust time server 10.211.37.1 offset 0.001333 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8217040', '/home/buildd/filecache-default/bcd5dc063ce51e1147d70d5a7a54c6f9cc3d3ea4'] Unpacking chroot for build PACKAGEBUILD-8217040 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8217040'] Mounting chroot for build PACKAGEBUILD-8217040 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8217040', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main', 'deb http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main', 'deb http://ftpmaster.internal/ubuntu trusty main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-8217040 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8217040', 'amd64'] Updating debian chroot for build PACKAGEBUILD-8217040 Ign http://ftpmaster.internal trusty InRelease Get:1 http://ftpmaster.internal trusty-security InRelease [64.4 kB] Get:2 http://ppa.launchpad.net trusty InRelease [15.4 kB] Get:3 http://ftpmaster.internal trusty-updates InRelease [64.4 kB] Get:4 http://ppa.launchpad.net trusty InRelease [15.4 kB] Get:5 http://ftpmaster.internal trusty Release.gpg [933 B] Get:6 http://ftpmaster.internal trusty Release [58.5 kB] Get:7 http://ftpmaster.internal trusty-security/main amd64 Packages [357 kB] Ign http://ppa.launchpad.net trusty InRelease Get:8 http://ppa.launchpad.net trusty/main amd64 Packages [52.3 kB] Get:9 http://ppa.launchpad.net trusty/main Translation-en [47.9 kB] Ign http://ppa.launchpad.net trusty InRelease Get:10 http://ppa.launchpad.net trusty/main amd64 Packages [8036 B] Get:11 http://ppa.launchpad.net trusty/main Translation-en [7177 B] Get:12 http://ftpmaster.internal trusty-security/restricted amd64 Packages [12.4 kB] Get:13 http://ftpmaster.internal trusty-security/universe amd64 Packages [117 kB] Get:14 http://ftpmaster.internal trusty-security/multiverse amd64 Packages [3688 B] Get:15 http://ftpmaster.internal trusty-security/main Translation-en [194 kB] Get:16 http://ftpmaster.internal trusty-security/multiverse Translation-en [1679 B] Get:17 http://ftpmaster.internal trusty-security/restricted Translation-en [3076 B] Get:18 http://ftpmaster.internal trusty-security/universe Translation-en [68.4 kB] Get:19 http://ftpmaster.internal trusty-updates/main amd64 Packages [638 kB] Get:20 http://ftpmaster.internal trusty-updates/restricted amd64 Packages [15.4 kB] Get:21 http://ftpmaster.internal trusty-updates/universe amd64 Packages [326 kB] Get:22 http://ftpmaster.internal trusty-updates/multiverse amd64 Packages [12.0 kB] Get:23 http://ftpmaster.internal trusty-updates/main Translation-en [309 kB] Get:24 http://ftpmaster.internal trusty-updates/multiverse Translation-en [6148 B] Get:25 http://ftpmaster.internal trusty-updates/restricted Translation-en [3569 B] Get:26 http://ftpmaster.internal trusty-updates/universe Translation-en [172 kB] Get:27 http://ftpmaster.internal trusty/main amd64 Packages [1350 kB] Get:28 http://ftpmaster.internal trusty/restricted amd64 Packages [13.0 kB] Get:29 http://ftpmaster.internal trusty/universe amd64 Packages [5859 kB] Get:30 http://ftpmaster.internal trusty/multiverse amd64 Packages [132 kB] Get:31 http://ftpmaster.internal trusty/main Translation-en [762 kB] Get:32 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:33 http://ftpmaster.internal trusty/restricted Translation-en [3457 B] Get:34 http://ftpmaster.internal trusty/universe Translation-en [4089 kB] Fetched 14.9 MB in 5s (2886 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net trusty InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 W: GPG error: http://ppa.launchpad.net trusty InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 5E25F516B04C661B Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files bash binutils bsdutils ca-certificates coreutils cpio cpp-4.8 dpkg dpkg-dev e2fslibs e2fsprogs g++-4.8 gcc-4.8 gcc-4.8-base gcc-4.9-base gnupg gpgv ifupdown initramfs-tools initramfs-tools-bin initscripts iproute2 libapt-pkg4.12 libasan0 libasn1-8-heimdal libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcgmanager0 libcomerr2 libcurl3-gnutls libdbus-1-3 libdpkg-perl libdrm2 libgcc-4.8-dev libgcc1 libgcrypt11 libgnutls26 libgomp1 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libjson-c2 libjson0 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libpcre3 libplymouth2 libprocps3 libquadmath0 libroken18-heimdal libselinux1 libsepol1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-4.8-dev libstdc++6 libtasn1-6 libtsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd patch pkg-create-dbgsym plymouth procps sysv-rc sysvinit-utils tzdata udev upstart util-linux 93 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 55.6 MB of archives. After this operation, 7469 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty-updates/main base-files amd64 7.2ubuntu5.3 [60.9 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty-security/main bash amd64 4.3-7ubuntu1.5 [576 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-security/main coreutils amd64 8.21-1ubuntu5.1 [1089 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-security/main dpkg amd64 1.17.5ubuntu5.4 [1954 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty-security/main libpcre3 amd64 1:8.31-2ubuntu2.1 [144 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty-updates/main libselinux1 amd64 2.2.2-1ubuntu0.1 [58.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty-updates/main sysv-rc all 2.88dsf-41ubuntu6.2 [36.4 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty-updates/main sysvinit-utils amd64 2.88dsf-41ubuntu6.2 [53.1 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty-updates/main mount amd64 2.20.1-5.1ubuntu20.7 [114 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty-updates/main passwd amd64 1:4.1.5.1-1ubuntu9.1 [755 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty-updates/main initscripts amd64 2.88dsf-41ubuntu6.2 [27.7 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty-security/main libdbus-1-3 amd64 1.6.18-0ubuntu4.3 [132 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty-security/main libjson-c2 amd64 0.11-3ubuntu1.2 [22.0 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty-updates/main libuuid1 amd64 2.20.1-5.1ubuntu20.7 [10.9 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty-updates/main libblkid1 amd64 2.20.1-5.1ubuntu20.7 [62.6 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty-updates/main libcgmanager0 amd64 0.24-0ubuntu7.5 [28.9 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty-security/main tzdata all 2015g-0ubuntu0.14.04 [164 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty-updates/main util-linux amd64 2.20.1-5.1ubuntu20.7 [458 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty-updates/main libprocps3 amd64 1:3.3.9-1ubuntu2.2 [31.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty-updates/main procps amd64 1:3.3.9-1ubuntu2.2 [209 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty-updates/main udev amd64 204-5ubuntu20.15 [735 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty-updates/main libudev1 amd64 204-5ubuntu20.15 [33.4 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty-updates/main iproute2 amd64 3.12.0-2ubuntu1 [401 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-updates/main ifupdown amd64 0.7.47.2ubuntu4.1 [52.1 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty-security/main libjson0 amd64 0.11-3ubuntu1.2 [1080 B] Get:26 http://ftpmaster.internal/ubuntu/ trusty-updates/main upstart amd64 1.12.1-0ubuntu4.2 [390 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty-security/main libc6-dev amd64 2.19-0ubuntu6.6 [1910 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty-security/main libc-dev-bin amd64 2.19-0ubuntu6.6 [68.9 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty-security/main linux-libc-dev amd64 3.13.0-66.108 [775 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty-security/main libc-bin amd64 2.19-0ubuntu6.6 [1168 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty-updates/main gcc-4.9-base amd64 4.9.1-0ubuntu1 [14.8 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgcc1 amd64 1:4.9.1-0ubuntu1 [39.2 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty-security/main libc6 amd64 2.19-0ubuntu6.6 [4735 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty-updates/main e2fslibs amd64 1.42.9-3ubuntu1.3 [182 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty-updates/main e2fsprogs amd64 1.42.9-3ubuntu1.3 [667 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty-updates/main login amd64 1:4.1.5.1-1ubuntu9.1 [301 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty-updates/main libtsan0 amd64 4.8.4-2ubuntu1~14.04 [94.7 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgomp1 amd64 4.8.4-2ubuntu1~14.04 [23.1 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty-updates/main libitm1 amd64 4.8.4-2ubuntu1~14.04 [28.6 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty-updates/main libatomic1 amd64 4.8.4-2ubuntu1~14.04 [8650 B] Get:41 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasan0 amd64 4.8.4-2ubuntu1~14.04 [63.0 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty-updates/main libquadmath0 amd64 4.8.4-2ubuntu1~14.04 [126 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty-updates/main g++-4.8 amd64 4.8.4-2ubuntu1~14.04 [15.0 MB] Get:44 http://ftpmaster.internal/ubuntu/ trusty-updates/main gcc-4.8 amd64 4.8.4-2ubuntu1~14.04 [5049 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty-updates/main cpp-4.8 amd64 4.8.4-2ubuntu1~14.04 [4597 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty-updates/main binutils amd64 2.24-5ubuntu14 [2076 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty-updates/main libstdc++-4.8-dev amd64 4.8.4-2ubuntu1~14.04 [1052 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgcc-4.8-dev amd64 4.8.4-2ubuntu1~14.04 [1687 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty-updates/main gcc-4.8-base amd64 4.8.4-2ubuntu1~14.04 [15.9 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty-updates/main libstdc++6 amd64 4.8.4-2ubuntu1~14.04 [259 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty-updates/main libapt-pkg4.12 amd64 1.0.1ubuntu2.10 [637 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty-security/main gpgv amd64 1.4.16-1ubuntu2.3 [161 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty-security/main gnupg amd64 1.4.16-1ubuntu2.3 [611 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty-updates/main apt amd64 1.0.1ubuntu2.10 [952 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty-updates/main bsdutils amd64 1:2.20.1-5.1ubuntu20.7 [33.8 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty-updates/main libcomerr2 amd64 1.42.9-3ubuntu1.3 [62.9 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty-updates/main libmount1 amd64 2.20.1-5.1ubuntu20.7 [60.2 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty-updates/main libsepol1 amd64 2.2-1ubuntu0.1 [107 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty-updates/main libss2 amd64 1.42.9-3ubuntu1.3 [67.1 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty-security/main libgcrypt11 amd64 1.5.3-2ubuntu4.2 [239 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty-security/main libtasn1-6 amd64 3.4-3ubuntu0.3 [43.6 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty-security/main libgnutls26 amd64 2.12.23-12ubuntu2.2 [393 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty-security/main libsqlite3-0 amd64 3.8.2-1ubuntu2.1 [342 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty-security/main libssl1.0.0 amd64 1.0.1f-1ubuntu2.15 [826 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty-updates/main libdrm2 amd64 2.4.60-2~ubuntu14.04.1 [23.5 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty-updates/main initramfs-tools all 0.103ubuntu4.2 [44.3 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty-updates/main initramfs-tools-bin amd64 0.103ubuntu4.2 [8922 B] Get:68 http://ftpmaster.internal/ubuntu/ trusty-security/main cpio amd64 2.11+dfsg-1ubuntu1.1 [73.3 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty-updates/main plymouth amd64 0.8.8-0ubuntu17.1 [98.6 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty-updates/main libplymouth2 amd64 0.8.8-0ubuntu17.1 [76.8 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty-updates/main libroken18-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [40.0 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasn1-8-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [161 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty-security/main libk5crypto3 amd64 1.12+dfsg-2ubuntu5.1 [79.8 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty-security/main libgssapi-krb5-2 amd64 1.12+dfsg-2ubuntu5.1 [113 kB] Get:75 http://ftpmaster.internal/ubuntu/ trusty-security/main libkrb5-3 amd64 1.12+dfsg-2ubuntu5.1 [262 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty-security/main libkrb5support0 amd64 1.12+dfsg-2ubuntu5.1 [30.4 kB] Get:77 http://ftpmaster.internal/ubuntu/ trusty-updates/main libhcrypto4-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [83.9 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty-updates/main libheimbase1-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [28.9 kB] Get:79 http://ftpmaster.internal/ubuntu/ trusty-updates/main libwind0-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [47.8 kB] Get:80 http://ftpmaster.internal/ubuntu/ trusty-updates/main libhx509-5-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [104 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty-updates/main libkrb5-26-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [196 kB] Get:82 http://ftpmaster.internal/ubuntu/ trusty-updates/main libheimntlm0-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [15.2 kB] Get:83 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgssapi3-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [89.8 kB] Get:84 http://ftpmaster.internal/ubuntu/ trusty-security/main libldap-2.4-2 amd64 2.4.31-1+nmu2ubuntu8.2 [153 kB] Get:85 http://ftpmaster.internal/ubuntu/ trusty-security/main libcurl3-gnutls amd64 7.35.0-1ubuntu2.5 [165 kB] Get:86 http://ftpmaster.internal/ubuntu/ trusty-security/main multiarch-support amd64 2.19-0ubuntu6.6 [4486 B] Get:87 http://ftpmaster.internal/ubuntu/ trusty-updates/main apt-transport-https amd64 1.0.1ubuntu2.10 [25.1 kB] Get:88 http://ftpmaster.internal/ubuntu/ trusty-security/main openssl amd64 1.0.1f-1ubuntu2.15 [489 kB] Get:89 http://ftpmaster.internal/ubuntu/ trusty-security/main ca-certificates all 20141019ubuntu0.14.04.1 [189 kB] Get:90 http://ftpmaster.internal/ubuntu/ trusty-security/main dpkg-dev all 1.17.5ubuntu5.4 [726 kB] Get:91 http://ftpmaster.internal/ubuntu/ trusty-security/main libdpkg-perl all 1.17.5ubuntu5.4 [179 kB] Get:92 http://ftpmaster.internal/ubuntu/ trusty-security/main patch amd64 2.7.1-4ubuntu2.3 [86.4 kB] Get:93 http://ftpmaster.internal/ubuntu/ trusty-security/main pkg-create-dbgsym all 0.67~trusty [8844 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.6 MB in 7s (7032 kB/s) (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu5.3_amd64.deb ... Unpacking base-files (7.2ubuntu5.3) over (7.2ubuntu5) ... Setting up base-files (7.2ubuntu5.3) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/os-release ... (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../bash_4.3-7ubuntu1.5_amd64.deb ... Unpacking bash (4.3-7ubuntu1.5) over (4.3-6ubuntu1) ... Setting up bash (4.3-7ubuntu1.5) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../coreutils_8.21-1ubuntu5.1_amd64.deb ... Unpacking coreutils (8.21-1ubuntu5.1) over (8.21-1ubuntu5) ... Setting up coreutils (8.21-1ubuntu5.1) ... 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Setting up libpcre3:amd64 (1:8.31-2ubuntu2.1) ... Processing triggers for libc-bin (2.19-0ubuntu6) ... (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../libselinux1_2.2.2-1ubuntu0.1_amd64.deb ... Unpacking libselinux1:amd64 (2.2.2-1ubuntu0.1) over (2.2.2-1) ... Setting up libselinux1:amd64 (2.2.2-1ubuntu0.1) ... Processing triggers for libc-bin (2.19-0ubuntu6) ... (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../sysv-rc_2.88dsf-41ubuntu6.2_all.deb ... Unpacking sysv-rc (2.88dsf-41ubuntu6.2) over (2.88dsf-41ubuntu6) ... Preparing to unpack .../sysvinit-utils_2.88dsf-41ubuntu6.2_amd64.deb ... Unpacking sysvinit-utils (2.88dsf-41ubuntu6.2) over (2.88dsf-41ubuntu6) ... Setting up sysvinit-utils (2.88dsf-41ubuntu6.2) ... Setting up sysv-rc (2.88dsf-41ubuntu6.2) ... (Reading database ... 11788 files and directories currently installed.) 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Setting up libsqlite3-0:amd64 (3.8.2-1ubuntu2.1) ... Setting up libssl1.0.0:amd64 (1.0.1f-1ubuntu2.15) ... Setting up libdrm2:amd64 (2.4.60-2~ubuntu14.04.1) ... Setting up initramfs-tools-bin (0.103ubuntu4.2) ... Setting up cpio (2.11+dfsg-1ubuntu1.1) ... Setting up initramfs-tools (0.103ubuntu4.2) ... update-initramfs: deferring update (trigger activated) Setting up libplymouth2:amd64 (0.8.8-0ubuntu17.1) ... Setting up plymouth (0.8.8-0ubuntu17.1) ... update-initramfs: deferring update (trigger activated) Setting up libroken18-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libasn1-8-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libkrb5support0:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libk5crypto3:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libkrb5-3:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libgssapi-krb5-2:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libhcrypto4-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libheimbase1-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libwind0-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libhx509-5-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libkrb5-26-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libheimntlm0-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libgssapi3-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libldap-2.4-2:amd64 (2.4.31-1+nmu2ubuntu8.2) ... Setting up libcurl3-gnutls:amd64 (7.35.0-1ubuntu2.5) ... Setting up apt-transport-https (1.0.1ubuntu2.10) ... Setting up openssl (1.0.1f-1ubuntu2.15) ... Setting up ca-certificates (20141019ubuntu0.14.04.1) ... Setting up libdpkg-perl (1.17.5ubuntu5.4) ... Setting up patch (2.7.1-4ubuntu2.3) ... Setting up dpkg-dev (1.17.5ubuntu5.4) ... Setting up pkg-create-dbgsym (0.67~trusty) ... Processing triggers for libc-bin (2.19-0ubuntu6.6) ... Processing triggers for initramfs-tools (0.103ubuntu4.2) ... Processing triggers for ca-certificates (20141019ubuntu0.14.04.1) ... Updating certificates in /etc/ssl/certs... 17 added, 8 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8217040', 'amd64', 'trusty', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=trusty', '--purge=never', '--nolog', '-A', 'trinityrnaseq_2.0.6+dfsg-0biolinux3.dsc'] Initiating build PACKAGEBUILD-8217040 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-24.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ trinityrnaseq 2.0.6+dfsg-0biolinux3 (amd64) 29 Oct 2015 09:59 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: trinityrnaseq Version: 2.0.6+dfsg-0biolinux3 Source Version: 2.0.6+dfsg-0biolinux3 Distribution: trusty Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/trinityrnaseq-WXWW41/trinityrnaseq-2.0.6+dfsg' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/trinityrnaseq-WXWW41' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8217040/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── trinityrnaseq_2.0.6+dfsg-0biolinux3.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-IyxH3E/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/766 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11840 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, jellyfish (>= 2.1.4), libjung-java, javahelper, libgetopt-java, default-jdk, parafly, jaligner Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, jellyfish (>= 2.1.4), libjung-java, javahelper, libgetopt-java, default-jdk, parafly, jaligner dpkg-deb: building package `sbuild-build-depends-trinityrnaseq-dummy' in `/«BUILDDIR»/resolver-1IokXY/apt_archive/sbuild-build-depends-trinityrnaseq-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install trinityrnaseq build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils ca-certificates-java dctrl-tools debhelper default-jdk default-jre default-jre-headless devscripts dh-apparmor dh-python file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner java-common javahelper jellyfish libarchive-zip-perl libasound2 libasound2-data libasprintf0c2 libasyncns0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcolt-java libcommons-collections4-java libconcurrent-java libcroco3 libcups2 libdatrie1 libexpat1 libflac8 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgif4 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libjai-core-java libjasper1 libjava3d-java libjava3d-jni libjbig0 libjellyfish-2.0-2 libjpeg-turbo8 libjpeg8 libjung-java liblcms2-2 libmagic1 libnspr4 libnss3 libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpipeline1 libpixman-1-0 libpulse0 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsctp1 libsndfile1 libthai-data libthai0 libtiff5 libunistring0 libvecmath-java libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 man-db mime-support openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless parafly po-debconf python3 python3-minimal python3.4 python3.4-minimal shared-mime-info tzdata-java ucf x11-common Suggested packages: wamerican wordlist whois vacation debtags dh-make bsd-mailx mailx cvs-buildpackage devscripts-el gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl libterm-size-perl libyaml-syck-perl mutt ssh-client svn-buildpackage w3m debian-keyring equivs liblwp-protocol-https-perl libsoap-lite-perl apparmor-easyprof gettext-doc groff cvs gawk tofrodos libasound2-plugins alsa-utils libcommons-collections4-java-doc cups-common libgetopt-java-doc librsvg2-common gvfs libjasper-runtime libjava3d-java-doc liblcms2-utils ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp pcscd pulseaudio less www-browser openjdk-7-demo openjdk-7-source visualvm icedtea-7-plugin icedtea-7-jre-jamvm libnss-mdns sun-java6-fonts fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei ttf-wqy-zenhei ttf-indic-fonts-core ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts libmail-box-perl python3-doc python3-tk python3.4-venv python3.4-doc binfmt-support Recommended packages: at dput dupload libdistro-info-perl libencode-locale-perl libjson-perl libparse-debcontrol-perl liburi-perl libwww-perl lintian patchutils python3-debian python3-magic strace unzip wdiff wget curl libasprintf-dev libgettextpo-dev libgl1-mesa-dri libglib2.0-data hicolor-icon-theme libgtk2.0-bin lksctp-tools tcpd xml-core libxt-dev libgnome2-0 libgnomevfs2-0 libgconf2-4 fonts-dejavu-extra libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils ca-certificates-java dctrl-tools debhelper default-jdk default-jre default-jre-headless devscripts dh-apparmor dh-python file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner java-common javahelper jellyfish libarchive-zip-perl libasound2 libasound2-data libasprintf0c2 libasyncns0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcolt-java libcommons-collections4-java libconcurrent-java libcroco3 libcups2 libdatrie1 libexpat1 libflac8 libfontconfig1 libfreetype6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgif4 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libjai-core-java libjasper1 libjava3d-java libjava3d-jni libjbig0 libjellyfish-2.0-2 libjpeg-turbo8 libjpeg8 libjung-java liblcms2-2 libmagic1 libnspr4 libnss3 libnss3-nssdb libogg0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpipeline1 libpixman-1-0 libpulse0 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsctp1 libsndfile1 libthai-data libthai0 libtiff5 libunistring0 libvecmath-java libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 man-db mime-support openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless parafly po-debconf python3 python3-minimal python3.4 python3.4-minimal sbuild-build-depends-trinityrnaseq-dummy shared-mime-info tzdata-java ucf x11-common 0 upgraded, 134 newly installed, 0 to remove and 0 not upgraded. Need to get 84.6 MB/84.6 MB of archives. After this operation, 179 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! jaligner libjellyfish-2.0-2 jellyfish libjung-java parafly sbuild-build-depends-trinityrnaseq-dummy Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ trusty-security/main libexpat1 amd64 2.1.0-4ubuntu1.1 [71.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty-security/main libmagic1 amd64 1:5.14-2ubuntu3.3 [185 kB] Get:3 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main jaligner all 1.0+dfsg-1biolinux1 [114 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpython3.4-minimal amd64 3.4.3-1ubuntu1~14.04.3 [461 kB] Get:5 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main libjellyfish-2.0-2 amd64 2.2.3-2biolinux2 [60.6 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty-security/main mime-support all 3.54ubuntu1.1 [29.3 kB] Get:7 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main jellyfish amd64 2.2.3-2biolinux2 [347 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpython3.4-stdlib amd64 3.4.3-1ubuntu1~14.04.3 [1986 kB] Get:9 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main libjung-java all 2.0.1-1biolinux1 [830 kB] Get:10 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main parafly amd64 0.0.2013.01.21-1biolinux2 [15.6 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty-updates/main python3.4-minimal amd64 3.4.3-1ubuntu1~14.04.3 [1223 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasprintf0c2 amd64 0.18.3.1-1ubuntu3 [6712 B] Get:13 http://ftpmaster.internal/ubuntu/ trusty-updates/main libglib2.0-0 amd64 2.40.2-0ubuntu1 [1058 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 amd64 1.3.0-1 [24.0 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libxau6 amd64 1:1.0.8-1 [8376 B] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libxdmcp6 amd64 1:1.1.1-1 [12.8 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libxcb1 amd64 1.10-2ubuntu1 [38.0 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libx11-data all 2:1.6.2-1ubuntu2 [111 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libx11-6 amd64 2:1.6.2-1ubuntu2 [560 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty-security/main libxext6 amd64 2:1.3.2-1ubuntu0.0.14.04.1 [28.8 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty-security/main libxml2 amd64 2.9.1+dfsg1-3ubuntu4.4 [570 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main groff-base amd64 1.22.2-5 [1053 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-updates/main man-db amd64 2.6.7.1-1ubuntu1 [857 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libasound2-data all 1.0.27.2-3ubuntu7 [26.3 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main libasound2 amd64 1.0.27.2-3ubuntu7 [327 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main libasyncns0 amd64 0.8-4ubuntu2 [11.9 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main libatk1.0-data all 2.10.0-2ubuntu2 [13.7 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main libatk1.0-0 amd64 2.10.0-2ubuntu2 [50.9 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgtk2.0-common all 2.24.23-0ubuntu1.3 [121 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main fonts-dejavu-core all 2.34-1ubuntu1 [1024 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main ucf all 3.0027+nmu1 [56.3 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty-updates/main fontconfig-config all 2.11.0-0ubuntu4.1 [47.4 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty-security/main libfreetype6 amd64 2.5.2-1ubuntu2.5 [304 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty-updates/main libfontconfig1 amd64 2.11.0-0ubuntu4.1 [123 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main libpixman-1-0 amd64 0.30.2-2ubuntu1 [227 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-render0 amd64 1.10-2ubuntu1 [11.0 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-shm0 amd64 1.10-2ubuntu1 [5432 B] Get:39 http://ftpmaster.internal/ubuntu/ trusty-security/main libxrender1 amd64 1:0.9.8-1build0.14.04.1 [17.9 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty-updates/main libcairo2 amd64 1.13.0~20140204-0ubuntu1.1 [535 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main libavahi-common-data amd64 0.6.31-4ubuntu1 [21.2 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main libavahi-common3 amd64 0.6.31-4ubuntu1 [21.7 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main libavahi-client3 amd64 0.6.31-4ubuntu1 [25.1 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty-security/main libcups2 amd64 1.7.2-0ubuntu1.6 [178 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg-turbo8 amd64 1.3.0-0ubuntu2 [104 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:47 http://ftpmaster.internal/ubuntu/ trusty-security/main libjasper1 amd64 1.900.1-14ubuntu3.2 [130 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty-security/main libjbig0 amd64 2.0-2ubuntu4.1 [26.1 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty-security/main libtiff5 amd64 4.0.3-7ubuntu0.3 [143 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty-security/main libgdk-pixbuf2.0-common all 2.30.7-0ubuntu1.2 [8826 B] Get:51 http://ftpmaster.internal/ubuntu/ trusty-security/main libgdk-pixbuf2.0-0 amd64 2.30.7-0ubuntu1.2 [160 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main libthai-data all 0.1.20-3 [130 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main libdatrie1 amd64 0.2.8-1 [16.7 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main libthai0 amd64 0.1.20-3 [16.9 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty-updates/main fontconfig amd64 2.11.0-0ubuntu4.1 [176 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpango-1.0-0 amd64 1.36.3-1ubuntu1.1 [149 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main libgraphite2-3 amd64 1.2.4-1ubuntu1 [53.8 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty-updates/main libharfbuzz0b amd64 0.9.27-1ubuntu1 [127 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpangoft2-1.0-0 amd64 1.36.3-1ubuntu1.1 [32.7 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpangocairo-1.0-0 amd64 1.36.3-1ubuntu1.1 [20.0 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main libxcomposite1 amd64 1:0.4.4-1 [7714 B] Get:62 http://ftpmaster.internal/ubuntu/ trusty-security/main libxfixes3 amd64 1:5.0.1-1ubuntu1.1 [10.4 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty/main libxcursor1 amd64 1:1.1.14-1 [22.8 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty/main libxdamage1 amd64 1:1.1.4-1ubuntu1 [7612 B] Get:65 http://ftpmaster.internal/ubuntu/ trusty-security/main libxi6 amd64 2:1.7.1.901-1ubuntu1.1 [27.9 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/main libxinerama1 amd64 2:1.1.3-1 [7908 B] Get:67 http://ftpmaster.internal/ubuntu/ trusty/main libxrandr2 amd64 2:1.4.2-1 [16.6 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/main shared-mime-info amd64 1.2-0ubuntu3 [415 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgtk2.0-0 amd64 2.24.23-0ubuntu1.3 [1738 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty-security/main libnspr4 amd64 2:4.10.7-0ubuntu0.14.04.1 [111 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty-security/main libnss3-nssdb all 2:3.19.2-0ubuntu0.14.04.1 [10.6 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty-security/main libnss3 amd64 2:3.19.2-0ubuntu0.14.04.1 [1103 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty/main ca-certificates-java all 20130815ubuntu1 [13.4 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty-security/main tzdata-java all 2015g-0ubuntu0.14.04 [69.6 kB] Get:75 http://ftpmaster.internal/ubuntu/ trusty/main java-common all 0.51 [130 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty/main liblcms2-2 amd64 2.5-0ubuntu4 [132 kB] Get:77 http://ftpmaster.internal/ubuntu/ trusty/main libpcsclite1 amd64 1.8.10-1ubuntu1 [20.9 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty/main libogg0 amd64 1.3.1-1ubuntu1 [17.0 kB] Get:79 http://ftpmaster.internal/ubuntu/ trusty-security/main libflac8 amd64 1.3.0-2ubuntu0.14.04.1 [80.2 kB] Get:80 http://ftpmaster.internal/ubuntu/ trusty/main libvorbis0a amd64 1.3.2-1.3ubuntu1 [87.2 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty/main libvorbisenc2 amd64 1.3.2-1.3ubuntu1 [84.5 kB] Get:82 http://ftpmaster.internal/ubuntu/ trusty/main libsndfile1 amd64 1.0.25-7ubuntu2 [136 kB] Get:83 http://ftpmaster.internal/ubuntu/ trusty/main libwrap0 amd64 7.6.q-25 [46.2 kB] Get:84 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpulse0 amd64 1:4.0-0ubuntu11.1 [225 kB] Get:85 http://ftpmaster.internal/ubuntu/ trusty/main libsctp1 amd64 1.0.15+dfsg-1 [9226 B] Get:86 http://ftpmaster.internal/ubuntu/ trusty-security/main openjdk-7-jre-headless amd64 7u85-2.6.1-5ubuntu0.14.04.1 [39.6 MB] Get:87 http://ftpmaster.internal/ubuntu/ trusty/main default-jre-headless amd64 2:1.7-51 [3834 B] Get:88 http://ftpmaster.internal/ubuntu/ trusty/main libgif4 amd64 4.1.6-11 [28.6 kB] Get:89 http://ftpmaster.internal/ubuntu/ trusty-updates/main x11-common all 1:7.7+1ubuntu8.1 [49.5 kB] Get:90 http://ftpmaster.internal/ubuntu/ trusty/main libxtst6 amd64 2:1.2.2-1 [14.1 kB] Get:91 http://ftpmaster.internal/ubuntu/ trusty-updates/main libglapi-mesa amd64 10.1.3-0ubuntu0.5 [20.6 kB] Get:92 http://ftpmaster.internal/ubuntu/ trusty/main libx11-xcb1 amd64 2:1.6.2-1ubuntu2 [9426 B] Get:93 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-dri2-0 amd64 1.10-2ubuntu1 [6710 B] Get:94 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-dri3-0 amd64 1.10-2ubuntu1 [5118 B] Get:95 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-glx0 amd64 1.10-2ubuntu1 [20.0 kB] Get:96 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-present0 amd64 1.10-2ubuntu1 [5254 B] Get:97 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-sync1 amd64 1.10-2ubuntu1 [8090 B] Get:98 http://ftpmaster.internal/ubuntu/ trusty/main libxshmfence1 amd64 1.1-2 [4644 B] Get:99 http://ftpmaster.internal/ubuntu/ trusty/main libxxf86vm1 amd64 1:1.1.3-1 [11.7 kB] Get:100 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgl1-mesa-glx amd64 10.1.3-0ubuntu0.5 [113 kB] Get:101 http://ftpmaster.internal/ubuntu/ trusty-security/main openjdk-7-jre amd64 7u85-2.6.1-5ubuntu0.14.04.1 [171 kB] Get:102 http://ftpmaster.internal/ubuntu/ trusty/main default-jre amd64 2:1.7-51 [940 B] Get:103 http://ftpmaster.internal/ubuntu/ trusty/main libatk-wrapper-java all 0.30.4-4 [30.2 kB] Get:104 http://ftpmaster.internal/ubuntu/ trusty/main libatk-wrapper-java-jni amd64 0.30.4-4 [25.2 kB] Get:105 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 amd64 0.6.8-2ubuntu1 [82.4 kB] Get:106 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] Get:107 http://ftpmaster.internal/ubuntu/ trusty-updates/main python3.4 amd64 3.4.3-1ubuntu1~14.04.3 [177 kB] Get:108 http://ftpmaster.internal/ubuntu/ trusty/main python3-minimal amd64 3.4.0-0ubuntu2 [23.2 kB] Get:109 http://ftpmaster.internal/ubuntu/ trusty/main libpython3-stdlib amd64 3.4.0-0ubuntu2 [6912 B] Get:110 http://ftpmaster.internal/ubuntu/ trusty/main python3 amd64 3.4.0-0ubuntu2 [8666 B] Get:111 http://ftpmaster.internal/ubuntu/ trusty-updates/main dh-python all 1.20140128-1ubuntu8.2 [51.1 kB] Get:112 http://ftpmaster.internal/ubuntu/ trusty-security/main file amd64 1:5.14-2ubuntu3.3 [18.9 kB] Get:113 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext-base amd64 0.18.3.1-1ubuntu3 [48.8 kB] Get:114 http://ftpmaster.internal/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] Get:115 http://ftpmaster.internal/ubuntu/ trusty/main dctrl-tools amd64 2.23ubuntu1 [101 kB] Get:116 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext amd64 0.18.3.1-1ubuntu3 [829 kB] Get:117 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:118 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:119 http://ftpmaster.internal/ubuntu/ trusty-updates/main dh-apparmor all 2.8.95~2430-0ubuntu5.3 [12.2 kB] Get:120 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] Get:121 http://ftpmaster.internal/ubuntu/ trusty-security/main openjdk-7-jdk amd64 7u85-2.6.1-5ubuntu0.14.04.1 [16.3 MB] Get:122 http://ftpmaster.internal/ubuntu/ trusty/main default-jdk amd64 2:1.7-51 [934 B] Get:123 http://ftpmaster.internal/ubuntu/ trusty-security/main devscripts amd64 2.14.1ubuntu0.1 [792 kB] Get:124 http://ftpmaster.internal/ubuntu/ trusty/main libarchive-zip-perl all 1.30-7 [90.1 kB] Get:125 http://ftpmaster.internal/ubuntu/ trusty/main javahelper all 0.45ubuntu1 [77.5 kB] Get:126 http://ftpmaster.internal/ubuntu/ trusty/universe libconcurrent-java all 1.3.4-4 [133 kB] Get:127 http://ftpmaster.internal/ubuntu/ trusty/multiverse libcolt-java all 1.2.0+dfsg-2 [510 kB] Get:128 http://ftpmaster.internal/ubuntu/ trusty/universe libcommons-collections4-java all 4.0-1 [553 kB] Get:129 http://ftpmaster.internal/ubuntu/ trusty/universe libgetopt-java all 1.0.14+dfsg-2 [23.5 kB] Get:130 http://ftpmaster.internal/ubuntu/ trusty/multiverse libjai-core-java amd64 1.1.4-3ubuntu1 [2805 kB] Get:131 http://ftpmaster.internal/ubuntu/ trusty/universe libjava3d-jni amd64 1.5.2+dfsg-9ubuntu1 [52.6 kB] Get:132 http://ftpmaster.internal/ubuntu/ trusty/universe libvecmath-java all 1.5.2-4 [118 kB] Get:133 http://ftpmaster.internal/ubuntu/ trusty/universe libjava3d-java all 1.5.2+dfsg-9ubuntu1 [1653 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.6 MB in 8s (9683 kB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 11840 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1.1_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-4ubuntu1.1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu3.3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.14-2ubuntu3.3) ... Selecting previously unselected package libpython3.4-minimal:amd64. Preparing to unpack .../libpython3.4-minimal_3.4.3-1ubuntu1~14.04.3_amd64.deb ... Unpacking libpython3.4-minimal:amd64 (3.4.3-1ubuntu1~14.04.3) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.54ubuntu1.1_all.deb ... Unpacking mime-support (3.54ubuntu1.1) ... Selecting previously unselected package libpython3.4-stdlib:amd64. Preparing to unpack .../libpython3.4-stdlib_3.4.3-1ubuntu1~14.04.3_amd64.deb ... Unpacking libpython3.4-stdlib:amd64 (3.4.3-1ubuntu1~14.04.3) ... 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Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d....done. Setting up libexpat1:amd64 (2.1.0-4ubuntu1.1) ... Setting up libmagic1:amd64 (1:5.14-2ubuntu3.3) ... Setting up libpython3.4-minimal:amd64 (3.4.3-1ubuntu1~14.04.3) ... Setting up mime-support (3.54ubuntu1.1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython3.4-stdlib:amd64 (3.4.3-1ubuntu1~14.04.3) ... Setting up python3.4-minimal (3.4.3-1ubuntu1~14.04.3) ... Setting up libasprintf0c2:amd64 (0.18.3.1-1ubuntu3) ... Setting up libglib2.0-0:amd64 (2.40.2-0ubuntu1) ... No schema files found: doing nothing. Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.10-2ubuntu1) ... Setting up libx11-data (2:1.6.2-1ubuntu2) ... Setting up libx11-6:amd64 (2:1.6.2-1ubuntu2) ... Setting up libxext6:amd64 (2:1.3.2-1ubuntu0.0.14.04.1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3ubuntu4.4) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.6.7.1-1ubuntu1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasound2-data (1.0.27.2-3ubuntu7) ... Setting up libasound2:amd64 (1.0.27.2-3ubuntu7) ... Setting up libasyncns0:amd64 (0.8-4ubuntu2) ... Setting up libatk1.0-data (2.10.0-2ubuntu2) ... Setting up libatk1.0-0:amd64 (2.10.0-2ubuntu2) ... Setting up libgtk2.0-common (2.24.23-0ubuntu1.3) ... Setting up fonts-dejavu-core (2.34-1ubuntu1) ... Setting up ucf (3.0027+nmu1) ... Setting up fontconfig-config (2.11.0-0ubuntu4.1) ... Setting up libfreetype6:amd64 (2.5.2-1ubuntu2.5) ... Setting up libfontconfig1:amd64 (2.11.0-0ubuntu4.1) ... Setting up libpixman-1-0:amd64 (0.30.2-2ubuntu1) ... Setting up libxcb-render0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-shm0:amd64 (1.10-2ubuntu1) ... Setting up libxrender1:amd64 (1:0.9.8-1build0.14.04.1) ... Setting up libcairo2:amd64 (1.13.0~20140204-0ubuntu1.1) ... Setting up libavahi-common-data:amd64 (0.6.31-4ubuntu1) ... Setting up libavahi-common3:amd64 (0.6.31-4ubuntu1) ... Setting up libavahi-client3:amd64 (0.6.31-4ubuntu1) ... Setting up libcups2:amd64 (1.7.2-0ubuntu1.6) ... Setting up libjpeg-turbo8:amd64 (1.3.0-0ubuntu2) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libjasper1:amd64 (1.900.1-14ubuntu3.2) ... Setting up libjbig0:amd64 (2.0-2ubuntu4.1) ... Setting up libtiff5:amd64 (4.0.3-7ubuntu0.3) ... Setting up libgdk-pixbuf2.0-common (2.30.7-0ubuntu1.2) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.30.7-0ubuntu1.2) ... Setting up libthai-data (0.1.20-3) ... Setting up libdatrie1:amd64 (0.2.8-1) ... Setting up libthai0:amd64 (0.1.20-3) ... Setting up fontconfig (2.11.0-0ubuntu4.1) ... Regenerating fonts cache... done. Setting up libpango-1.0-0:amd64 (1.36.3-1ubuntu1.1) ... Setting up libgraphite2-3:amd64 (1.2.4-1ubuntu1) ... Setting up libharfbuzz0b:amd64 (0.9.27-1ubuntu1) ... Setting up libpangoft2-1.0-0:amd64 (1.36.3-1ubuntu1.1) ... Setting up libpangocairo-1.0-0:amd64 (1.36.3-1ubuntu1.1) ... Setting up libxcomposite1:amd64 (1:0.4.4-1) ... Setting up libxfixes3:amd64 (1:5.0.1-1ubuntu1.1) ... Setting up libxcursor1:amd64 (1:1.1.14-1) ... Setting up libxdamage1:amd64 (1:1.1.4-1ubuntu1) ... Setting up libxi6:amd64 (2:1.7.1.901-1ubuntu1.1) ... Setting up libxinerama1:amd64 (2:1.1.3-1) ... Setting up libxrandr2:amd64 (2:1.4.2-1) ... Setting up shared-mime-info (1.2-0ubuntu3) ... Setting up libgtk2.0-0:amd64 (2.24.23-0ubuntu1.3) ... Setting up libnspr4:amd64 (2:4.10.7-0ubuntu0.14.04.1) ... Setting up tzdata-java (2015g-0ubuntu0.14.04) ... Setting up java-common (0.51) ... Setting up liblcms2-2:amd64 (2.5-0ubuntu4) ... Setting up libpcsclite1:amd64 (1.8.10-1ubuntu1) ... Setting up libogg0:amd64 (1.3.1-1ubuntu1) ... Setting up libflac8:amd64 (1.3.0-2ubuntu0.14.04.1) ... Setting up libvorbis0a:amd64 (1.3.2-1.3ubuntu1) ... Setting up libvorbisenc2:amd64 (1.3.2-1.3ubuntu1) ... Setting up libsndfile1:amd64 (1.0.25-7ubuntu2) ... Setting up libwrap0:amd64 (7.6.q-25) ... Setting up libpulse0:amd64 (1:4.0-0ubuntu11.1) ... Setting up libsctp1:amd64 (1.0.15+dfsg-1) ... Setting up libgif4:amd64 (4.1.6-11) ... Setting up x11-common (1:7.7+1ubuntu8.1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libxtst6:amd64 (2:1.2.2-1) ... Setting up libglapi-mesa:amd64 (10.1.3-0ubuntu0.5) ... Setting up libx11-xcb1:amd64 (2:1.6.2-1ubuntu2) ... Setting up libxcb-dri2-0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-dri3-0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-glx0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-present0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-sync1:amd64 (1.10-2ubuntu1) ... Setting up libxshmfence1:amd64 (1.1-2) ... Setting up libxxf86vm1:amd64 (1:1.1.3-1) ... Setting up libgl1-mesa-glx:amd64 (10.1.3-0ubuntu0.5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf (x86_64-linux-gnu_gl_conf) in auto mode Setting up libcroco3:amd64 (0.6.8-2ubuntu1) ... Setting up libunistring0:amd64 (0.9.3-5ubuntu3) ... Setting up python3.4 (3.4.3-1ubuntu1~14.04.3) ... Setting up python3-minimal (3.4.0-0ubuntu2) ... Setting up libpython3-stdlib:amd64 (3.4.0-0ubuntu2) ... Setting up file (1:5.14-2ubuntu3.3) ... Setting up gettext-base (0.18.3.1-1ubuntu3) ... Setting up autotools-dev (20130810.1) ... Setting up dctrl-tools (2.23ubuntu1) ... Setting up gettext (0.18.3.1-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.8.95~2430-0ubuntu5.3) ... Setting up debhelper (9.20131227ubuntu1) ... Setting up libarchive-zip-perl (1.30-7) ... Setting up libjellyfish-2.0-2 (2.2.3-2biolinux2) ... Setting up jellyfish (2.2.3-2biolinux2) ... Setting up libcommons-collections4-java (4.0-1) ... Setting up libgetopt-java (1.0.14+dfsg-2) ... Setting up libjai-core-java (1.1.4-3ubuntu1) ... Setting up libjava3d-jni (1.5.2+dfsg-9ubuntu1) ... Setting up libvecmath-java (1.5.2-4) ... Setting up libjava3d-java (1.5.2+dfsg-9ubuntu1) ... Setting up parafly (0.0.2013.01.21-1biolinux2) ... Setting up python3 (3.4.0-0ubuntu2) ... Setting up dh-python (1.20140128-1ubuntu8.2) ... Setting up devscripts (2.14.1ubuntu0.1) ... Setting up javahelper (0.45ubuntu1) ... Setting up libnss3-nssdb (2:3.19.2-0ubuntu0.14.04.1) ... Setting up libnss3:amd64 (2:3.19.2-0ubuntu0.14.04.1) ... Setting up openjdk-7-jre-headless:amd64 (7u85-2.6.1-5ubuntu0.14.04.1) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up default-jre-headless (2:1.7-51) ... Setting up libatk-wrapper-java (0.30.4-4) ... Setting up libatk-wrapper-java-jni:amd64 (0.30.4-4) ... Setting up openjdk-7-jre:amd64 (7u85-2.6.1-5ubuntu0.14.04.1) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up default-jre (2:1.7-51) ... Setting up openjdk-7-jdk:amd64 (7u85-2.6.1-5ubuntu0.14.04.1) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode Setting up default-jdk (2:1.7-51) ... Setting up jaligner (1.0+dfsg-1biolinux1) ... Setting up libconcurrent-java (1.3.4-4) ... Setting up libcolt-java (1.2.0+dfsg-2) ... Setting up libjung-java (2.0.1-1biolinux1) ... Setting up sbuild-build-depends-trinityrnaseq-dummy (0.invalid.0) ... Setting up ca-certificates-java (20130815ubuntu1) ... Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:AddTrust_External_Root.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:ComSign_Secured_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:ACEDICOM_Root.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Izenpe.com.pem Adding debian:StartCom_Certification_Authority_G2.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Certum_Root_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:PSCProcert.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem Adding debian:A-Trust-nQual-03.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:America_Online_Root_Certification_Authority_2.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:SG_TRUST_SERVICES_RACINE.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:America_Online_Root_Certification_Authority_1.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:TC_TrustCenter_Class_2_CA_II.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Thawte_Premium_Server_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:SecureTrust_CA.pem Adding debian:EC-ACC.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:UTN_DATACorp_SGC_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Thawte_Server_CA.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:StartCom_Certification_Authority_2.pem Adding debian:WoSign.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Certigna.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Juur-SK.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:WoSign_China.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:GTE_CyberTrust_Global_Root.pem Adding debian:Taiwan_GRCA.pem Adding debian:CA_Disig.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Equifax_Secure_CA.pem Adding debian:spi-cacert-2008.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:IGC_A.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Buypass_Class_3_CA_1.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:ComSign_CA.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:CNNIC_ROOT.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:ACCVRAIZ1.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:TC_TrustCenter_Universal_CA_I.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Microsec_e-Szigno_Root_CA.pem done. Processing triggers for libc-bin (2.19-0ubuntu6.6) ... Processing triggers for ca-certificates (20141019ubuntu0.14.04.1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d.... done. done. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.19.0-31-generic amd64 (x86_64) Toolchain package versions: binutils_2.24-5ubuntu14 dpkg-dev_1.17.5ubuntu5.4 g++-4.8_4.8.4-2ubuntu1~14.04 gcc-4.8_4.8.4-2ubuntu1~14.04 libc6-dev_2.19-0ubuntu6.6 libstdc++-4.8-dev_4.8.4-2ubuntu1~14.04 libstdc++6_4.8.4-2ubuntu1~14.04 linux-libc-dev_3.13.0-66.108 Package versions: adduser_3.113+nmu3ubuntu3 advancecomp_1.18-1 apt_1.0.1ubuntu2.10 apt-transport-https_1.0.1ubuntu2.10 autotools-dev_20130810.1 base-files_7.2ubuntu5.3 base-passwd_3.5.33 bash_4.3-7ubuntu1.5 binutils_2.24-5ubuntu14 bsdmainutils_9.0.5ubuntu1 bsdutils_1:2.20.1-5.1ubuntu20.7 build-essential_11.6ubuntu6 busybox-initramfs_1:1.21.0-1ubuntu1 bzip2_1.0.6-5 ca-certificates_20141019ubuntu0.14.04.1 ca-certificates-java_20130815ubuntu1 coreutils_8.21-1ubuntu5.1 cpio_2.11+dfsg-1ubuntu1.1 cpp_4:4.8.2-1ubuntu6 cpp-4.8_4.8.4-2ubuntu1~14.04 dash_0.5.7-4ubuntu1 dctrl-tools_2.23ubuntu1 debconf_1.5.51ubuntu2 debhelper_9.20131227ubuntu1 debianutils_4.4 default-jdk_2:1.7-51 default-jre_2:1.7-51 default-jre-headless_2:1.7-51 devscripts_2.14.1ubuntu0.1 dh-apparmor_2.8.95~2430-0ubuntu5.3 dh-python_1.20140128-1ubuntu8.2 diffutils_1:3.3-1 dpkg_1.17.5ubuntu5.4 dpkg-dev_1.17.5ubuntu5.4 e2fslibs_1.42.9-3ubuntu1.3 e2fsprogs_1.42.9-3ubuntu1.3 fakeroot_1.20-3ubuntu2 file_1:5.14-2ubuntu3.3 findutils_4.4.2-7 fontconfig_2.11.0-0ubuntu4.1 fontconfig-config_2.11.0-0ubuntu4.1 fonts-dejavu-core_2.34-1ubuntu1 g++_4:4.8.2-1ubuntu6 g++-4.8_4.8.4-2ubuntu1~14.04 gcc_4:4.8.2-1ubuntu6 gcc-4.8_4.8.4-2ubuntu1~14.04 gcc-4.8-base_4.8.4-2ubuntu1~14.04 gcc-4.9-base_4.9.1-0ubuntu1 gettext_0.18.3.1-1ubuntu3 gettext-base_0.18.3.1-1ubuntu3 gnupg_1.4.16-1ubuntu2.3 gpgv_1.4.16-1ubuntu2.3 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3ubuntu1 hostname_3.15ubuntu1 ifupdown_0.7.47.2ubuntu4.1 initramfs-tools_0.103ubuntu4.2 initramfs-tools-bin_0.103ubuntu4.2 initscripts_2.88dsf-41ubuntu6.2 insserv_1.14.0-5ubuntu2 intltool-debian_0.35.0+20060710.1 iproute2_3.12.0-2ubuntu1 jaligner_1.0+dfsg-1biolinux1 java-common_0.51 javahelper_0.45ubuntu1 jellyfish_2.2.3-2biolinux2 klibc-utils_2.0.3-0ubuntu1 kmod_15-0ubuntu6 libacl1_2.2.52-1 libapt-pkg4.12_1.0.1ubuntu2.10 libarchive-zip-perl_1.30-7 libasan0_4.8.4-2ubuntu1~14.04 libasn1-8-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libasound2_1.0.27.2-3ubuntu7 libasound2-data_1.0.27.2-3ubuntu7 libasprintf0c2_0.18.3.1-1ubuntu3 libasyncns0_0.8-4ubuntu2 libatk-wrapper-java_0.30.4-4 libatk-wrapper-java-jni_0.30.4-4 libatk1.0-0_2.10.0-2ubuntu2 libatk1.0-data_2.10.0-2ubuntu2 libatomic1_4.8.4-2ubuntu1~14.04 libattr1_1:2.4.47-1ubuntu1 libaudit-common_1:2.3.2-2ubuntu1 libaudit1_1:2.3.2-2ubuntu1 libavahi-client3_0.6.31-4ubuntu1 libavahi-common-data_0.6.31-4ubuntu1 libavahi-common3_0.6.31-4ubuntu1 libblkid1_2.20.1-5.1ubuntu20.7 libbz2-1.0_1.0.6-5 libc-bin_2.19-0ubuntu6.6 libc-dev-bin_2.19-0ubuntu6.6 libc6_2.19-0ubuntu6.6 libc6-dev_2.19-0ubuntu6.6 libcairo2_1.13.0~20140204-0ubuntu1.1 libcap2_1:2.24-0ubuntu2 libcgmanager0_0.24-0ubuntu7.5 libcloog-isl4_0.18.2-1 libcolt-java_1.2.0+dfsg-2 libcomerr2_1.42.9-3ubuntu1.3 libcommons-collections4-java_4.0-1 libconcurrent-java_1.3.4-4 libcroco3_0.6.8-2ubuntu1 libcups2_1.7.2-0ubuntu1.6 libcurl3-gnutls_7.35.0-1ubuntu2.5 libdatrie1_0.2.8-1 libdb5.3_5.3.28-3ubuntu3 libdbus-1-3_1.6.18-0ubuntu4.3 libdebconfclient0_0.187ubuntu1 libdpkg-perl_1.17.5ubuntu5.4 libdrm2_2.4.60-2~ubuntu14.04.1 libexpat1_2.1.0-4ubuntu1.1 libfakeroot_1.20-3ubuntu2 libffi6_3.1~rc1+r3.0.13-12 libflac8_1.3.0-2ubuntu0.14.04.1 libfontconfig1_2.11.0-0ubuntu4.1 libfreetype6_2.5.2-1ubuntu2.5 libgcc-4.8-dev_4.8.4-2ubuntu1~14.04 libgcc1_1:4.9.1-0ubuntu1 libgcrypt11_1.5.3-2ubuntu4.2 libgdbm3_1.8.3-12build1 libgdk-pixbuf2.0-0_2.30.7-0ubuntu1.2 libgdk-pixbuf2.0-common_2.30.7-0ubuntu1.2 libgetopt-java_1.0.14+dfsg-2 libgif4_4.1.6-11 libgl1-mesa-glx_10.1.3-0ubuntu0.5 libglapi-mesa_10.1.3-0ubuntu0.5 libglib2.0-0_2.40.2-0ubuntu1 libgmp10_2:5.1.3+dfsg-1ubuntu1 libgnutls26_2.12.23-12ubuntu2.2 libgomp1_4.8.4-2ubuntu1~14.04 libgpg-error0_1.12-0.2ubuntu1 libgraphite2-3_1.2.4-1ubuntu1 libgssapi-krb5-2_1.12+dfsg-2ubuntu5.1 libgssapi3-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libgtk2.0-0_2.24.23-0ubuntu1.3 libgtk2.0-common_2.24.23-0ubuntu1.3 libharfbuzz0b_0.9.27-1ubuntu1 libhcrypto4-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libheimbase1-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libheimntlm0-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libhx509-5-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libidn11_1.28-1ubuntu2 libisl10_0.12.2-1 libitm1_4.8.4-2ubuntu1~14.04 libjai-core-java_1.1.4-3ubuntu1 libjasper1_1.900.1-14ubuntu3.2 libjava3d-java_1.5.2+dfsg-9ubuntu1 libjava3d-jni_1.5.2+dfsg-9ubuntu1 libjbig0_2.0-2ubuntu4.1 libjellyfish-2.0-2_2.2.3-2biolinux2 libjpeg-turbo8_1.3.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjson-c2_0.11-3ubuntu1.2 libjson0_0.11-3ubuntu1.2 libjung-java_2.0.1-1biolinux1 libk5crypto3_1.12+dfsg-2ubuntu5.1 libkeyutils1_1.5.6-1 libklibc_2.0.3-0ubuntu1 libkmod2_15-0ubuntu6 libkrb5-26-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libkrb5-3_1.12+dfsg-2ubuntu5.1 libkrb5support0_1.12+dfsg-2ubuntu5.1 liblcms2-2_2.5-0ubuntu4 libldap-2.4-2_2.4.31-1+nmu2ubuntu8.2 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.14-2ubuntu3.3 libmount1_2.20.1-5.1ubuntu20.7 libmpc3_1.0.1-1ubuntu1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1ubuntu1 libncursesw5_5.9+20140118-1ubuntu1 libnih-dbus1_1.0.3-4ubuntu25 libnih1_1.0.3-4ubuntu25 libnspr4_2:4.10.7-0ubuntu0.14.04.1 libnss3_2:3.19.2-0ubuntu0.14.04.1 libnss3-nssdb_2:3.19.2-0ubuntu0.14.04.1 libogg0_1.3.1-1ubuntu1 libp11-kit0_0.20.2-2ubuntu2 libpam-modules_1.1.8-1ubuntu2 libpam-modules-bin_1.1.8-1ubuntu2 libpam-runtime_1.1.8-1ubuntu2 libpam0g_1.1.8-1ubuntu2 libpango-1.0-0_1.36.3-1ubuntu1.1 libpangocairo-1.0-0_1.36.3-1ubuntu1.1 libpangoft2-1.0-0_1.36.3-1ubuntu1.1 libpcre3_1:8.31-2ubuntu2.1 libpcsclite1_1.8.10-1ubuntu1 libpipeline1_1.3.0-1 libpixman-1-0_0.30.2-2ubuntu1 libplymouth2_0.8.8-0ubuntu17.1 libpng12-0_1.2.50-1ubuntu2 libprocps3_1:3.3.9-1ubuntu2.2 libpulse0_1:4.0-0ubuntu11.1 libpython3-stdlib_3.4.0-0ubuntu2 libpython3.4-minimal_3.4.3-1ubuntu1~14.04.3 libpython3.4-stdlib_3.4.3-1ubuntu1~14.04.3 libquadmath0_4.8.4-2ubuntu1~14.04 libreadline6_6.3-4ubuntu2 libroken18-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 librtmp0_2.4+20121230.gitdf6c518-1 libsasl2-2_2.1.25.dfsg1-17build1 libsasl2-modules-db_2.1.25.dfsg1-17build1 libsctp1_1.0.15+dfsg-1 libselinux1_2.2.2-1ubuntu0.1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1ubuntu0.1 libslang2_2.2.4-15ubuntu1 libsndfile1_1.0.25-7ubuntu2 libsqlite3-0_3.8.2-1ubuntu2.1 libss2_1.42.9-3ubuntu1.3 libssl1.0.0_1.0.1f-1ubuntu2.15 libstdc++-4.8-dev_4.8.4-2ubuntu1~14.04 libstdc++6_4.8.4-2ubuntu1~14.04 libtasn1-6_3.4-3ubuntu0.3 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff5_4.0.3-7ubuntu0.3 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1ubuntu1 libtsan0_4.8.4-2ubuntu1~14.04 libudev1_204-5ubuntu20.15 libunistring0_0.9.3-5ubuntu3 libusb-0.1-4_2:0.1.12-23.3ubuntu1 libustr-1.0-1_1.0.4-3ubuntu2 libuuid1_2.20.1-5.1ubuntu20.7 libvecmath-java_1.5.2-4 libvorbis0a_1.3.2-1.3ubuntu1 libvorbisenc2_1.3.2-1.3ubuntu1 libwind0-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libwrap0_7.6.q-25 libx11-6_2:1.6.2-1ubuntu2 libx11-data_2:1.6.2-1ubuntu2 libx11-xcb1_2:1.6.2-1ubuntu2 libxau6_1:1.0.8-1 libxcb-dri2-0_1.10-2ubuntu1 libxcb-dri3-0_1.10-2ubuntu1 libxcb-glx0_1.10-2ubuntu1 libxcb-present0_1.10-2ubuntu1 libxcb-render0_1.10-2ubuntu1 libxcb-shm0_1.10-2ubuntu1 libxcb-sync1_1.10-2ubuntu1 libxcb1_1.10-2ubuntu1 libxcomposite1_1:0.4.4-1 libxcursor1_1:1.1.14-1 libxdamage1_1:1.1.4-1ubuntu1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1ubuntu0.0.14.04.1 libxfixes3_1:5.0.1-1ubuntu1.1 libxi6_2:1.7.1.901-1ubuntu1.1 libxinerama1_2:1.1.3-1 libxml2_2.9.1+dfsg1-3ubuntu4.4 libxrandr2_2:1.4.2-1 libxrender1_1:0.9.8-1build0.14.04.1 libxshmfence1_1.1-2 libxtst6_2:1.2.2-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.13.0-66.108 lockfile-progs_0.1.17 login_1:4.1.5.1-1ubuntu9.1 lsb-base_4.1+Debian11ubuntu6 make_3.81-8.2ubuntu3 makedev_2.3.1-93ubuntu1 man-db_2.6.7.1-1ubuntu1 mawk_1.3.3-17ubuntu2 mime-support_3.54ubuntu1.1 module-init-tools_15-0ubuntu6 mount_2.20.1-5.1ubuntu20.7 mountall_2.53 multiarch-support_2.19-0ubuntu6.6 ncurses-base_5.9+20140118-1ubuntu1 ncurses-bin_5.9+20140118-1ubuntu1 openjdk-7-jdk_7u85-2.6.1-5ubuntu0.14.04.1 openjdk-7-jre_7u85-2.6.1-5ubuntu0.14.04.1 openjdk-7-jre-headless_7u85-2.6.1-5ubuntu0.14.04.1 openssl_1.0.1f-1ubuntu2.15 optipng_0.6.4-1build1 parafly_0.0.2013.01.21-1biolinux2 passwd_1:4.1.5.1-1ubuntu9.1 patch_2.7.1-4ubuntu2.3 perl_5.18.2-2ubuntu1 perl-base_5.18.2-2ubuntu1 perl-modules_5.18.2-2ubuntu1 pkg-create-dbgsym_0.67~trusty pkgbinarymangler_121 plymouth_0.8.8-0ubuntu17.1 po-debconf_1.0.16+nmu2ubuntu1 policyrcd-script-zg2_0.1-2 procps_1:3.3.9-1ubuntu2.2 python3_3.4.0-0ubuntu2 python3-minimal_3.4.0-0ubuntu2 python3.4_3.4.3-1ubuntu1~14.04.3 python3.4-minimal_3.4.3-1ubuntu1~14.04.3 readline-common_6.3-4ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-trinityrnaseq-dummy_0.invalid.0 sed_4.2.2-4ubuntu1 sensible-utils_0.0.9 shared-mime-info_1.2-0ubuntu3 sysv-rc_2.88dsf-41ubuntu6.2 sysvinit-utils_2.88dsf-41ubuntu6.2 tar_1.27.1-1 tzdata_2015g-0ubuntu0.14.04 tzdata-java_2015g-0ubuntu0.14.04 ubuntu-keyring_2012.05.19 ucf_3.0027+nmu1 udev_204-5ubuntu20.15 upstart_1.12.1-0ubuntu4.2 util-linux_2.20.1-5.1ubuntu20.7 x11-common_1:7.7+1ubuntu8.1 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-1ubuntu1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Thu Oct 29 09:58:04 2015 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./trinityrnaseq_2.0.6+dfsg-0biolinux3.dsc dpkg-source: info: extracting trinityrnaseq in trinityrnaseq-2.0.6+dfsg dpkg-source: info: unpacking trinityrnaseq_2.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking trinityrnaseq_2.0.6+dfsg-0biolinux3.debian.tar.gz dpkg-source: info: applying chrysalis-make-tweak dpkg-source: info: applying noExitTester dpkg-source: info: applying jellyfish-path dpkg-source: info: applying update-paths dpkg-source: info: applying collections15-to-4 dpkg-source: info: applying fix_system_paths.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package trinityrnaseq dpkg-buildpackage: source version 2.0.6+dfsg-0biolinux3 dpkg-buildpackage: source distribution trusty dpkg-source --before-build trinityrnaseq-2.0.6+dfsg dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel --with javahelper dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust; do dh_autotools-dev_restoreconfig \ -O--sourcedirectory=${target}; dh_auto_clean \ --sourcedirectory=${target}; done make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Chrysalis' Makefile:79: ---------------------------------------------------------- Makefile:80: using g++ version 4.8 Makefile:81: -------------------------------------------------------- for file in BreakTransByPairs Chrysalis CreateIwormFastaBundle GraphFromFasta GraphFromFasta_MPI IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts ReadsToTranscripts_MPI ReadsToTranscripts_MPI_chang RunButterfly TranscriptomeFromVaryK ; do rm -f ./$file; done rm -f MakeDepend ./MakeDepend contigs.out my.permanent.log.file \ core a.out Makefile.bak bsubin BasevectorTables.h ./checkLock find obj -name '*.o' -exec rm {} \; || /bin/true find: `obj': No such file or directory rm -rf cxx_repository rm -f lib_*_temp.a make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Chrysalis' make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' rm -f *.o fastool make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make clean; done <<< src >>> make[3]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust/src' rm -f slcluster.o graph.o graphnode.o cmd_line_opts.o core a.out *~ \#* slclust Makefile.bak make[3]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust' rm Chrysalis/Makefile_auto #These seem to get missed by the cleanup rm -f trinity-plugins/slclust/bin/slclust rm -f Butterfly/src/sample_data/RawComps.0/comp0.allProbPaths.fasta rm -f *.jar make[1]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' jh_clean -O--parallel dh_clean -O--parallel debian/rules build dh build --parallel --with javahelper dh_testdir -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust; do dh_autotools-dev_updateconfig \ -O--sourcedirectory=${target}; dh_auto_configure \ --sourcedirectory=${target} -- \ --prefix=/usr/lib/trinityrnaseq/${target}; done configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for library containing cos... none required configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' jh_linkjars -O--parallel debian/rules override_dh_auto_build make[1]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust; do dh_auto_build \ -O--sourcedirectory=${target}; done make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make all-recursive make[3]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' Making all in src make[4]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm/src' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o Fasta_entry.o Fasta_entry.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o IRKE_run.o IRKE_run.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sequenceUtil.o sequenceUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o IRKE.o IRKE.cpp sequenceUtil.cpp: In function 'bool contains_non_gatc(std::string)': sequenceUtil.cpp:35:20: warning: array subscript has type 'char' [-Wchar-subscripts] if (_base_to_int[c] > 3) ^ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o KmerCounter.o KmerCounter.cpp sequenceUtil.cpp: In function 'kmer_int_type_t kmer_to_intval(std::string)': sequenceUtil.cpp:260:26: warning: array subscript has type 'char' [-Wchar-subscripts] int val = _base_to_int[c]; ^ sequenceUtil.cpp: In function 'std::string replace_nonGATC_chars_with_A(std::string&)': sequenceUtil.cpp:403:27: warning: array subscript has type 'char' [-Wchar-subscripts] if (_base_to_int[c] > 3) ^ IRKE.cpp:34:1: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ IRKE.cpp:71:6: warning: unused parameter 'reassembleIworm' [-Wunused-parameter] void IRKE::build_graph(const string& fasta_filename, bool reassembleIworm, bool useKmers) { ^ IRKE.cpp: In member function 'void IRKE::compute_sequence_assemblies(KmerCounter&, float, unsigned int, unsigned int, bool, bool, std::string)': IRKE.cpp:572:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (contig_length >= MIN_ASSEMBLY_LENGTH && avg_cov >= MIN_ASSEMBLY_COVERAGE) { ^ IRKE.cpp:644:26: warning: unused variable 'contig_length' [-Wunused-variable] unsigned int contig_length = sequence.length(); ^ IRKE.cpp: At global scope: IRKE.cpp:714:6: warning: unused parameter 'min_connectivity' [-Wunused-parameter] bool IRKE::is_good_seed_kmer(kmer_int_type_t kmer, unsigned int kmer_count, unsigned int kmer_length, ^ IRKE.cpp:759:26: warning: unused parameter 'PARALLEL_IWORM' [-Wunused-parameter] vector IRKE::build_inchworm_contig_from_seed(kmer_int_type_t kmer, KmerCounter& kcounter, ^ IRKE.cpp: In member function 'Path_n_count_pair IRKE::inchworm_step(KmerCounter&, char, Kmer_Occurence_Pair, Kmer_visitor&, Kmer_visitor&, unsigned int, unsigned int, float, unsigned int)': IRKE.cpp:1052:80: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (IRKE_COMMON::__DEVEL_no_tie_breaking || recurse_cap >= MAX_RECURSION_HARD_STOP) { ^ IRKE.cpp: At global scope: IRKE.cpp:1174:6: warning: unused parameter 'kcounter' [-Wunused-parameter] bool IRKE::exceeds_min_connectivity (KmerCounter& kcounter, Kmer_Occurence_Pair kmerA, Kmer_Occurence_Pair kmerB, float min_connectivity) { ^ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o string_util.o string_util.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o Fasta_reader.o Fasta_reader.cpp IRKE.cpp: In member function 'kmer_int_type_t IRKE::extract_best_seed(std::vector&, KmerCounter&, float)': IRKE.cpp:1365:21: warning: 'best_seed' may be used uninitialized in this function [-Wmaybe-uninitialized] return(best_seed); ^ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o stacktrace.o stacktrace.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o argProcessor.o argProcessor.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cigar_tweaker.o cigar_tweaker.cpp In file included from cigar_tweaker.cpp:10:0: Cigar.hpp:23:26: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] char strand = NULL); ^ cigar_tweaker.cpp: In function 'int run(int, char**)': cigar_tweaker.cpp:114:75: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] string new_cigar = Cigar::construct_cigar(new_v, sequence.length(), ""); ^ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o SAM_entry.o SAM_entry.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o SAM_reader.o SAM_reader.cpp In file included from SAM_entry.cpp:6:0: Cigar.hpp:23:26: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] char strand = NULL); ^ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o Cigar.o Cigar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o pull_reads_with_kmers.o pull_reads_with_kmers.cpp In file included from Cigar.cpp:1:0: Cigar.hpp:23:26: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] char strand = NULL); ^ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o FastaToDeBruijn.o FastaToDeBruijn.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o DeBruijnGraph.o DeBruijnGraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o fastaToKmerCoverageStats.o fastaToKmerCoverageStats.cpp FastaToDeBruijn.cpp:42:8: warning: unused parameter 'args' [-Wunused-parameter] string usage (ArgProcessor args) { ^ FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': FastaToDeBruijn.cpp:155:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < fasta_file_names.size(); i++) { ^ FastaToDeBruijn.cpp:197:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s = 0; s < seq_regions.size(); s++) { ^ FastaToDeBruijn.cpp: In function 'DeBruijnGraph constructDeBruijnGraph(std::vector >, int, int, bool, ArgProcessor)': FastaToDeBruijn.cpp:252:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < fasta_file_names.size(); i++) { ^ FastaToDeBruijn.cpp:271:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int s = 0; s < seq_regions.size(); s++) { ^ DeBruijnGraph.cpp: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': DeBruijnGraph.cpp:430:22: warning: variable 'rdk' set but not used [-Wunused-but-set-variable] DeBruijnKmer rdk = _kmer_map.find(rk)->second; ^ DeBruijnGraph.cpp: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': DeBruijnGraph.cpp:578:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < left_extensions.size(); i++) { ^ DeBruijnGraph.cpp:581:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0; j < right_extensions.size(); j++) { ^ DeBruijnGraph.cpp: In member function 'void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t, std::vector&, std::vector >&, char, std::map&, int)': DeBruijnGraph.cpp:618:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < adjacent_kmers.size(); i++) { ^ DeBruijnGraph.cpp:632:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (kmer_extension_chars.size() == flank_extension_length) { ^ fastaToKmerCoverageStats.cpp: In function 'int runMe(int, char**)': fastaToKmerCoverageStats.cpp:135:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < kmer_coverage.size(); i++) { ^ fastaToKmerCoverageStats.cpp:137:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i != kmer_coverage.size() - 1) { ^ fastaToKmerCoverageStats.cpp:97:15: warning: unused variable 'filewriter' [-Wunused-variable] ofstream* filewriter = NULL; ^ fastaToKmerCoverageStats.cpp:98:15: warning: unused variable 'covwriter' [-Wunused-variable] ofstream* covwriter = NULL; ^ fastaToKmerCoverageStats.cpp: In function 'void populate_kmer_counter(KmerCounter&, std::string&)': fastaToKmerCoverageStats.cpp:194:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(seq.length() != KMER_SIZE) { ^ fastaToKmerCoverageStats.cpp: At global scope: fastaToKmerCoverageStats.cpp:255:8: warning: unused parameter 'args' [-Wunused-parameter] string usage(ArgProcessor args) { ^ g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o inchworm Fasta_entry.o IRKE_run.o sequenceUtil.o IRKE.o KmerCounter.o string_util.o Fasta_reader.o stacktrace.o argProcessor.o g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o cigar_tweaker cigar_tweaker.o SAM_entry.o sequenceUtil.o SAM_reader.o Cigar.o string_util.o stacktrace.o Fasta_reader.o Fasta_entry.o g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o pull_reads_with_kmers pull_reads_with_kmers.o Fasta_reader.o Fasta_entry.o sequenceUtil.o KmerCounter.o string_util.o stacktrace.o argProcessor.o g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o fastaToKmerCoverageStats fastaToKmerCoverageStats.o argProcessor.o Fasta_reader.o Fasta_entry.o sequenceUtil.o string_util.o stacktrace.o KmerCounter.o g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o FastaToDeBruijn FastaToDeBruijn.o argProcessor.o Fasta_reader.o Fasta_entry.o sequenceUtil.o string_util.o stacktrace.o DeBruijnGraph.o make[4]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm/src' make[4]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[4]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[3]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Chrysalis' Makefile:79: ---------------------------------------------------------- Makefile:80: using g++ version 4.8 Makefile:81: -------------------------------------------------------- ./MakeDepend.cc: In member function 'bool makefile_builder::dependency::operator<(const makefile_builder::dependency&) const': ./MakeDepend.cc:93:47: warning: suggest parentheses around '&&' within '||' [-Wparentheses] dependent_ == other.dependent_ && ^ ./MakeDepend.cc: In member function 'bool makefile_builder::subdir_and_target::operator<(const makefile_builder::subdir_and_target&) const': ./MakeDepend.cc:130:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] subdir_ == other.subdir_ && ^ ./MakeDepend.cc: In function 'int main(int, char**)': ./MakeDepend.cc:223:20: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char * options = "Ad:g:u:fh"; ^ ./MakeDepend.cc: In member function 'void makefile_builder::DumpDependencies(const string&)': ./MakeDepend.cc:491:46: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! this->FileIsSource( dependent ) && ! this->FileIsHeader( dependent ) || ^ ./MakeDepend.cc:493:44: warning: suggest parentheses around '&&' within '||' [-Wparentheses] this->FileIsHeader( dependent ) && this->FileIsSource( provider ) ) { ^ ./MakeDepend.cc: In member function 'bool makefile_builder::FileIsHeader(const string&) const': ./MakeDepend.cc:1339:32: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return ( filename.size() > 2 && ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:00:57 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:00:57 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/AACodons.cc -o obj/analysis/AACodons.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:00:57 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/BreakTransByPairs.cc -o obj/analysis/BreakTransByPairs.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:00:57 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/DNAVector.cc -o obj/analysis/DNAVector.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:00:57 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/KmerTable.cc -o obj/analysis/KmerTable.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:00:59 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/NonRedKmerTable.cc -o obj/analysis/NonRedKmerTable.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:01 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./base/ErrorHandling.cc -o obj/base/ErrorHandling.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:01 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./base/FileParser.cc -o obj/base/FileParser.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:01 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./base/StringUtil.cc -o obj/base/StringUtil.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:01 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./util/mutil.cc -o obj/util/mutil.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:02 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/Chrysalis.cc -o obj/analysis/Chrysalis.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:03 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/TranscriptomeGraph.cc -o obj/analysis/TranscriptomeGraph.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:03 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/CreateIwormFastaBundle.cc -o obj/analysis/CreateIwormFastaBundle.o ./analysis/Chrysalis.cc: In function 'void write_deBruijn_graphs(std::vector > >&, std::vector >&, ComponentFileMgr&, std::string, std::string, bool, std::map&)': ./analysis/Chrysalis.cc:109:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < bundled.size(); i++) { ^ ./analysis/Chrysalis.cc: In function 'void write_iworm_bundle(std::string, std::vector > >&, std::vector >&, ComponentFileMgr&)': ./analysis/Chrysalis.cc:186:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < bundled.size(); i++) { ^ ./analysis/CreateIwormFastaBundle.cc: In function 'void write_iworm_bundle(std::string, std::vector > >&, std::vector >&)': ./analysis/CreateIwormFastaBundle.cc:50:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < bundled.size(); i++) { ^ ./analysis/Chrysalis.cc: In function 'int main(int, char**)': ./analysis/Chrysalis.cc:384:28: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:03 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/DeBruijnGraph.cc -o obj/analysis/DeBruijnGraph.o ./analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': ./analysis/DeBruijnGraph.cc:473:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < left_extensions.size(); i++) { ^ ./analysis/DeBruijnGraph.cc:476:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0; j < right_extensions.size(); j++) { ^ ./analysis/DeBruijnGraph.cc: In member function 'void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t, std::vector&, std::vector >&, char, std::map&, int)': ./analysis/DeBruijnGraph.cc:513:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < adjacent_kmers.size(); i++) { ^ ./analysis/DeBruijnGraph.cc:527:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (kmer_extension_chars.size() == flank_extension_length) { ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:05 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/GraphFromFasta.cc -o obj/analysis/GraphFromFasta.o ./analysis/GraphFromFasta.cc: In member function 'void Pool::exclude(int)': ./analysis/GraphFromFasta.cc:93:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0; j < m_index.size(); j++) { ^ ./analysis/GraphFromFasta.cc: In function 'svec bubble_up_cluster_growth(std::map&, std::map&)': ./analysis/GraphFromFasta.cc:685:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./analysis/GraphFromFasta.cc:706:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./analysis/GraphFromFasta.cc:813:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./analysis/GraphFromFasta.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': ./analysis/GraphFromFasta.cc:858:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:07 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/sequenceUtil.cc -o obj/analysis/sequenceUtil.o ./analysis/GraphFromFasta.cc: In function 'int main(int, char**)': ./analysis/GraphFromFasta.cc:1763:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int j = 0; j < p.size(); j++) { ^ ./analysis/GraphFromFasta.cc:1776:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int j = 0; j < p.size(); j++) { ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:08 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/stacktrace.cc -o obj/analysis/stacktrace.o ./analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': ./analysis/sequenceUtil.cc:33:20: warning: array subscript has type 'char' [-Wchar-subscripts] if (_base_to_int[c] > 3) ^ ./analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': ./analysis/sequenceUtil.cc:264:26: warning: array subscript has type 'char' [-Wchar-subscripts] int val = _base_to_int[c]; ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:08 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./GraphFromFasta_MPI.cc -o obj/GraphFromFasta_MPI.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:08 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/IsoformAugment.cc -o obj/analysis/IsoformAugment.o ./GraphFromFasta_MPI.cc: In member function 'void Pool::exclude(int)': ./GraphFromFasta_MPI.cc:127:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0; j < m_index.size(); j++) { ^ ./GraphFromFasta_MPI.cc: In function 'svec bubble_up_cluster_growth(std::map&, std::map&)': ./GraphFromFasta_MPI.cc:706:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./GraphFromFasta_MPI.cc:727:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./GraphFromFasta_MPI.cc:834:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./GraphFromFasta_MPI.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': ./GraphFromFasta_MPI.cc:879:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < pool_vec.size(); i++) { ^ ./GraphFromFasta_MPI.cc: In function 'int main(int, char**)': ./GraphFromFasta_MPI.cc:2483:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int j = 0; j < p.size(); j++) { ^ ./GraphFromFasta_MPI.cc:2496:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned int j = 0; j < p.size(); j++) { ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:08 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/JoinTransByPairs.cc -o obj/analysis/JoinTransByPairs.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:09 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/QuantifyGraph.cc -o obj/analysis/QuantifyGraph.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:12 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/ReadsToTranscripts.cc -o obj/analysis/ReadsToTranscripts.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:14 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./ReadsToTranscripts_MPI.cc -o obj/ReadsToTranscripts_MPI.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:15 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./ReadsToTranscripts_MPI_chang.cc -o obj/ReadsToTranscripts_MPI_chang.o g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:16 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/RunButterfly.cc -o obj/analysis/RunButterfly.o ./analysis/RunButterfly.cc: In member function 'void JobControl::ClearFiles()': ./analysis/RunButterfly.cc:107:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(rm.c_str()); ^ ./analysis/RunButterfly.cc: In member function 'void JobControl::Submit()': ./analysis/RunButterfly.cc:77:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(theCmmd.c_str()); ^ ./analysis/RunButterfly.cc:85:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(theCmmd.c_str()); ^ g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Thu Oct 29 10:01:17 UTC 2015"' -DMAKE_OS_RELEASE='"3.19.0-31-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/TranscriptomeFromVaryK.cc -o obj/analysis/TranscriptomeFromVaryK.o /bin/rm -f lib_BreakTransByPairs_temp.a ar -qc lib_BreakTransByPairs_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/BreakTransByPairs.o obj/analysis/DNAVector.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./BreakTransByPairs g++ -ggdb3 -fopenmp -o ./BreakTransByPairs obj/analysis/BreakTransByPairs.o -L. -lm -pthread -l_BreakTransByPairs_temp /bin/rm lib_BreakTransByPairs_temp.a /bin/rm -f lib_Chrysalis_temp.a ar -qc lib_Chrysalis_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/Chrysalis.o obj/analysis/DNAVector.o obj/analysis/TranscriptomeGraph.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./Chrysalis g++ -ggdb3 -fopenmp -o ./Chrysalis obj/analysis/Chrysalis.o -L. -lm -pthread -l_Chrysalis_temp /bin/rm lib_Chrysalis_temp.a /bin/rm -f lib_CreateIwormFastaBundle_temp.a ar -qc lib_CreateIwormFastaBundle_temp.a obj/analysis/AACodons.o obj/analysis/CreateIwormFastaBundle.o obj/analysis/DNAVector.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./CreateIwormFastaBundle g++ -ggdb3 -fopenmp -o ./CreateIwormFastaBundle obj/analysis/CreateIwormFastaBundle.o -L. -lm -pthread -l_CreateIwormFastaBundle_temp /bin/rm lib_CreateIwormFastaBundle_temp.a /bin/rm -f lib_GraphFromFasta_temp.a ar -qc lib_GraphFromFasta_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/DeBruijnGraph.o obj/analysis/GraphFromFasta.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/sequenceUtil.o obj/analysis/stacktrace.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./GraphFromFasta g++ -ggdb3 -fopenmp -o ./GraphFromFasta obj/analysis/GraphFromFasta.o -L. -lm -pthread -l_GraphFromFasta_temp /bin/rm lib_GraphFromFasta_temp.a /bin/rm -f lib_GraphFromFasta_MPI_temp.a ar -qc lib_GraphFromFasta_MPI_temp.a obj/GraphFromFasta_MPI.o obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/DeBruijnGraph.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/sequenceUtil.o obj/analysis/stacktrace.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./GraphFromFasta_MPI g++ -ggdb3 -fopenmp -o ./GraphFromFasta_MPI obj/GraphFromFasta_MPI.o -L. -lm -pthread -l_GraphFromFasta_MPI_temp /bin/rm -f lib_IsoformAugment_temp.a ar -qc lib_IsoformAugment_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/IsoformAugment.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./IsoformAugment g++ -ggdb3 -fopenmp -o ./IsoformAugment obj/analysis/IsoformAugment.o -L. -lm -pthread -l_IsoformAugment_temp /bin/rm lib_GraphFromFasta_MPI_temp.a /bin/rm -f lib_JoinTransByPairs_temp.a ar -qc lib_JoinTransByPairs_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/JoinTransByPairs.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./JoinTransByPairs g++ -ggdb3 -fopenmp -o ./JoinTransByPairs obj/analysis/JoinTransByPairs.o -L. -lm -pthread -l_JoinTransByPairs_temp /bin/rm lib_IsoformAugment_temp.a /bin/rm -f lib_QuantifyGraph_temp.a ar -qc lib_QuantifyGraph_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/QuantifyGraph.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./QuantifyGraph g++ -ggdb3 -fopenmp -o ./QuantifyGraph obj/analysis/QuantifyGraph.o -L. -lm -pthread -l_QuantifyGraph_temp /bin/rm lib_QuantifyGraph_temp.a /bin/rm -f lib_ReadsToTranscripts_temp.a /bin/rm lib_JoinTransByPairs_temp.a ar -qc lib_ReadsToTranscripts_temp.a obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/NonRedKmerTable.o obj/analysis/ReadsToTranscripts.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o /bin/rm -f lib_ReadsToTranscripts_MPI_temp.a ar -qc lib_ReadsToTranscripts_MPI_temp.a obj/ReadsToTranscripts_MPI.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./ReadsToTranscripts g++ -ggdb3 -fopenmp -o ./ReadsToTranscripts obj/analysis/ReadsToTranscripts.o -L. -lm -pthread -l_ReadsToTranscripts_temp ./checkLock ./ReadsToTranscripts_MPI g++ -ggdb3 -fopenmp -o ./ReadsToTranscripts_MPI obj/ReadsToTranscripts_MPI.o -L. -lm -pthread -l_ReadsToTranscripts_MPI_temp /bin/rm -f lib_RunButterfly_temp.a ar -qc lib_RunButterfly_temp.a obj/analysis/RunButterfly.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./RunButterfly g++ -ggdb3 -fopenmp -o ./RunButterfly obj/analysis/RunButterfly.o -L. -lm -pthread -l_RunButterfly_temp /bin/rm lib_ReadsToTranscripts_temp.a /bin/rm -f lib_ReadsToTranscripts_MPI_chang_temp.a ar -qc lib_ReadsToTranscripts_MPI_chang_temp.a obj/ReadsToTranscripts_MPI_chang.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./ReadsToTranscripts_MPI_chang g++ -ggdb3 -fopenmp -o ./ReadsToTranscripts_MPI_chang obj/ReadsToTranscripts_MPI_chang.o -L. -lm -pthread -l_ReadsToTranscripts_MPI_chang_temp /bin/rm lib_RunButterfly_temp.a /bin/rm lib_ReadsToTranscripts_MPI_temp.a /bin/rm lib_ReadsToTranscripts_MPI_chang_temp.a /bin/rm -f lib_TranscriptomeFromVaryK_temp.a ar -qc lib_TranscriptomeFromVaryK_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/TranscriptomeFromVaryK.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o ./checkLock ./TranscriptomeFromVaryK g++ -ggdb3 -fopenmp -o ./TranscriptomeFromVaryK obj/analysis/TranscriptomeFromVaryK.o -L. -lm -pthread -l_TranscriptomeFromVaryK_temp /bin/rm lib_TranscriptomeFromVaryK_temp.a make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Chrysalis' make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' gcc -O2 -std=c99 -Werror fastool.c -o fastool make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/fstrozzi-Fastool-7c3e034f05' make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make all; done <<< src >>> make[3]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust/src' g++ -I../include -Wall -c slcluster.cpp g++ -I../include -Wall -c graph.cpp g++ -I../include -Wall -c graphnode.cpp g++ -I../include -Wall -c cmd_line_opts.cpp g++ -I../include -Wall slcluster.o graph.o graphnode.o cmd_line_opts.o -o slclust chmod 755 slclust make[3]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust' jh_build Butterfly.jar Butterfly/src/src find Butterfly/src/src -name *.java -and -type f -print0 | xargs -0 /usr/lib/jvm/default-java/bin/javac -cp /usr/share/java/commons-collections4.jar:/usr/share/java/gnu-getopt.jar:/usr/share/java/jung-algorithms.jar:/usr/share/java/jung-api.jar:/usr/share/java/jung-graph-impl.jar:/usr/share/java/jaligner.jar:debian/_jh_build.Butterfly -d debian/_jh_build.Butterfly -source 1.5 -target 1.5 warning: [options] bootstrap class path not set in conjunction with -source 1.5 Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 13 warnings find Butterfly/src/src -name *.java -and -type f -print0 | xargs -0 /usr/lib/jvm/default-java/bin/javadoc -classpath /usr/share/java/commons-collections4.jar:/usr/share/java/gnu-getopt.jar:/usr/share/java/jung-algorithms.jar:/usr/share/java/jung-api.jar:/usr/share/java/jung-graph-impl.jar:/usr/share/java/jaligner.jar:debian/_jh_build.Butterfly -d debian/_jh_build.javadoc/api -quiet -source 1.5 Creating destination directory: "debian/_jh_build.javadoc/api/" warning: [options] bootstrap class path not set in conjunction with -source 1.5 Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:16: warning: unmappable character for encoding ASCII L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:17: warning: unmappable character for encoding ASCII S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:37: warning: unmappable character for encoding ASCII //L ??? Empty list that will contain the sorted elements ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/TopologicalSort.java:40: warning: unmappable character for encoding ASCII // S ??? Set of all nodes with no incoming edges ^ Butterfly/src/src/GraphPath.java:42: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:202: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:221: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:245: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:316: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:389: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:421: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:450: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:469: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:482: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:501: warning - @return tag has no arguments. Butterfly/src/src/IsoformExpressionLearning.java:514: warning - @return tag has no arguments. Butterfly/src/src/My_DFS.java:563: warning - @return tag has no arguments. Butterfly/src/src/My_DFS.java:32: warning - @param argument "roots" is not a parameter name. Butterfly/src/src/PairPath.java:178: warning - @return tag has no arguments. Butterfly/src/src/PairPath.java:126: warning - @param argument "isCircular" is not a parameter name. Butterfly/src/src/Read.java:62: warning - @return tag has no arguments. Butterfly/src/src/Read.java:70: warning - @return tag has no arguments. Butterfly/src/src/Read.java:78: warning - @return tag has no arguments. Butterfly/src/src/Read.java:88: warning - @return tag has no arguments. Butterfly/src/src/Read.java:96: warning - @return tag has no arguments. Butterfly/src/src/Read.java:104: warning - @return tag has no arguments. Butterfly/src/src/Read.java:20: warning - @param argument "toV" is not a parameter name. Butterfly/src/src/SeqVertex.java:373: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:413: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:421: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:429: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:469: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:493: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:521: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:655: warning - @return tag has no arguments. Butterfly/src/src/SeqVertex.java:84: warning - @param argument "nextID" is not a parameter name. Butterfly/src/src/SeqVertex.java:84: warning - @param argument "l" is not a parameter name. Butterfly/src/src/SeqVertex.java:157: warning - @param argument "_origButterflyID" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "name" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "weight" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "name2" is not a parameter name. Butterfly/src/src/SeqVertex.java:771: warning - @param argument "weight2" is not a parameter name. Butterfly/src/src/TransAssembly_allProbPaths.java:14369: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:8375: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:8424: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:8865: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:8901: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:9024: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:9166: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10265: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10337: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10386: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10405: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10753: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10856: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:10919: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11031: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11180: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11232: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11263: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11282: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11296: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11406: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11500: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:11595: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:12107: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:12376: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:12538: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:12568: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:12586: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:13142: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:13515: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:13821: warning - @return tag has no arguments. Butterfly/src/src/TransAssembly_allProbPaths.java:14369: warning - @param argument "candidateNodes" is not a parameter name. Butterfly/src/src/TransAssembly_allProbPaths.java:14369: warning - @param argument "l" is not a parameter name. 84 warnings /usr/lib/jvm/default-java/bin/jar cfm /«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Butterfly.jar ../_jh_manifest.Butterfly AlignmentStats.class BFLY_GLOBALS.class BipartiteMatching.class DFS.class GraphPath.class IsoformExpressionLearning.class ListComparator.class LocInGraph.class My_DFS$1.class My_DFS$2.class My_DFS.class NWalign.class NumPathNodeLoopsEdgeComparator.class PairPath.class PairPathWOrig.class PasaVertex$1.class PasaVertex.class Path.class PathEndSeqVertexFinishTimeComparator.class PathExpressionComparator.class PathOverlap.class PathReadSupportComparator.class PathWithOrig.class Path_n_MM_count$Vertex_path_position.class Path_n_MM_count.class Read.class ScoredPath.class SeqComparator.class SeqVertex.class SeqVertexDepthComparator.class SeqVertexFinishTimeComparator.class SeqVertexNodeDepthComparator.class SimpleEdge.class SimpleEdgeComparator.class SimplePathNodeEdge.class TopologicalSort.class TransAssembly_allProbPaths$1.class TransAssembly_allProbPaths$10.class TransAssembly_allProbPaths$11.class TransAssembly_allProbPaths$12.class TransAssembly_allProbPaths$13.class TransAssembly_allProbPaths$14.class TransAssembly_allProbPaths$15.class TransAssembly_allProbPaths$16.class TransAssembly_allProbPaths$17.class TransAssembly_allProbPaths$18.class TransAssembly_allProbPaths$19.class TransAssembly_allProbPaths$2.class TransAssembly_allProbPaths$20.class TransAssembly_allProbPaths$3.class TransAssembly_allProbPaths$4.class TransAssembly_allProbPaths$5.class TransAssembly_allProbPaths$6.class TransAssembly_allProbPaths$7.class TransAssembly_allProbPaths$8.class TransAssembly_allProbPaths$9.class TransAssembly_allProbPaths$FinalPaths.class TransAssembly_allProbPaths.class UniquePathContentComparator.class Visitor.class ZipperAlignment.class edu numLoopsEdgeComparator.class make[1]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' jh_build -O--parallel debian/rules override_dh_auto_test make[1]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' java -cp Butterfly.jar TransAssembly_allProbPaths -N 100 -L 100 -F 300 \ -C Butterfly/src/sample_data/RawComps.0/comp0 --stderr -V 18 Started using Path alignment for path comparisons combine paths if (identity=(numberOfMatches/shorterLen) > 98.0% or if we have <= 2 mismatches) and if we have internal gap lengths <= 10 path reinforcement distance computed based on 25% of max pair distance: 300 = 75 bases SECTION ================ Parsing de Bruijn graph ====================== preProcessGraphFile: Butterfly/src/sample_data/RawComps.0/comp0.out SECTION ================== buildNewGraph ======================== buildNewGraphFirstLetter: Butterfly/src/sample_data/RawComps.0/comp0.out KMER_SIZE=24 [17] [34] [51] [68] [85] [102] [119] [136] [153] [170] [187] [204] [221] [238] [255] [272] [289] [306] [323] [340] [357] [374] [391] [408] [425] [442] [459] [476] [493] [510] [527] [544] [561] [578] [595] [612] [629] [646] [663] [680] [697] [714] [731] [748] [765] Graph is built fixExtremeleyHighSingleEdges() fixExtremelyHighSingleEdges() removeLightEdges() removeLightEdges() SECTION ================= REMOVING LIGHT In EDGES ================= SECTION ================= REMOVING LIGHT OUT EDGES ================= SECTION ================= REMOVING LIGHT FLOW EDGES ================= compactLinearPaths() SECTION ================= COMPACTING THE GRAPH ================= SNP_collapse candidates: TCAGAACAGTCATTGATATTCTTT:W5(V337_D1) len: 24 and CCAGAACAGTC:W21(V104_D1) len: 11 SECTION ==================== Removing small components. ==================== ComponentDivision: 0 contains the following vertices: node_id: 0 node_id: 115 node_id: 337 node_id: 128 node_id: 361 node_id: 104 number of good components: 1 SECTION ==================== Threading reads through the graph ========================= Threading read: SRR039231.14043245_FC42DB6AAXX:2:78:825:704, length: 75, allowing for 4 max mismatches. Read SRR039231.14043245_FC42DB6AAXX:2:78:825:704 seq TAAAGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:75,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.14043245_FC42DB6AAXX:2:78:825:704 : [0] ReadPath@Init: SRR039231.14043245_FC42DB6AAXX:2:78:825:704 : [0] Threading read: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794, length: 74, allowing for 4 max mismatches. Read SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 seq AGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:77,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] ReadPath@Init: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] Threading read: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158, length: 74, allowing for 4 max mismatches. Read SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 seq AGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:77,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0] ReadPath@Init: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0] Threading read: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027, length: 74, allowing for 4 max mismatches. Read SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 seq GGGGATCATGGTCTGAACGGAAGTTCATGANACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:78,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] ReadPath@Init: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] Threading read: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256, length: 65, allowing for 4 max mismatches. Read SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 seq AGGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:68,readEnd:65] , trimmed to: [0] Threaded Read as: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0] ReadPath@Init: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0] Threading read: SRR039231.238223_FC42DB6AAXX:2:2:467:595, length: 74, allowing for 4 max mismatches. Read SRR039231.238223_FC42DB6AAXX:2:2:467:595 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:78,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] ReadPath@Init: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] Threading read: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969, length: 59, allowing for 3 max mismatches. Read SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 seq AACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:78,readEnd:59] , trimmed to: [0] Threaded Read as: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] ReadPath@Init: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] Threading read: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615, length: 75, allowing for 4 max mismatches. Read SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:79,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] ReadPath@Init: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] Threading read: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278, length: 59, allowing for 3 max mismatches. Read SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:63,readEnd:59] , trimmed to: [0] Threaded Read as: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] ReadPath@Init: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] Threading read: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587, length: 59, allowing for 3 max mismatches. Read SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 seq GGGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:63,readEnd:59] , trimmed to: [0] Threaded Read as: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0] ReadPath@Init: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0] Threading read: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090, length: 61, allowing for 4 max mismatches. Read SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 seq GGGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:66,readEnd:61] , trimmed to: [0] Threaded Read as: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0] ReadPath@Init: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0] Threading read: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133, length: 75, allowing for 4 max mismatches. Read SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 seq GGATCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:81,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0] ReadPath@Init: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0] Threading read: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500, length: 75, allowing for 4 max mismatches. Read SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 seq ATCATGGTCTGAACGGAAGTTCATGATAACTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:83,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 : [0] ReadPath@Init: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 : [0] Threading read: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638, length: 74, allowing for 4 max mismatches. Read SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 seq TCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:83,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0] ReadPath@Init: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0] Threading read: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567, length: 75, allowing for 4 max mismatches. Read SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 seq TCATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:84,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 : [0] ReadPath@Init: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 : [0] Threading read: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026, length: 75, allowing for 4 max mismatches. Read SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 seq TCATGGTCTGAACGGAAGTTCATGATGCCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:84,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 : [0] ReadPath@Init: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 : [0] Threading read: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951, length: 70, allowing for 4 max mismatches. Read SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 seq TCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:85,readEnd:70] , trimmed to: [0] Threaded Read as: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 : [0] ReadPath@Init: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 : [0] Threading read: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016, length: 70, allowing for 4 max mismatches. Read SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 seq ATGGTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:81,readEnd:70] , trimmed to: [0] Threaded Read as: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0] ReadPath@Init: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0] Threading read: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547, length: 74, allowing for 4 max mismatches. Read SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 seq GTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:88,readEnd:74] , trimmed to: [0] Threaded Read as: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0] ReadPath@Init: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0] Threading read: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849, length: 75, allowing for 4 max mismatches. Read SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 seq GTCTGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:89,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0] ReadPath@Init: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0] Threading read: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746, length: 75, allowing for 4 max mismatches. Read SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 seq TGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:92,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 : [0] ReadPath@Init: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 : [0] Threading read: SRR039231.14173065_FC42DB6AAXX:2:79:322:765, length: 75, allowing for 4 max mismatches. Read SRR039231.14173065_FC42DB6AAXX:2:79:322:765 seq TGAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:92,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.14173065_FC42DB6AAXX:2:79:322:765 : [0] ReadPath@Init: SRR039231.14173065_FC42DB6AAXX:2:79:322:765 : [0] Threading read: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344, length: 69, allowing for 4 max mismatches. Read SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 seq GAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:92,readEnd:69] , trimmed to: [0] Threaded Read as: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 : [0] ReadPath@Init: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 : [0] Threading read: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828, length: 75, allowing for 4 max mismatches. Read SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 seq GAACGGAAGTTCATGATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:93,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 : [0] ReadPath@Init: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 : [0] Threading read: SRR039231.238223_FC42DB6AAXX:2:2:467:595, length: 75, allowing for 4 max mismatches. Read SRR039231.238223_FC42DB6AAXX:2:2:467:595 seq GATACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:107,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] ReadPath@Init: SRR039231.238223_FC42DB6AAXX:2:2:467:595 : [0] Threading read: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442, length: 75, allowing for 4 max mismatches. Read SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 seq TACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:109,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 : [0] ReadPath@Init: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 : [0] Threading read: SRR039231.21589259_FC42DB6AAXX:2:119:947:546, length: 75, allowing for 4 max mismatches. Read SRR039231.21589259_FC42DB6AAXX:2:119:947:546 seq ACCTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:110,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.21589259_FC42DB6AAXX:2:119:947:546 : [0] ReadPath@Init: SRR039231.21589259_FC42DB6AAXX:2:119:947:546 : [0] Threading read: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833, length: 75, allowing for 4 max mismatches. Read SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 seq CTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:112,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0] ReadPath@Init: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0] Threading read: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177, length: 75, allowing for 4 max mismatches. Read SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 seq CTAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:112,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0] ReadPath@Init: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0] Threading read: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867, length: 68, allowing for 4 max mismatches. Read SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 seq TAGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:106,readEnd:68] , trimmed to: [0] Threaded Read as: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [0] ReadPath@Init: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [0] Threading read: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027, length: 75, allowing for 4 max mismatches. Read SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 seq AGAATAATAATTATGATATGATGGTGGATCTAGAAGAGGCNTCTGGTACATTTCATGGCTGAGAAAACATTTTTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0] positions: [0,nodeEnd:114,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] ReadPath@Init: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 : [0] Threading read: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536, length: 64, allowing for 4 max mismatches. Read SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 seq ATAATAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:106,readEnd:64] , trimmed to: [0] Threaded Read as: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0] ReadPath@Init: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0] Threading read: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794, length: 75, allowing for 4 max mismatches. Read SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] ReadPath@Init: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 : [0] Threading read: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615, length: 75, allowing for 4 max mismatches. Read SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] ReadPath@Init: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 : [0] Threading read: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278, length: 75, allowing for 4 max mismatches. Read SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] ReadPath@Init: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 : [0] Threading read: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969, length: 75, allowing for 4 max mismatches. Read SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 seq TAATTATGATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:121,readEnd:75] , trimmed to: [0] Threaded Read as: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] ReadPath@Init: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 : [0] Threading read: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090, length: 75, allowing for 4 max mismatches. Read SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 seq GATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:74] [337,nodeEnd:24,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0, 337] ReadPath@Init: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 : [0, 337] Threading read: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849, length: 75, allowing for 4 max mismatches. Read SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 seq GATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:74] [104,nodeEnd:24,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0, 104] ReadPath@Init: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 : [0, 104] Threading read: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158, length: 75, allowing for 4 max mismatches. Read SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 seq ATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:73] [104,nodeEnd:25,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0, 104] ReadPath@Init: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 : [0, 104] Threading read: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016, length: 74, allowing for 4 max mismatches. Read SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 seq ATATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:73] [104,nodeEnd:24,readEnd:74] , trimmed to: [0, 104] Threaded Read as: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0, 104] ReadPath@Init: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 : [0, 104] Threading read: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547, length: 75, allowing for 4 max mismatches. Read SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 seq ATGATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:71] [104,nodeEnd:27,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0, 104] ReadPath@Init: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 : [0, 104] Threading read: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638, length: 75, allowing for 4 max mismatches. Read SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 seq GATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:69] [337,nodeEnd:29,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0, 337] ReadPath@Init: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 : [0, 337] Threading read: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587, length: 75, allowing for 4 max mismatches. Read SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 seq GATGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:69] [104,nodeEnd:29,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0, 104] ReadPath@Init: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 : [0, 104] Threading read: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288, length: 75, allowing for 4 max mismatches. Read SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 seq TGGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:67] [104,nodeEnd:31,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104] ReadPath@Init: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104] Threading read: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333, length: 72, allowing for 4 max mismatches. Read SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:66] [104,nodeEnd:29,readEnd:72] , trimmed to: [0, 104] Threaded Read as: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [0, 104] ReadPath@Init: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [0, 104] Threading read: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450, length: 53, allowing for 3 max mismatches. Read SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 seq GGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:44] [337,nodeEnd:32,readEnd:53] , trimmed to: [0, 337] Threaded Read as: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [0, 337] ReadPath@Init: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [0, 337] Threading read: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595, length: 72, allowing for 4 max mismatches. Read SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:66] [337,nodeEnd:29,readEnd:72] , trimmed to: [0, 337] Threaded Read as: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [0, 337] ReadPath@Init: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [0, 337] Threading read: SRR039231.2140780_FC42DB6AAXX:2:12:746:731, length: 56, allowing for 3 max mismatches. Read SRR039231.2140780_FC42DB6AAXX:2:12:746:731 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:117,readEnd:56] , trimmed to: [0] Threaded Read as: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0] ReadPath@Init: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0] Threading read: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289, length: 69, allowing for 4 max mismatches. Read SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:66] [104,nodeEnd:26,readEnd:69] , trimmed to: [0, 104] Threaded Read as: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [0, 104] ReadPath@Init: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [0, 104] Threading read: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566, length: 57, allowing for 3 max mismatches. Read SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 seq GGTGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0] positions: [0,nodeEnd:118,readEnd:57] , trimmed to: [0] Threaded Read as: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [0] ReadPath@Init: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [0] Threading read: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161, length: 70, allowing for 4 max mismatches. Read SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 seq TCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAGT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:60] [337,nodeEnd:33,readEnd:70] , trimmed to: [0, 337] Threaded Read as: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [0, 337] ReadPath@Init: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [0, 337] Threading read: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256, length: 75, allowing for 4 max mismatches. Read SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 seq TGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:64] [104,nodeEnd:34,readEnd:75] , trimmed to: [0, 104] Threaded Read as: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0, 104] ReadPath@Init: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 : [0, 104] Threading read: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133, length: 75, allowing for 4 max mismatches. Read SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 seq TGGATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:64] [337,nodeEnd:34,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0, 337] ReadPath@Init: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 : [0, 337] Threading read: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457, length: 75, allowing for 4 max mismatches. Read SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 seq GATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAATCAGAACAGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 337] positions: [0,nodeEnd:127,readEnd:62] [337,nodeEnd:36,readEnd:75] , trimmed to: [0, 337] Threaded Read as: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [0, 337] ReadPath@Init: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [0, 337] Threading read: SRR039231.21001541_FC42DB6AAXX:2:116:708:497, length: 75, allowing for 4 max mismatches. Read SRR039231.21001541_FC42DB6AAXX:2:116:708:497 seq ATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:61] [104,nodeEnd:34,readEnd:72] [115,nodeEnd:26,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115] ReadPath@Init: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115] Threading read: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375, length: 75, allowing for 4 max mismatches. Read SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 seq ATCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:61] [104,nodeEnd:34,readEnd:72] [115,nodeEnd:26,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [0, 104, 115] ReadPath@Init: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [0, 104, 115] Threading read: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254, length: 74, allowing for 4 max mismatches. Read SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 seq TCTAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:60] [104,nodeEnd:34,readEnd:71] [115,nodeEnd:26,readEnd:74] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [0, 104, 115] ReadPath@Init: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [0, 104, 115] Threading read: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346, length: 75, allowing for 4 max mismatches. Read SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 seq TAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:58] [104,nodeEnd:34,readEnd:69] [115,nodeEnd:29,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [0, 104, 115] ReadPath@Init: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [0, 104, 115] Threading read: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604, length: 67, allowing for 4 max mismatches. Read SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 seq TAGAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:58] [104,nodeEnd:32,readEnd:67] , trimmed to: [0, 104] Threaded Read as: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [0, 104] ReadPath@Init: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [0, 104] Threading read: SRR039231.14735089_FC42DB6AAXX:2:82:509:413, length: 75, allowing for 4 max mismatches. WARNING, Tied paths from vertex [V0 ]: Path A: PATH_N_MM_COUNT: mismatches=0, path= [104, 115] positions: [104,nodeEnd:34,readEnd:67] [115,nodeEnd:31,readEnd:75] vs. Path B: PATH_N_MM_COUNT: mismatches=1, path= [337] positions: [337,nodeEnd:42,readEnd:75] WARNING: TIED_READ_PATH Read SRR039231.14735089_FC42DB6AAXX:2:82:509:413 seq GAAGAGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTTATGGTTTGATGAACCAGAACAGTCATTGATAT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:56] [104,nodeEnd:34,readEnd:67] [115,nodeEnd:31,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [0, 104, 115] ReadPath@Init: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [0, 104, 115] Threading read: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833, length: 75, allowing for 4 max mismatches. Read SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 seq AGGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:52] [104,nodeEnd:34,readEnd:63] [115,nodeEnd:35,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0, 104, 115] ReadPath@Init: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 : [0, 104, 115] Threading read: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177, length: 75, allowing for 4 max mismatches. WARNING, Tied paths from vertex [V0 ]: Path A: PATH_N_MM_COUNT: mismatches=0, path= [104, 115] positions: [104,nodeEnd:34,readEnd:62] [115,nodeEnd:36,readEnd:75] vs. Path B: PATH_N_MM_COUNT: mismatches=1, path= [337] positions: [337,nodeEnd:47,readEnd:75] WARNING: TIED_READ_PATH Read SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 seq GGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGGTGGTTTGATGAACCAGAACAGTCATTGATATTCTTT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:51] [104,nodeEnd:34,readEnd:62] [115,nodeEnd:36,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0, 104, 115] ReadPath@Init: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 : [0, 104, 115] Threading read: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560, length: 75, allowing for 4 max mismatches. Read SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 seq GGCATCTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115] positions: [0,nodeEnd:127,readEnd:51] [104,nodeEnd:34,readEnd:62] [115,nodeEnd:36,readEnd:75] , trimmed to: [0, 104, 115] Threaded Read as: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [0, 104, 115] ReadPath@Init: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [0, 104, 115] Threading read: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562, length: 51, allowing for 3 max mismatches. Read SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 seq CTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104] positions: [0,nodeEnd:127,readEnd:46] [104,nodeEnd:28,readEnd:51] , trimmed to: [0, 104] Threaded Read as: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 : [0, 104] ReadPath@Init: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 : [0, 104] Threading read: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691, length: 75, allowing for 4 max mismatches. Read SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 seq CTGGTACATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:46] [104,nodeEnd:34,readEnd:57] [115,nodeEnd:36,readEnd:70] [128,nodeEnd:28,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 : [0, 104, 115, 128] ReadPath@Init: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 : [0, 104, 115, 128] Threading read: SRR039231.2140780_FC42DB6AAXX:2:12:746:731, length: 75, allowing for 4 max mismatches. Read SRR039231.2140780_FC42DB6AAXX:2:12:746:731 seq ATTTCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:39] [104,nodeEnd:34,readEnd:50] [115,nodeEnd:36,readEnd:63] [128,nodeEnd:35,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0, 104, 115, 128] ReadPath@Init: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 : [0, 104, 115, 128] Threading read: SRR039231.21001541_FC42DB6AAXX:2:116:708:497, length: 75, allowing for 4 max mismatches. Read SRR039231.21001541_FC42DB6AAXX:2:116:708:497 seq TCATGGCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:36] [104,nodeEnd:34,readEnd:47] [115,nodeEnd:36,readEnd:60] [128,nodeEnd:38,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115, 128] ReadPath@Init: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 : [0, 104, 115, 128] Threading read: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110, length: 70, allowing for 4 max mismatches. Read SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 seq GAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:26] [104,nodeEnd:34,readEnd:37] [115,nodeEnd:36,readEnd:50] [128,nodeEnd:43,readEnd:70] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [0, 104, 115, 128] ReadPath@Init: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [0, 104, 115, 128] Threading read: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536, length: 75, allowing for 4 max mismatches. -running Needleman-Wunsch alignment of vertex to read Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh construct INFO: Started... Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh construct INFO: Finished. Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh traceback INFO: Started... Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. Vertex 1 TCAGAACAGTCATTGATATTCTTT 24 .||||||||||||:|||||||||| Read 1 CCAGAACAGTCATNGATATTCTTT 24 Read SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 seq GCTGAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATNGATATTCTTTATAAGCATATTCAAGCGCAC threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:31] [104,nodeEnd:34,readEnd:42] [115,nodeEnd:36,readEnd:55] [128,nodeEnd:43,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0, 104, 115, 128] ReadPath@Init: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 : [0, 104, 115, 128] Threading read: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35, length: 75, allowing for 4 max mismatches. Read SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 seq GAGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:28] [104,nodeEnd:34,readEnd:39] [115,nodeEnd:36,readEnd:52] [128,nodeEnd:46,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [0, 104, 115, 128] ReadPath@Init: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [0, 104, 115, 128] Threading read: SRR039231.142909_FC42DB6AAXX:2:1:1346:135, length: 75, allowing for 4 max mismatches. Read SRR039231.142909_FC42DB6AAXX:2:1:1346:135 seq AGAAAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:27] [104,nodeEnd:34,readEnd:38] [115,nodeEnd:36,readEnd:51] [128,nodeEnd:47,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [0, 104, 115, 128] ReadPath@Init: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [0, 104, 115, 128] Threading read: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560, length: 75, allowing for 4 max mismatches. Read SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 seq GAAAACATTTTTGGTGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [361, 115, 128] positions: [361,nodeEnd:47,readEnd:37] [115,nodeEnd:36,readEnd:50] [128,nodeEnd:48,readEnd:75] , trimmed to: [361, 115, 128] Threaded Read as: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [361, 115, 128] ReadPath@Init: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 : [361, 115, 128] Threading read: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968, length: 75, allowing for 4 max mismatches. -running Needleman-Wunsch alignment of vertex to read Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh construct INFO: Started... Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh construct INFO: Finished. Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh traceback INFO: Started... Oct 29, 2015 10:01:34 AM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. Vertex 1 TCAGAACAGTCATTGATATTCTTT 24 .|||||||||||||:||||||||| Read 1 CCAGAACAGTCATTNATATTCTTT 24 Read SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 seq AAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTNATATTCTTTATAAGCATATTCAAGCGCACTGGAAAT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:24] [104,nodeEnd:34,readEnd:35] [115,nodeEnd:36,readEnd:48] [128,nodeEnd:50,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [0, 104, 115, 128] ReadPath@Init: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [0, 104, 115, 128] Threading read: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288, length: 75, allowing for 4 max mismatches. Read SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 seq AAACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [0, 104, 115, 128] positions: [0,nodeEnd:127,readEnd:24] [104,nodeEnd:34,readEnd:35] [115,nodeEnd:36,readEnd:48] [128,nodeEnd:50,readEnd:75] , trimmed to: [0, 104, 115, 128] Threaded Read as: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104, 115, 128] ReadPath@Init: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 : [0, 104, 115, 128] Threading read: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867, length: 75, allowing for 4 max mismatches. Read SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 seq AACATTTTTGATGGTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [104, 115, 128] positions: [104,nodeEnd:34,readEnd:34] [115,nodeEnd:36,readEnd:47] [128,nodeEnd:51,readEnd:75] , trimmed to: [104, 115, 128] Threaded Read as: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [104, 115, 128] ReadPath@Init: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 : [104, 115, 128] Threading read: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457, length: 75, allowing for 4 max mismatches. Read SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 seq TTTTGATGGTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:42] [128,nodeEnd:56,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [337, 128] ReadPath@Init: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 : [337, 128] Threading read: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450, length: 67, allowing for 4 max mismatches. Read SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 seq TTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:33] [128,nodeEnd:57,readEnd:67] , trimmed to: [337, 128] Threaded Read as: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [337, 128] ReadPath@Init: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 : [337, 128] Threading read: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595, length: 75, allowing for 4 max mismatches. Read SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 seq TTTGATGGTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:41] [128,nodeEnd:57,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [337, 128] ReadPath@Init: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 : [337, 128] Threading read: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566, length: 58, allowing for 3 max mismatches. Read SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:57,readEnd:58] , trimmed to: [115, 128] Threaded Read as: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [115, 128] ReadPath@Init: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 : [115, 128] Threading read: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333, length: 60, allowing for 3 max mismatches. Read SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:59,readEnd:60] , trimmed to: [115, 128] Threaded Read as: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [115, 128] ReadPath@Init: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 : [115, 128] Threading read: SRR039231.390226_FC42DB6AAXX:2:3:125:1502, length: 75, allowing for 4 max mismatches. Read SRR039231.390226_FC42DB6AAXX:2:3:125:1502 seq GGTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:35] [128,nodeEnd:63,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] ReadPath@Init: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] Threading read: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312, length: 75, allowing for 4 max mismatches. Read SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 seq GTTTGATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [337, 128] ReadPath@Init: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [337, 128] Threading read: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958, length: 75, allowing for 4 max mismatches. Read SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 seq GTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [115, 128] ReadPath@Init: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [115, 128] Threading read: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254, length: 75, allowing for 4 max mismatches. Read SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 seq GTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [115, 128] ReadPath@Init: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 : [115, 128] Threading read: SRR039231.8633607_FC42DB6AAXX:2:48:203:527, length: 75, allowing for 4 max mismatches. Read SRR039231.8633607_FC42DB6AAXX:2:48:203:527 seq GTTTGATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:34] [128,nodeEnd:64,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [115, 128] ReadPath@Init: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [115, 128] Threading read: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161, length: 75, allowing for 4 max mismatches. Read SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 seq ATGAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [337, 128] positions: [337,nodeEnd:47,readEnd:29] [128,nodeEnd:69,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [337, 128] ReadPath@Init: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 : [337, 128] Threading read: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289, length: 66, allowing for 4 max mismatches. Read SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 seq ATGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:29] [128,nodeEnd:60,readEnd:66] , trimmed to: [115, 128] Threaded Read as: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [115, 128] ReadPath@Init: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 : [115, 128] Threading read: SRR039231.14735089_FC42DB6AAXX:2:82:509:413, length: 75, allowing for 4 max mismatches. Read SRR039231.14735089_FC42DB6AAXX:2:82:509:413 seq TGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:28] [128,nodeEnd:70,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [115, 128] ReadPath@Init: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 : [115, 128] Threading read: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769, length: 65, allowing for 4 max mismatches. Read SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 seq CAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:70,readEnd:65] , trimmed to: [128] Threaded Read as: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 : [128] ReadPath@Init: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 : [128] Threading read: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35, length: 69, allowing for 4 max mismatches. Read SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 seq AGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:70,readEnd:69] , trimmed to: [128] Threaded Read as: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [128] ReadPath@Init: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 : [128] Threading read: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375, length: 75, allowing for 4 max mismatches. Read SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 seq TGAACCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:28] [128,nodeEnd:70,readEnd:75] , trimmed to: [115, 128] Threaded Read as: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [115, 128] ReadPath@Init: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 : [115, 128] Threading read: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604, length: 72, allowing for 4 max mismatches. Read SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:71,readEnd:72] , trimmed to: [115, 128] Threaded Read as: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [115, 128] ReadPath@Init: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 : [115, 128] Threading read: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887, length: 70, allowing for 4 max mismatches. Read SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 seq AGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:71,readEnd:70] , trimmed to: [128] Threaded Read as: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 : [128] ReadPath@Init: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 : [128] Threading read: SRR039231.390226_FC42DB6AAXX:2:3:125:1502, length: 75, allowing for 4 max mismatches. Read SRR039231.390226_FC42DB6AAXX:2:3:125:1502 seq GAATCAGAACAGTCATTGATATTCTTTATAAGCATATTCAATCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [337, 128] positions: [337,nodeEnd:47,readEnd:27] [128,nodeEnd:71,readEnd:75] , trimmed to: [337, 128] Threaded Read as: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] ReadPath@Init: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 : [337, 128] Threading read: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968, length: 72, allowing for 4 max mismatches. Read SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 seq CCAGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [115, 128] positions: [115,nodeEnd:36,readEnd:24] [128,nodeEnd:71,readEnd:72] , trimmed to: [115, 128] Threaded Read as: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [115, 128] ReadPath@Init: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 : [115, 128] Threading read: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346, length: 75, allowing for 4 max mismatches. Read SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 seq AGAACAGTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:76,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [128] ReadPath@Init: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 : [128] Threading read: SRR039231.142909_FC42DB6AAXX:2:1:1346:135, length: 75, allowing for 4 max mismatches. Read SRR039231.142909_FC42DB6AAXX:2:1:1346:135 seq GTCATTGATATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:82,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [128] ReadPath@Init: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 : [128] Threading read: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958, length: 75, allowing for 4 max mismatches. Read SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 seq TATTCTTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:90,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [128] ReadPath@Init: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 : [128] Threading read: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312, length: 57, allowing for 3 max mismatches. Read SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 seq CAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:91,readEnd:57] , trimmed to: [128] Threaded Read as: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [128] ReadPath@Init: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 : [128] Threading read: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110, length: 75, allowing for 4 max mismatches. Read SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 seq TTTATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:95,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [128] ReadPath@Init: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 : [128] Threading read: SRR039231.8633607_FC42DB6AAXX:2:48:203:527, length: 75, allowing for 4 max mismatches. Read SRR039231.8633607_FC42DB6AAXX:2:48:203:527 seq TATAAGCATATTCAAGCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:97,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [128] ReadPath@Init: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 : [128] Threading read: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158, length: 64, allowing for 4 max mismatches. Read SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 seq AATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:111,readEnd:64] , trimmed to: [128] Threaded Read as: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 : [128] ReadPath@Init: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 : [128] Threading read: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404, length: 75, allowing for 4 max mismatches. Read SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 seq GCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:112,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 : [128] ReadPath@Init: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 : [128] Threading read: SRR039231.16895577_FC42DB6AAXX:2:94:163:51, length: 75, allowing for 4 max mismatches. Read SRR039231.16895577_FC42DB6AAXX:2:94:163:51 seq GCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:112,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.16895577_FC42DB6AAXX:2:94:163:51 : [128] ReadPath@Init: SRR039231.16895577_FC42DB6AAXX:2:94:163:51 : [128] Threading read: SRR039231.3014932_FC42DB6AAXX:2:17:237:179, length: 75, allowing for 4 max mismatches. Read SRR039231.3014932_FC42DB6AAXX:2:17:237:179 seq GCGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:112,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] ReadPath@Init: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] Threading read: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782, length: 75, allowing for 4 max mismatches. Read SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 seq CGCACTGGAAATGGTTTTCAGGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:113,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] ReadPath@Init: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] Threading read: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065, length: 75, allowing for 4 max mismatches. Read SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 seq GGTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:133,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] ReadPath@Init: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] Threading read: SRR039231.21734868_FC42DB6AAXX:2:120:549:795, length: 75, allowing for 4 max mismatches. Read SRR039231.21734868_FC42DB6AAXX:2:120:549:795 seq GTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:134,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] ReadPath@Init: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] Threading read: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782, length: 75, allowing for 4 max mismatches. Read SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 seq GTCATTTTCCATACTCTTTGCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:134,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] ReadPath@Init: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 : [128] Threading read: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880, length: 74, allowing for 4 max mismatches. Read SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:152,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] ReadPath@Init: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] Threading read: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996, length: 74, allowing for 4 max mismatches. Read SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:152,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] ReadPath@Init: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] Threading read: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670, length: 75, allowing for 4 max mismatches. Read SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 : [128] ReadPath@Init: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 : [128] Threading read: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397, length: 70, allowing for 4 max mismatches. Read SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 seq GTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:70] , trimmed to: [128] Threaded Read as: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] ReadPath@Init: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] Threading read: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147, length: 75, allowing for 4 max mismatches. Read SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] ReadPath@Init: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] Threading read: SRR039231.624520_FC42DB6AAXX:2:4:581:550, length: 75, allowing for 4 max mismatches. Read SRR039231.624520_FC42DB6AAXX:2:4:581:550 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] ReadPath@Init: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] Threading read: SRR039231.939493_FC42DB6AAXX:2:5:1771:471, length: 75, allowing for 4 max mismatches. Read SRR039231.939493_FC42DB6AAXX:2:5:1771:471 seq GCCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:153,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] ReadPath@Init: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] Threading read: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734, length: 65, allowing for 4 max mismatches. Read SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 seq GACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:154,readEnd:65] , trimmed to: [128] Threaded Read as: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] ReadPath@Init: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] Threading read: SRR039231.16173078_FC42DB6AAXX:2:90:254:422, length: 75, allowing for 4 max mismatches. Read SRR039231.16173078_FC42DB6AAXX:2:90:254:422 seq CCCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:154,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] ReadPath@Init: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] Threading read: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895, length: 75, allowing for 4 max mismatches. Read SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 : [128] ReadPath@Init: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 : [128] Threading read: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229, length: 67, allowing for 4 max mismatches. Read SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 seq CGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:67] , trimmed to: [128] Threaded Read as: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] ReadPath@Init: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] Threading read: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281, length: 75, allowing for 4 max mismatches. Read SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] ReadPath@Init: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] Threading read: SRR039231.17068078_FC42DB6AAXX:2:95:58:257, length: 75, allowing for 4 max mismatches. Read SRR039231.17068078_FC42DB6AAXX:2:95:58:257 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] ReadPath@Init: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] Threading read: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670, length: 75, allowing for 4 max mismatches. Read SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] ReadPath@Init: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] Threading read: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073, length: 75, allowing for 4 max mismatches. Read SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 : [128] ReadPath@Init: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 : [128] Threading read: SRR039231.9196619_FC42DB6AAXX:2:51:473:936, length: 75, allowing for 4 max mismatches. Read SRR039231.9196619_FC42DB6AAXX:2:51:473:936 seq CCAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:155,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] ReadPath@Init: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] Threading read: SRR039231.1328085_FC42DB6AAXX:2:8:132:68, length: 75, allowing for 4 max mismatches. Read SRR039231.1328085_FC42DB6AAXX:2:8:132:68 seq CAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:156,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] ReadPath@Init: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] Threading read: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591, length: 75, allowing for 4 max mismatches. Read SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 seq CAGTTTTCGACATCTCCTATTTCTTNGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGC threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:156,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] ReadPath@Init: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] Threading read: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689, length: 75, allowing for 4 max mismatches. Read SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 seq CAGTTTTCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:156,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] ReadPath@Init: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] Threading read: SRR039231.3014932_FC42DB6AAXX:2:17:237:179, length: 75, allowing for 4 max mismatches. Read SRR039231.3014932_FC42DB6AAXX:2:17:237:179 seq TCGACATCTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:162,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] ReadPath@Init: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 : [128] Threading read: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859, length: 75, allowing for 4 max mismatches. Read SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 seq CTCCTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:169,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] ReadPath@Init: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] Threading read: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065, length: 39, allowing for 2 max mismatches. Read SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 seq AAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:170,readEnd:39] , trimmed to: [128] Threaded Read as: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] ReadPath@Init: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 : [128] Threading read: SRR039231.5836358_FC42DB6AAXX:2:32:993:352, length: 75, allowing for 4 max mismatches. Read SRR039231.5836358_FC42DB6AAXX:2:32:993:352 seq CTATTTCTTTGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:172,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] ReadPath@Init: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] Threading read: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689, length: 75, allowing for 4 max mismatches. Read SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 seq TGAGAGCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:181,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] ReadPath@Init: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 : [128] Threading read: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723, length: 72, allowing for 4 max mismatches. Read SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 seq GCTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:183,readEnd:72] , trimmed to: [128] Threaded Read as: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] ReadPath@Init: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] Threading read: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021, length: 71, allowing for 4 max mismatches. Read SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 seq CATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGGTTAGCAAAAGTAAGGGCACTTTGATGGAGT threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:186,readEnd:71] , trimmed to: [128] Threaded Read as: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 : [128] ReadPath@Init: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 : [128] Threading read: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391, length: 75, allowing for 4 max mismatches. Read SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 seq CTCCATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:187,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 : [128] ReadPath@Init: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 : [128] Threading read: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880, length: 66, allowing for 4 max mismatches. Read SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 seq TTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAAC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:189,readEnd:66] , trimmed to: [128] Threaded Read as: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] ReadPath@Init: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 : [128] Threading read: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481, length: 75, allowing for 4 max mismatches. Read SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 seq CATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:190,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 : [128] ReadPath@Init: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 : [128] Threading read: SRR039231.939493_FC42DB6AAXX:2:5:1771:471, length: 75, allowing for 4 max mismatches. Read SRR039231.939493_FC42DB6AAXX:2:5:1771:471 seq CATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:190,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] ReadPath@Init: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 : [128] Threading read: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099, length: 75, allowing for 4 max mismatches. Read SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 seq ATTAAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:191,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] ReadPath@Init: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] Threading read: SRR039231.1328085_FC42DB6AAXX:2:8:132:68, length: 46, allowing for 3 max mismatches. Read SRR039231.1328085_FC42DB6AAXX:2:8:132:68 seq CAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:173,readEnd:46] , trimmed to: [128] Threaded Read as: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] ReadPath@Init: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 : [128] Threading read: SRR039231.17068078_FC42DB6AAXX:2:95:58:257, length: 75, allowing for 4 max mismatches. Read SRR039231.17068078_FC42DB6AAXX:2:95:58:257 seq AAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:194,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] ReadPath@Init: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 : [128] Threading read: SRR039231.21734868_FC42DB6AAXX:2:120:549:795, length: 75, allowing for 4 max mismatches. Read SRR039231.21734868_FC42DB6AAXX:2:120:549:795 seq AAAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:194,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] ReadPath@Init: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 : [128] Threading read: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734, length: 75, allowing for 4 max mismatches. Read SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 seq AAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:195,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] ReadPath@Init: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 : [128] Threading read: SRR039231.16173078_FC42DB6AAXX:2:90:254:422, length: 75, allowing for 4 max mismatches. Read SRR039231.16173078_FC42DB6AAXX:2:90:254:422 seq AAATTATCAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:195,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] ReadPath@Init: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 : [128] Threading read: SRR039231.624520_FC42DB6AAXX:2:4:581:550, length: 68, allowing for 4 max mismatches. Read SRR039231.624520_FC42DB6AAXX:2:4:581:550 seq CAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:195,readEnd:68] , trimmed to: [128] Threaded Read as: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] ReadPath@Init: SRR039231.624520_FC42DB6AAXX:2:4:581:550 : [128] Threading read: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397, length: 66, allowing for 4 max mismatches. Read SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 seq GGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:199,readEnd:66] , trimmed to: [128] Threaded Read as: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] ReadPath@Init: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 : [128] Threading read: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147, length: 74, allowing for 4 max mismatches. Read SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 seq CAACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:201,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] ReadPath@Init: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 : [128] Threading read: SRR039231.9196619_FC42DB6AAXX:2:51:473:936, length: 68, allowing for 4 max mismatches. Read SRR039231.9196619_FC42DB6AAXX:2:51:473:936 seq GGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCA threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:201,readEnd:68] , trimmed to: [128] Threaded Read as: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] ReadPath@Init: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 : [128] Threading read: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281, length: 75, allowing for 4 max mismatches. Read SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 seq AACAAGGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:203,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] ReadPath@Init: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 : [128] Threading read: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996, length: 71, allowing for 4 max mismatches. Read SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 seq GGGAGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:204,readEnd:71] , trimmed to: [128] Threaded Read as: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] ReadPath@Init: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 : [128] Threading read: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592, length: 65, allowing for 4 max mismatches. Read SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 seq CATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:206,readEnd:65] , trimmed to: [128] Threaded Read as: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 : [128] ReadPath@Init: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 : [128] Threading read: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670, length: 75, allowing for 4 max mismatches. Read SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 seq AGAGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:211,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] ReadPath@Init: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 : [128] Threading read: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229, length: 75, allowing for 4 max mismatches. Read SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 seq AGCCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:213,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] ReadPath@Init: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 : [128] Threading read: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859, length: 75, allowing for 4 max mismatches. Read SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 seq CCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:215,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] ReadPath@Init: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 : [128] Threading read: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591, length: 74, allowing for 4 max mismatches. Read SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 seq CCATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:214,readEnd:74] , trimmed to: [128] Threaded Read as: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] ReadPath@Init: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 : [128] Threading read: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499, length: 75, allowing for 4 max mismatches. Read SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 seq ATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:217,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 : [128] ReadPath@Init: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 : [128] Threading read: SRR039231.5836358_FC42DB6AAXX:2:32:993:352, length: 75, allowing for 4 max mismatches. Read SRR039231.5836358_FC42DB6AAXX:2:32:993:352 seq ATTGTTGAGTCTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGAT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:217,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] ReadPath@Init: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 : [128] Threading read: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473, length: 70, allowing for 4 max mismatches. Read SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 seq GTTGAGTCTGCTTAGCAAAAGTAAGAGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:215,readEnd:70] , trimmed to: [128] Threaded Read as: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 : [128] ReadPath@Init: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 : [128] Threading read: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099, length: 75, allowing for 4 max mismatches. Read SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 seq CTGCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGC threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:227,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] ReadPath@Init: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 : [128] Threading read: SRR039231.1908187_FC42DB6AAXX:2:11:306:275, length: 75, allowing for 4 max mismatches. Read SRR039231.1908187_FC42DB6AAXX:2:11:306:275 seq GCTTAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGCTT threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:229,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.1908187_FC42DB6AAXX:2:11:306:275 : [128] ReadPath@Init: SRR039231.1908187_FC42DB6AAXX:2:11:306:275 : [128] Threading read: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711, length: 72, allowing for 4 max mismatches. Read SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 seq AGCAAAAGTAAGGGCACTTTGATGGATTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGCTTG threaded as: PATH_N_MM_COUNT: mismatches=1, path= [128] positions: [128,nodeEnd:230,readEnd:72] , trimmed to: [128] Threaded Read as: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 : [128] ReadPath@Init: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 : [128] Threading read: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723, length: 75, allowing for 4 max mismatches. Read SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 seq TAGCAAAAGTAAGGGCACTTTGATGGAGTAACTTTGCTTCTGCATCCAGTCGCTTTTGATTCAAATATGCTTGTG threaded as: PATH_N_MM_COUNT: mismatches=0, path= [128] positions: [128,nodeEnd:232,readEnd:75] , trimmed to: [128] Threaded Read as: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] ReadPath@Init: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 : [128] number of reads found = 163 (from total of 163) which came from 96 pairs Read name to pairing info: SRR039231.1666142_FC42DB6AAXX:2:9:1550:312 => [337, 128][128] Read name to pairing info: SRR039231.13728972_FC42DB6AAXX:2:76:1282:833 => [0][0, 104, 115] Read name to pairing info: SRR039231.14487335_FC42DB6AAXX:2:80:1636:450 => [0, 337][337, 128] Read name to pairing info: SRR039231.2103331_FC42DB6AAXX:2:12:391:1567 => [0] Read name to pairing info: SRR039231.21829784_FC42DB6AAXX:2:120:1439:177 => [0][0, 104, 115] Read name to pairing info: SRR039231.21734868_FC42DB6AAXX:2:120:549:795 => [128][128] Read name to pairing info: SRR039231.21078379_FC42DB6AAXX:2:116:1435:1547 => [0][0, 104] Read name to pairing info: SRR039231.3927545_FC42DB6AAXX:2:22:138:1536 => [0][0, 104, 115, 128] Read name to pairing info: SRR039231.4096942_FC42DB6AAXX:2:22:1764:1073 => [128] Read name to pairing info: SRR039231.14510947_FC42DB6AAXX:2:81:84:1895 => [128] Read name to pairing info: SRR039231.624520_FC42DB6AAXX:2:4:581:550 => [128][128] Read name to pairing info: SRR039231.21382512_FC42DB6AAXX:2:118:769:1375 => [0, 104, 115][115, 128] Read name to pairing info: SRR039231.9625434_FC42DB6AAXX:2:53:1210:1288 => [0, 104][0, 104, 115, 128] Read name to pairing info: SRR039231.6233377_FC42DB6AAXX:2:34:1346:591 => [128][128] Read name to pairing info: SRR039231.17068078_FC42DB6AAXX:2:95:58:257 => [128][128] Read name to pairing info: SRR039231.892387_FC42DB6AAXX:2:5:1324:1026 => [0] Read name to pairing info: SRR039231.21001541_FC42DB6AAXX:2:116:708:497 => [0, 104, 115][0, 104, 115, 128] Read name to pairing info: SRR039231.13707404_FC42DB6AAXX:2:76:1069:604 => [0, 104][115, 128] Read name to pairing info: SRR039231.8543228_FC42DB6AAXX:2:47:1078:711 => [128] Read name to pairing info: SRR039231.238223_FC42DB6AAXX:2:2:467:595 => [0][0] Read name to pairing info: SRR039231.13264799_FC42DB6AAXX:2:74:237:1090 => [0][0, 337] Read name to pairing info: SRR039231.1282721_FC42DB6AAXX:2:7:1475:1500 => [0] Read name to pairing info: SRR039231.10363944_FC42DB6AAXX:2:57:1495:794 => [0][0] Read name to pairing info: SRR039231.5093995_FC42DB6AAXX:2:28:781:1782 => [128][128] Read name to pairing info: SRR039231.17800444_FC42DB6AAXX:2:99:56:1147 => [128][128] Read name to pairing info: SRR039231.15270417_FC42DB6AAXX:2:85:381:1158 => [0][0, 104] Read name to pairing info: SRR039231.5230525_FC42DB6AAXX:2:29:349:1587 => [0][0, 104] Read name to pairing info: SRR039231.15313573_FC42DB6AAXX:2:85:806:1481 => [128] Read name to pairing info: SRR039231.9506053_FC42DB6AAXX:2:52:1789:1689 => [128][128] Read name to pairing info: SRR039231.8928386_FC42DB6AAXX:2:49:1340:1691 => [0, 104, 115, 128] Read name to pairing info: SRR039231.19344867_FC42DB6AAXX:2:107:840:1473 => [128] Read name to pairing info: SRR039231.20100594_FC42DB6AAXX:2:111:1008:1849 => [0][0, 104] Read name to pairing info: SRR039231.12658759_FC42DB6AAXX:2:70:1304:1333 => [0, 104][115, 128] Read name to pairing info: SRR039231.14043245_FC42DB6AAXX:2:78:825:704 => [0] Read name to pairing info: SRR039231.2140780_FC42DB6AAXX:2:12:746:731 => [0][0, 104, 115, 128] Read name to pairing info: SRR039231.1580103_FC42DB6AAXX:2:9:737:1229 => [128][128] Read name to pairing info: SRR039231.10188932_FC42DB6AAXX:2:56:1521:723 => [128][128] Read name to pairing info: SRR039231.15839695_FC42DB6AAXX:2:88:581:1670 => [128] Read name to pairing info: SRR039231.12877170_FC42DB6AAXX:2:71:1700:1065 => [128][128] Read name to pairing info: SRR039231.15920717_FC42DB6AAXX:2:88:1368:397 => [128][128] Read name to pairing info: SRR039231.9196619_FC42DB6AAXX:2:51:473:936 => [128][128] Read name to pairing info: SRR039231.21670612_FC42DB6AAXX:2:119:1723:1158 => [128] Read name to pairing info: SRR039231.18386017_FC42DB6AAXX:2:102:421:1161 => [0, 337][337, 128] Read name to pairing info: SRR039231.19732435_FC42DB6AAXX:2:109:1038:1442 => [0] Read name to pairing info: SRR039231.21527302_FC42DB6AAXX:2:119:363:1289 => [0, 104][115, 128] Read name to pairing info: SRR039231.2762040_FC42DB6AAXX:2:15:1357:1099 => [128][128] Read name to pairing info: SRR039231.16895577_FC42DB6AAXX:2:94:163:51 => [128] Read name to pairing info: SRR039231.15919613_FC42DB6AAXX:2:88:1358:281 => [128][128] Read name to pairing info: SRR039231.7894225_FC42DB6AAXX:2:43:1741:968 => [0, 104, 115, 128][115, 128] Read name to pairing info: SRR039231.142909_FC42DB6AAXX:2:1:1346:135 => [0, 104, 115, 128][128] Read name to pairing info: SRR039231.21446475_FC42DB6AAXX:2:118:1372:1867 => [0][104, 115, 128] Read name to pairing info: SRR039231.18849210_FC42DB6AAXX:2:104:1359:1828 => [0] Read name to pairing info: SRR039231.6565424_FC42DB6AAXX:2:36:1061:969 => [0][0] Read name to pairing info: SRR039231.13481733_FC42DB6AAXX:2:75:614:1615 => [0][0] Read name to pairing info: SRR039231.18088731_FC42DB6AAXX:2:100:1090:1499 => [128] Read name to pairing info: SRR039231.939493_FC42DB6AAXX:2:5:1771:471 => [128][128] Read name to pairing info: SRR039231.18110959_FC42DB6AAXX:2:100:1305:958 => [115, 128][128] Read name to pairing info: SRR039231.10910792_FC42DB6AAXX:2:60:1619:404 => [128] Read name to pairing info: SRR039231.8633607_FC42DB6AAXX:2:48:203:527 => [115, 128][128] Read name to pairing info: SRR039231.2284997_FC42DB6AAXX:2:13:349:1110 => [0, 104, 115, 128][128] Read name to pairing info: SRR039231.13448095_FC42DB6AAXX:2:75:280:1746 => [0] Read name to pairing info: SRR039231.15246719_FC42DB6AAXX:2:85:149:1887 => [128] Read name to pairing info: SRR039231.5836358_FC42DB6AAXX:2:32:993:352 => [128][128] Read name to pairing info: SRR039231.20711733_FC42DB6AAXX:2:114:1506:133 => [0][0, 337] Read name to pairing info: SRR039231.390226_FC42DB6AAXX:2:3:125:1502 => [337, 128][337, 128] Read name to pairing info: SRR039231.7673168_FC42DB6AAXX:2:42:1340:391 => [128] Read name to pairing info: SRR039231.10010027_FC42DB6AAXX:2:55:1503:1027 => [0][0] Read name to pairing info: SRR039231.1328085_FC42DB6AAXX:2:8:132:68 => [128][128] Read name to pairing info: SRR039231.12346824_FC42DB6AAXX:2:68:1758:1346 => [0, 104, 115][128] Read name to pairing info: SRR039231.17587629_FC42DB6AAXX:2:97:1549:1670 => [128][128] Read name to pairing info: SRR039231.15012333_FC42DB6AAXX:2:83:1432:595 => [0, 337][337, 128] Read name to pairing info: SRR039231.6669437_FC42DB6AAXX:2:37:324:1344 => [0] Read name to pairing info: SRR039231.5174963_FC42DB6AAXX:2:28:1572:254 => [0, 104, 115][115, 128] Read name to pairing info: SRR039231.14481949_FC42DB6AAXX:2:80:1583:1278 => [0][0] Read name to pairing info: SRR039231.11705473_FC42DB6AAXX:2:65:662:1592 => [128] Read name to pairing info: SRR039231.5276511_FC42DB6AAXX:2:29:797:1951 => [0] Read name to pairing info: SRR039231.14396657_FC42DB6AAXX:2:80:740:1859 => [128][128] Read name to pairing info: SRR039231.13719753_FC42DB6AAXX:2:76:1191:1256 => [0][0, 104] Read name to pairing info: SRR039231.21589259_FC42DB6AAXX:2:119:947:546 => [0] Read name to pairing info: SRR039231.1908187_FC42DB6AAXX:2:11:306:275 => [128] Read name to pairing info: SRR039231.16147670_FC42DB6AAXX:2:90:3:1638 => [0][0, 337] Read name to pairing info: SRR039231.16173078_FC42DB6AAXX:2:90:254:422 => [128][128] Read name to pairing info: SRR039231.17582312_FC42DB6AAXX:2:97:1496:2016 => [0][0, 104] Read name to pairing info: SRR039231.13009251_FC42DB6AAXX:2:72:1245:1880 => [128][128] Read name to pairing info: SRR039231.20146338_FC42DB6AAXX:2:111:1444:35 => [0, 104, 115, 128][128] Read name to pairing info: SRR039231.19933512_FC42DB6AAXX:2:110:1189:2021 => [128] Read name to pairing info: SRR039231.17788793_FC42DB6AAXX:2:98:1726:769 => [128] Read name to pairing info: SRR039231.6179653_FC42DB6AAXX:2:34:822:1560 => [0, 104, 115][361, 115, 128] Read name to pairing info: SRR039231.10679582_FC42DB6AAXX:2:59:1098:1734 => [128][128] Read name to pairing info: SRR039231.14173065_FC42DB6AAXX:2:79:322:765 => [0] Read name to pairing info: SRR039231.11984981_FC42DB6AAXX:2:66:1684:1562 => [0, 104] Read name to pairing info: SRR039231.16902890_FC42DB6AAXX:2:94:234:1996 => [128][128] Read name to pairing info: SRR039231.19866284_FC42DB6AAXX:2:110:546:1457 => [0, 337][337, 128] Read name to pairing info: SRR039231.14735089_FC42DB6AAXX:2:82:509:413 => [0, 104, 115][115, 128] Read name to pairing info: SRR039231.3014932_FC42DB6AAXX:2:17:237:179 => [128][128] Read name to pairing info: SRR039231.7136667_FC42DB6AAXX:2:39:1376:566 => [0][115, 128] SECTION ================== Pairing up the reads into PairPaths =========================== we have 1 reads supporting the path: PairPath [_paths=[[337, 128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115]]] we have 1 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115, 128]]] we have 2 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104], [0, 104, 115, 128]]] we have 3 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 4 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [0, 104, 115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [0, 337]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 5 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 6 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 3 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 7 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 4 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 104], [115, 128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 104, 115, 128]]] we have 8 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 9 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 10 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 11 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 12 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 104], [115, 128]]] we have 13 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 14 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [115, 128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [104, 115, 128]]] we have 3 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 4 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 15 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[115, 128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[115, 128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [128]]] we have 16 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 2 reads supporting the path: PairPath [_paths=[[0], [0, 337]]] we have 1 reads supporting the path: PairPath [_paths=[[337, 128], [337, 128]]] we have 5 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 17 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [128]]] we have 18 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 2 reads supporting the path: PairPath [_paths=[[0, 104, 115], [115, 128]]] we have 6 reads supporting the path: PairPath [_paths=[[0], [0]]] we have 19 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 5 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 3 reads supporting the path: PairPath [_paths=[[0], [0, 337]]] we have 20 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 6 reads supporting the path: PairPath [_paths=[[0], [0, 104]]] we have 21 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 104, 115, 128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0, 104, 115], [361, 115, 128]]] we have 22 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 23 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 4 reads supporting the path: PairPath [_paths=[[0, 337], [337, 128]]] we have 3 reads supporting the path: PairPath [_paths=[[0, 104, 115], [115, 128]]] we have 24 reads supporting the path: PairPath [_paths=[[128], [128]]] we have 1 reads supporting the path: PairPath [_paths=[[0], [115, 128]]] number of reads used = 96 ## Read PathPair results: 29 singletons, num pairs: 67, num pairs discarded: 0 Printing Pair Paths ------------------ Start Vertex:0 PairPaths@Init: PairPath [_paths=[[0], [115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0], [0, 104, 115]]]=2 PairPaths@Init: PairPath [_paths=[[0], [0, 104]]]=6 PairPaths@Init: PairPath [_paths=[[0], [0, 337]]]=3 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [361, 115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [115, 128]]]=3 PairPaths@Init: PairPath [_paths=[[0, 104], [0, 104, 115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115, 128], [115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 337], [337, 128]]]=4 PairPaths@Init: PairPath [_paths=[[0, 104], [115, 128]]]=3 PairPaths@Init: PairPath [_paths=[[0], [0]]]=6 PairPaths@Init: PairPath [_paths=[[0, 104, 115, 128], []]]=1 PairPaths@Init: PairPath [_paths=[[0, 104], []]]=1 PairPaths@Init: PairPath [_paths=[[0], []]]=11 PairPaths@Init: PairPath [_paths=[[0], [104, 115, 128]]]=1 PairPaths@Init: PairPath [_paths=[[0, 104, 115, 128], [128]]]=3 PairPaths@Init: PairPath [_paths=[[0], [0, 104, 115, 128]]]=2 PairPaths@Init: PairPath [_paths=[[0, 104, 115], [0, 104, 115, 128]]]=1 Start Vertex:115 PairPaths@Init: PairPath [_paths=[[115, 128], [128]]]=2 Start Vertex:337 PairPaths@Init: PairPath [_paths=[[337, 128], [128]]]=1 PairPaths@Init: PairPath [_paths=[[337, 128], [337, 128]]]=1 Start Vertex:128 PairPaths@Init: PairPath [_paths=[[128], [128]]]=24 PairPaths@Init: PairPath [_paths=[[128], []]]=16 SECTION ======== Create DAG from Overlap Layout ============ Noncontained paths: [[0, 104, 115, 128], [361, 115, 128], [337, 128], [0, 337]] Node[128] has repeat count: 3 Node[0] has repeat count: 2 Node[115] has repeat count: 2 Node[337] has repeat count: 2 Node[361] has repeat count: 1 Node[104] has repeat count: 1 path PN1::[0, 104, 115, 128] extends no path path PN2::[361, 115, 128] extends no path PathNode Overlap Detected: [overlap: 1] PN4::[0, 337] extended by PN3::[337, 128] extension of: PN4::[0, 337] by PN3::[337, 128] has 1 terminal matches. path PN4::[0, 337] extends no path PathNodeDescription: PN1::[0, 104, 115, 128] PathNodeDescription: PN3::[337, 128] PathNodeDescription: PN4::[0, 337] PathNodeDescription: PN2::[361, 115, 128] // Breaking cycles in Path Overlap Graph (POG), Round: 1 SECTION ======== Convert Path-DAG to SeqVertex-DAG ============ prep_for_DAG_collapse: PN1 CurrVert:[385, 386, 387, 388], OrigVert:[0, 104, 115, 128] prep_for_DAG_collapse: PN3 CurrVert:[389, 390], OrigVert:[337, 128] prep_for_DAG_collapse: PN4 CurrVert:[391, 392], OrigVert:[0, 337] prep_for_DAG_collapse: PN2 CurrVert:[393, 394, 395], OrigVert:[361, 115, 128] DFS_path_to_graph: targeting: PN1::[0, 104, 115, 128] DFS_path_to_graph: targeting: PN4::[0, 337] DFS_path_to_graph: targeting: PN3::[337, 128] DFS_path_to_graph: targeting: PN2::[361, 115, 128] ## Round: 1 Zipping up. ## zip_up() attempt_zip_merge_SeqVertices([TCAGAACAGTCATTGATATTCTTT:W5(V392_337_D6), AACATTTTTG...GATATTCTTT:W5(V389_337_D3)]) UpZipMerging nodes: [AACATTTTTG...GATATTCTTT:W5(V392_337_D6), AACATTTTTG...GATATTCTTT:W5(V389_337_D3)] to TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D3) Zip up merged: 2 nodes. ## Round: 2 Zipping up. Zip up merged: 0 nodes. ## Round: 3 Zipping down. Zip down merged: 0 nodes. ## Round: 4 Zipping up. Zip up merged: 0 nodes. ## Round: 5 Zipping down. Zip down merged: 0 nodes. Old_to_new_vertex_id_mapping: 393 => 393 (stays same) Old_to_new_vertex_id_mapping: 385 => 385 (stays same) Old_to_new_vertex_id_mapping: 391 => 391 (stays same) Old_to_new_vertex_id_mapping: 394 => 394 (stays same) Old_to_new_vertex_id_mapping: 386 => 386 (stays same) Old_to_new_vertex_id_mapping: 392 => 396 Old_to_new_vertex_id_mapping: 389 => 396 Old_to_new_vertex_id_mapping: 395 => 395 (stays same) Old_to_new_vertex_id_mapping: 387 => 387 (stays same) Old_to_new_vertex_id_mapping: 390 => 390 (stays same) Old_to_new_vertex_id_mapping: 388 => 388 (stays same) Old-to-new-path mappings: {[361, 115, 128]=[393, 394, 395], [0, 337]=[391, 396], [337, 128]=[396, 390], [0, 104, 115, 128]=[385, 386, 387, 388]} LONG_READ_PATH_MAP is:{} LONG_READ_NAME_TO_PPath is : {} LONG_READ_PATH_MAP updated to:{} LONG_READ_NAME_TO_PPath updated to : {} Printing Pair Paths ------------------ Start Vertex:396 PairPaths@PostOverlapLayout: PairPath [_paths=[[396, 390], [388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[396, 390], [396, 390]]]=1 Start Vertex:387 PairPaths@PostOverlapLayout: PairPath [_paths=[[387, 388], [388]]]=2 Start Vertex:385 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [386, 387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], []]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], [387, 388]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386], [385, 386, 387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [388]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], []]]=11 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385, 386, 387]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [393, 394, 395]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], [387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385, 386]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385, 386, 387, 388]]]=2 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [385]]]=6 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [387, 388]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387, 388], []]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [387, 388]]]=1 PairPaths@PostOverlapLayout: PairPath [_paths=[[385], [391, 396]]]=3 PairPaths@PostOverlapLayout: PairPath [_paths=[[385, 386, 387], [385, 386, 387, 388]]]=1 Start Vertex:391 PairPaths@PostOverlapLayout: PairPath [_paths=[[391, 396], [396, 390]]]=4 Start Vertex:388 PairPaths@PostOverlapLayout: PairPath [_paths=[[388], [388]]]=24 PairPaths@PostOverlapLayout: PairPath [_paths=[[388], []]]=16 SECTION ======= Reorganize Read Pairings ========= NODE_DESCR: ATAAGCATAT...TATGCTTGTG:W20(V395_128_D2) Preds: [ATTGATATTCTTT:W17(V394_115_D1) ] Succ: [] NODE_DESCR: ATTGATATTCTTT:W17(V394_115_D1) Preds: [TCATGGCTGA...CAGAACAGTC:W2(V393_361_D0) ] Succ: [ATAAGCATAT...TATGCTTGTG:W20(V395_128_D2) ] NODE_DESCR: TCATGGCTGA...CAGAACAGTC:W2(V393_361_D0) Preds: [] Succ: [ATTGATATTCTTT:W17(V394_115_D1) ] NODE_DESCR: TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) Preds: [TAAAGGGGAT...GTTTGATGAA:W21(V391_0_D0) ] Succ: [ATAAGCATAT...TATGCTTGTG:W20(V390_128_D2) ] NODE_DESCR: ATTGATATTCTTT:W17(V387_115_D2) Preds: [CCAGAACAGTC:W21(V386_104_D1) ] Succ: [ATAAGCATAT...TATGCTTGTG:W20(V388_128_D3) ] NODE_DESCR: CCAGAACAGTC:W21(V386_104_D1) Preds: [TAAAGGGGAT...GTTTGATGAA:W21(V385_0_D0) ] Succ: [ATTGATATTCTTT:W17(V387_115_D2) ] NODE_DESCR: TAAAGGGGAT...GTTTGATGAA:W21(V385_0_D0) Preds: [] Succ: [CCAGAACAGTC:W21(V386_104_D1) ] NODE_DESCR: TAAAGGGGAT...GTTTGATGAA:W21(V391_0_D0) Preds: [] Succ: [TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) ] NODE_DESCR: ATAAGCATAT...TATGCTTGTG:W20(V390_128_D2) Preds: [TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1) ] Succ: [] NODE_DESCR: ATAAGCATAT...TATGCTTGTG:W20(V388_128_D3) Preds: [ATTGATATTCTTT:W17(V387_115_D2) ] Succ: [] combinePaths: [396, 390], [388] we have 1 reads supporting the path: PairPath [_paths=[[396, 390], []]] we have 1 reads supporting the path: PairPath [_paths=[[388], []]] Warning... pp: PairPath [_paths=[[396, 390], [388]]] needed to be split into: PairPath [_paths=[[396, 390], []]] and PairPath [_paths=[[388], []]] combinePaths: [396, 390], [396, 390] we have 2 reads supporting the path: PairPath [_paths=[[396, 390], []]] OK pp update to new DAG: PairPath [_paths=[[396, 390], [396, 390]]] => PairPath [_paths=[[396, 390], []]] combinePaths: [387, 388], [388] we have 2 reads supporting the path: PairPath [_paths=[[387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[387, 388], [388]]] => PairPath [_paths=[[387, 388], []]] combinePaths: [385], [386, 387, 388] Could Impute path connectingPairPath [_paths=[[385], [386, 387, 388]]] containing intervening nodes: [] we have 1 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385], [386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] we have 1 reads supporting the path: PairPath [_paths=[[385, 386], []]] combinePaths: [385, 386], [387, 388] Could Impute path connectingPairPath [_paths=[[385, 386], [387, 388]]] containing intervening nodes: [] we have 4 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387], [388] Could Impute path connectingPairPath [_paths=[[385, 386, 387], [388]]] containing intervening nodes: [] we have 5 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387], [388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386], [385, 386, 387, 388] we have 6 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386], [385, 386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385, 386, 387, 388], [388] we have 9 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387, 388], [388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] we have 11 reads supporting the path: PairPath [_paths=[[385], []]] combinePaths: [385], [385, 386, 387] we have 2 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385, 386, 387]]] => PairPath [_paths=[[385, 386, 387], []]] combinePaths: [385, 386, 387], [393, 394, 395] we have 3 reads supporting the path: PairPath [_paths=[[385, 386, 387], []]] we have 1 reads supporting the path: PairPath [_paths=[[393, 394, 395], []]] Warning... pp: PairPath [_paths=[[385, 386, 387], [393, 394, 395]]] needed to be split into: PairPath [_paths=[[385, 386, 387], []]] and PairPath [_paths=[[393, 394, 395], []]] combinePaths: [385, 386, 387, 388], [387, 388] we have 10 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387, 388], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [385, 386] we have 7 reads supporting the path: PairPath [_paths=[[385, 386], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385, 386]]] => PairPath [_paths=[[385, 386], []]] combinePaths: [385], [385, 386, 387, 388] we have 12 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385, 386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [385] we have 17 reads supporting the path: PairPath [_paths=[[385], []]] OK pp update to new DAG: PairPath [_paths=[[385], [385]]] => PairPath [_paths=[[385], []]] combinePaths: [385, 386, 387], [387, 388] we have 15 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] we have 16 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [387, 388] Could Impute path connectingPairPath [_paths=[[385], [387, 388]]] containing intervening nodes: [386] we have 17 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385], [387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [385], [391, 396] we have 20 reads supporting the path: PairPath [_paths=[[385], []]] we have 3 reads supporting the path: PairPath [_paths=[[391, 396], []]] Warning... pp: PairPath [_paths=[[385], [391, 396]]] needed to be split into: PairPath [_paths=[[385], []]] and PairPath [_paths=[[391, 396], []]] combinePaths: [385, 386, 387], [385, 386, 387, 388] we have 18 reads supporting the path: PairPath [_paths=[[385, 386, 387, 388], []]] OK pp update to new DAG: PairPath [_paths=[[385, 386, 387], [385, 386, 387, 388]]] => PairPath [_paths=[[385, 386, 387, 388], []]] combinePaths: [391, 396], [396, 390] we have 4 reads supporting the path: PairPath [_paths=[[391, 396, 390], []]] OK pp update to new DAG: PairPath [_paths=[[391, 396], [396, 390]]] => PairPath [_paths=[[391, 396, 390], []]] combinePaths: [388], [388] we have 25 reads supporting the path: PairPath [_paths=[[388], []]] OK pp update to new DAG: PairPath [_paths=[[388], [388]]] => PairPath [_paths=[[388], []]] we have 41 reads supporting the path: PairPath [_paths=[[388], []]] Start Vertex:393 PairPaths@AfterPairReorganization: PairPath [_paths=[[393, 394, 395], []]]=1 Start Vertex:396 PairPaths@AfterPairReorganization: PairPath [_paths=[[396, 390], []]]=2 Start Vertex:387 PairPaths@AfterPairReorganization: PairPath [_paths=[[387, 388], []]]=2 Start Vertex:385 PairPaths@AfterPairReorganization: PairPath [_paths=[[385, 386, 387, 388], []]]=18 PairPaths@AfterPairReorganization: PairPath [_paths=[[385, 386], []]]=7 PairPaths@AfterPairReorganization: PairPath [_paths=[[385, 386, 387], []]]=3 PairPaths@AfterPairReorganization: PairPath [_paths=[[385], []]]=20 Start Vertex:391 PairPaths@AfterPairReorganization: PairPath [_paths=[[391, 396], []]]=3 PairPaths@AfterPairReorganization: PairPath [_paths=[[391, 396, 390], []]]=4 Start Vertex:388 PairPaths@AfterPairReorganization: PairPath [_paths=[[388], []]]=41 ComponentDivision: 0 contains the following vertices: node_id: 387 node_id: 386 node_id: 385 node_id: 388 ComponentDivision: 1 contains the following vertices: node_id: 396 node_id: 391 node_id: 390 ComponentDivision: 2 contains the following vertices: node_id: 395 node_id: 394 node_id: 393 total number of components = 3 Searching for kmer set: TCAGAACAGTCATTGATATTCTTT -> CAGAACAGTCATTGATATTCTTTA Searching for kmer set: CCAGAACAGTCATTGATATTCTTT -> CAGAACAGTCATTGATATTCTTTA Searching for kmer set: CCAGAACAGTCATTGATATTCTTT -> CAGAACAGTCATTGATATTCTTTA Searching for kmer set: GTGGTTTGATGAACCAGAACAGTC -> TGGTTTGATGAACCAGAACAGTCA Searching for kmer set: ATGGTTTGATGAACCAGAACAGTC -> TGGTTTGATGAACCAGAACAGTCA Searching for kmer set: AAACATTTTTGATGGTTTGATGAA -> AACATTTTTGATGGTTTGATGAAC Searching for kmer set: AAACATTTTTGATGGTTTGATGAA -> AACATTTTTGATGGTTTGATGAAT SECTION ============= Begin Assembly =============== Assembling subcomponent 0 Subcomponent: 0, adding pairpath: PairPath [_paths=[[387, 388], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[385, 386, 387, 388], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[385, 386], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[385, 386, 387], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[385], []]] Subcomponent: 0, adding pairpath: PairPath [_paths=[[388], []]] #### Component Read Summary BEFORE PairPath-per-node Reduction componentReadHash, start node: 387 has size: 1 componentReadHash, start node: 385 has size: 4 componentReadHash, start node: 388 has size: 1 ***** PairPath Counts ***** Node: 387 has 1 pairpaths stored: PairPath [_paths=[[387, 388], []]] has read support: 2 Node: 385 has 4 pairpaths stored: PairPath [_paths=[[385], []]] has read support: 20 PairPath [_paths=[[385, 386, 387, 388], []]] has read support: 18 PairPath [_paths=[[385, 386], []]] has read support: 7 PairPath [_paths=[[385, 386, 387], []]] has read support: 3 Node: 388 has 1 pairpaths stored: PairPath [_paths=[[388], []]] has read support: 41 ## Total number of pairpaths: 6 #### Component Read Summary AFTER PairPath-per-node Reduction componentReadHash, start node: 387 has size: 1 componentReadHash, start node: 385 has size: 4 componentReadHash, start node: 388 has size: 1 ### Extracting triplets from reads. Setting initial triplet adjacency_path for central node: 386 => [385, 386, 387] Setting initial triplet adjacency_path for central node: 387 => [386, 387, 388] triplet adjacency_path of node: 386 => [385, 386, 387] already captured. ### 2 nodes have locked-in triplet paths: Triplet locks for: 387 : [[386, 387, 388]] Triplet locks for: 386 : [[385, 386, 387]] ### Extracting complex path prefixes from reads. -capturing path prefixes -removing prefixes that are subpaths of other prefixes EXTENDED_TRIPLET_CAPTURED: [385, 386, 387] EXTENDED_TRIPLET_CAPTURED: [385, 386, 387, 388] #### Extended triplets from reads: Complex prefix paths for: 387 : [[385, 386, 387]] Complex prefix paths for: 388 : [[385, 386, 387, 388]] SECTION ############### ## Starting Butterfly Assembly ## ################### PairPaths to assemble: Start Vertex:387 PairPaths@BflyStart: PairPath [_paths=[[387, 388], []]]=2 Start Vertex:385 PairPaths@BflyStart: PairPath [_paths=[[385, 386, 387, 388], []]]=18 PairPaths@BflyStart: PairPath [_paths=[[385, 386], []]]=7 PairPaths@BflyStart: PairPath [_paths=[[385, 386, 387], []]]=3 PairPaths@BflyStart: PairPath [_paths=[[385], []]]=20 Start Vertex:-1 PairPaths@BflyStart: PairPath [_paths=[[-1, 385], []]]=1 Start Vertex:388 PairPaths@BflyStart: PairPath [_paths=[[388], []]]=41 PairPaths@BflyStart: PairPath [_paths=[[388, -2], []]]=1 QUEUE IS: [:W2147483647(V-1_D-1)] #### getAllProbablePaths() The next node in the queue C is -1 ***** PairPath Counts ***** Node: 387 has 1 pairpaths stored: PairPath [_paths=[[387, 388], []]] has read support: 2 Node: 385 has 4 pairpaths stored: PairPath [_paths=[[385], []]] has read support: 20 PairPath [_paths=[[385, 386, 387, 388], []]] has read support: 18 PairPath [_paths=[[385, 386], []]] has read support: 7 PairPath [_paths=[[385, 386, 387], []]] has read support: 3 Node: 388 has 1 pairpaths stored: PairPath [_paths=[[388], []]] has read support: 41 ## Total number of pairpaths: 6 butterfly pct done: 1 / 4 = 25.0% pct done. ReadsStartingAtV_START_BFLY, Node: -1 read: PairPath [_paths=[[-1, 385], []]] Exploring extension of: 1 paths that end at vertex: -1 == Current Paths Constructed Up To Vertex: -1 : PathPartialReconstruction@[-1] : [-1] Adding the reads {PairPath [_paths=[[-1, 385], []]]=1} to the path [-1] ################################################ ###### Exploring extension of v: -1 by successor: 385 ################################################ Count of paths ending at v: -1 = 1 path_ending_at_v: [-1] # [PathCounter(385)=0 Examining potential extension of path ending at node V: -1 by successor: 385, via path=[-1] path [-1] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] -checking if subPath has enough read support. Exploring sub path: [385] -readsOfPathUntilV: PairPath [_paths=[[-1, 385], []]] -checking if pp: PairPath [_paths=[[-1, 385], []]] supports extension of [-1, 385] => true examining subPath: [385] for reinforcement by read: [[-1, 385], []] :true the read PairPath [_paths=[[-1, 385], []]](1) enforces the sub-path ([385]) -found: 1 reads supporting subpath. the sub-path ([385]) has PASSED Successful extension of 385 to generate path [-1, 385] updateReadsOfPath: [-1, 385] read PairPath [_paths=[[-1, 385], []]] is consistent with 385 pct_contained_propagated: 0.0% 385 was added to the queue QUEUE IS: [GAAGTTCATG...GTTTGATGAA:W21(V385_0_D0)] #### getAllProbablePaths() The next node in the queue C is 385 butterfly pct done: 2 / 4 = 50.0% pct done. ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385, 386], []]] ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385, 386, 387], []]] ReadsStartingAtV_START_BFLY, Node: 385 read: PairPath [_paths=[[385], []]] Exploring extension of: 1 paths that end at vertex: 385 == Current Paths Constructed Up To Vertex: 385 : PathPartialReconstruction@[385] : [-1, 385] Adding the reads {PairPath [_paths=[[385, 386, 387, 388], []]]=18, PairPath [_paths=[[385, 386], []]]=7, PairPath [_paths=[[385, 386, 387], []]]=3, PairPath [_paths=[[385], []]]=20} to the path [-1, 385] ################################################ ###### Exploring extension of v: 385 by successor: 386 ################################################ Count of paths ending at v: 385 = 1 path_ending_at_v: [-1, 385] # [PathCounter(386)=0 Examining potential extension of path ending at node V: 385 by successor: 386, via path=[-1, 385] path [-1, 385] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1, 385] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] -checking if subPath has enough read support. Exploring sub path: [385, 386] -readsOfPathUntilV: PairPath [_paths=[[-1, 385], []]] -checking if pp: PairPath [_paths=[[-1, 385], []]] supports extension of [-1, 385, 386] => false examining subPath: [385, 386] for reinforcement by read: [[-1, 385], []] :false the read PairPath [_paths=[[-1, 385], []]](1) does not enforce the sub-path ([385, 386]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387, 388], []]] -checking if pp: PairPath [_paths=[[385, 386, 387, 388], []]] supports extension of [-1, 385, 386] => true examining subPath: [385, 386] for reinforcement by read: [[385, 386, 387, 388], []] :true the read PairPath [_paths=[[385, 386, 387, 388], []]](18) enforces the sub-path ([385, 386]) -found: 18 reads supporting subpath. the sub-path ([385, 386]) has PASSED Successful extension of 386 to generate path [-1, 385, 386] updateReadsOfPath: [-1, 385, 386] read PairPath [_paths=[[385, 386, 387, 388], []]] is consistent with 386 read PairPath [_paths=[[385, 386], []]] is consistent with 386 read PairPath [_paths=[[385, 386, 387], []]] is consistent with 386 read PairPath [_paths=[[385], []]] is consistent with 386 pct_contained_propagated: 20.0% 386 was added to the queue QUEUE IS: [CCAGAACAGTC:W21(V386_104_D1)] #### getAllProbablePaths() The next node in the queue C is 386 butterfly pct done: 3 / 4 = 75.0% pct done. ReadsStartingAtV_START_BFLY386 EMPTY Exploring extension of: 1 paths that end at vertex: 386 == Current Paths Constructed Up To Vertex: 386 : PathPartialReconstruction@[386] : [-1, 385, 386] ################################################ ###### Exploring extension of v: 386 by successor: 387 ################################################ Count of paths ending at v: 386 = 1 path_ending_at_v: [-1, 385, 386] # [PathCounter(387)=0 Examining potential extension of path ending at node V: 386 by successor: 387, via path=[-1, 385, 386] TripletMapper doesnt contain node: 386 ReadsOfPathUntilV: PATH: [-1, 385, 386] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] -checking if subPath has enough read support. Exploring sub path: [385, 386, 387] -readsOfPathUntilV: PairPath [_paths=[[-1, 385], []]] -checking if pp: PairPath [_paths=[[-1, 385], []]] supports extension of [-1, 385, 386, 387] => false examining subPath: [385, 386, 387] for reinforcement by read: [[-1, 385], []] :false the read PairPath [_paths=[[-1, 385], []]](1) does not enforce the sub-path ([385, 386, 387]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387, 388], []]] -checking if pp: PairPath [_paths=[[385, 386, 387, 388], []]] supports extension of [-1, 385, 386, 387] => true examining subPath: [385, 386, 387] for reinforcement by read: [[385, 386, 387, 388], []] :true the read PairPath [_paths=[[385, 386, 387, 388], []]](18) enforces the sub-path ([385, 386, 387]) -found: 18 reads supporting subpath. the sub-path ([385, 386, 387]) has PASSED Successful extension of 387 to generate path [-1, 385, 386, 387] updateReadsOfPath: [-1, 385, 386, 387] read PairPath [_paths=[[385, 386, 387, 388], []]] is consistent with 387 read PairPath [_paths=[[385, 386, 387], []]] is consistent with 387 pct_contained_propagated: 60.000004% 387 was added to the queue QUEUE IS: [ATTGATATTCTTT:W17(V387_115_D2)] #### getAllProbablePaths() The next node in the queue C is 387 butterfly pct done: 4 / 4 = 100.0% pct done. ReadsStartingAtV_START_BFLY, Node: 387 read: PairPath [_paths=[[387, 388], []]] Exploring extension of: 1 paths that end at vertex: 387 == Current Paths Constructed Up To Vertex: 387 : PathPartialReconstruction@[387] : [-1, 385, 386, 387] Adding the reads {PairPath [_paths=[[387, 388], []]]=2} to the path [-1, 385, 386, 387] ################################################ ###### Exploring extension of v: 387 by successor: 388 ################################################ Count of paths ending at v: 387 = 1 path_ending_at_v: [-1, 385, 386, 387] # [PathCounter(388)=0 Examining potential extension of path ending at node V: 387 by successor: 388, via path=[-1, 385, 386, 387] TripletMapper doesnt contain node: 387 ReadsOfPathUntilV: PATH: [-1, 385, 386, 387] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] -checking if subPath has enough read support. Exploring sub path: [388] -readsOfPathUntilV: PairPath [_paths=[[-1, 385], []]] -checking if pp: PairPath [_paths=[[-1, 385], []]] supports extension of [-1, 385, 386, 387, 388] => false examining subPath: [388] for reinforcement by read: [[-1, 385], []] :false the read PairPath [_paths=[[-1, 385], []]](1) does not enforce the sub-path ([388]) -readsOfPathUntilV: PairPath [_paths=[[387, 388], []]] -checking if pp: PairPath [_paths=[[387, 388], []]] supports extension of [-1, 385, 386, 387, 388] => true examining subPath: [388] for reinforcement by read: [[387, 388], []] :true the read PairPath [_paths=[[387, 388], []]](2) enforces the sub-path ([388]) -found: 2 reads supporting subpath. the sub-path ([388]) has PASSED Successful extension of 388 to generate path [-1, 385, 386, 387, 388] updateReadsOfPath: [-1, 385, 386, 387, 388] read PairPath [_paths=[[387, 388], []]] is consistent with 388 read PairPath [_paths=[[385, 386, 387, 388], []]] is consistent with 388 pct_contained_propagated: 66.66667% 388 was added to the queue QUEUE IS: [ATAAGCATAT...TATGCTTGTG:W20(V388_128_D3)] #### getAllProbablePaths() The next node in the queue C is 388 butterfly pct done: 5 / 4 = 125.0% pct done. ReadsStartingAtV_START_BFLY, Node: 388 read: PairPath [_paths=[[388], []]] ReadsStartingAtV_START_BFLY, Node: 388 read: PairPath [_paths=[[388, -2], []]] Exploring extension of: 1 paths that end at vertex: 388 == Current Paths Constructed Up To Vertex: 388 : PathPartialReconstruction@[388] : [-1, 385, 386, 387, 388] Adding the reads {PairPath [_paths=[[388], []]]=41, PairPath [_paths=[[388, -2], []]]=1} to the path [-1, 385, 386, 387, 388] ################################################ ###### Exploring extension of v: 388 by successor: -2 ################################################ Count of paths ending at v: 388 = 1 path_ending_at_v: [-1, 385, 386, 387, 388] # [PathCounter(-2)=0 Examining potential extension of path ending at node V: 388 by successor: -2, via path=[-1, 385, 386, 387, 388] TripletMapper doesnt contain node: 388 ReadsOfPathUntilV: PATH: [-1, 385, 386, 387, 388] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387, 388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385, 386, 387], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[388], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[385], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[388, -2], []]] -checking if subPath has enough read support. Exploring sub path: [388, -2] -readsOfPathUntilV: PairPath [_paths=[[-1, 385], []]] -checking if pp: PairPath [_paths=[[-1, 385], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[-1, 385], []] :false the read PairPath [_paths=[[-1, 385], []]](1) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[387, 388], []]] -checking if pp: PairPath [_paths=[[387, 388], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[387, 388], []] :false the read PairPath [_paths=[[387, 388], []]](2) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387, 388], []]] -checking if pp: PairPath [_paths=[[385, 386, 387, 388], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[385, 386, 387, 388], []] :false the read PairPath [_paths=[[385, 386, 387, 388], []]](18) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[385, 386], []]] -checking if pp: PairPath [_paths=[[385, 386], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[385, 386], []] :false the read PairPath [_paths=[[385, 386], []]](7) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[385, 386, 387], []]] -checking if pp: PairPath [_paths=[[385, 386, 387], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[385, 386, 387], []] :false the read PairPath [_paths=[[385, 386, 387], []]](3) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[388], []]] -checking if pp: PairPath [_paths=[[388], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[388], []] :false the read PairPath [_paths=[[388], []]](41) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[385], []]] -checking if pp: PairPath [_paths=[[385], []]] supports extension of [-1, 385, 386, 387, 388, -2] => false examining subPath: [388, -2] for reinforcement by read: [[385], []] :false the read PairPath [_paths=[[385], []]](20) does not enforce the sub-path ([388, -2]) -readsOfPathUntilV: PairPath [_paths=[[388, -2], []]] -checking if pp: PairPath [_paths=[[388, -2], []]] supports extension of [-1, 385, 386, 387, 388, -2] => true examining subPath: [388, -2] for reinforcement by read: [[388, -2], []] :true the read PairPath [_paths=[[388, -2], []]](1) enforces the sub-path ([388, -2]) -found: 1 reads supporting subpath. the sub-path ([388, -2]) has PASSED Successful extension of -2 to generate path [-1, 385, 386, 387, 388, -2] updateReadsOfPath: [-1, 385, 386, 387, 388, -2] read PairPath [_paths=[[388], []]] is consistent with -2 read PairPath [_paths=[[388, -2], []]] is consistent with -2 pct_contained_propagated: 75.0% -2 was added to the queue QUEUE IS: [:W-1(V-2_D-1)] #### getAllProbablePaths() The next node in the queue C is -2 butterfly pct done: 6 / 4 = 150.0% pct done. ReadsStartingAtV_START_BFLY-2 EMPTY Exploring extension of: 1 paths that end at vertex: -2 == Current Paths Constructed Up To Vertex: -2 : PathPartialReconstruction@[-2] : [-1, 385, 386, 387, 388, -2] the finished path: [-1, 385, 386, 387, 388, -2] was added to the final paths, with 93 support FinalPath@BeforeFiltering: [-1, 385, 386, 387, 388, -2] Grouping paths into genes IsoformClustering, number of clusters = 0 Sep Gene IDs:{[-1, 385, 386, 387, 388, -2]=1} FinalPath@AfterFiltering: [-1, 385, 386, 387, 388, -2] Final Paths: 1 Final path reported: comp0_g1_i1 len=360 path=[385:0-126 386:127-137 387:138-150 388:151-359] [-1, 385, 386, 387, 388, -2] SECTION ============= Begin Assembly =============== Assembling subcomponent 1 Subcomponent: 1, adding pairpath: PairPath [_paths=[[396, 390], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[391, 396], []]] Subcomponent: 1, adding pairpath: PairPath [_paths=[[391, 396, 390], []]] #### Component Read Summary BEFORE PairPath-per-node Reduction componentReadHash, start node: 396 has size: 1 componentReadHash, start node: 391 has size: 2 #### Component Read Summary AFTER PairPath-per-node Reduction componentReadHash, start node: 396 has size: 1 componentReadHash, start node: 391 has size: 2 ### Extracting triplets from reads. Setting initial triplet adjacency_path for central node: 396 => [391, 396, 390] ### 1 nodes have locked-in triplet paths: Triplet locks for: 396 : [[391, 396, 390]] ### Extracting complex path prefixes from reads. -capturing path prefixes -removing prefixes that are subpaths of other prefixes EXTENDED_TRIPLET_CAPTURED: [391, 396, 390] #### Extended triplets from reads: Complex prefix paths for: 390 : [[391, 396, 390]] SECTION ############### ## Starting Butterfly Assembly ## ################### PairPaths to assemble: Start Vertex:396 PairPaths@BflyStart: PairPath [_paths=[[396, 390], []]]=2 Start Vertex:391 PairPaths@BflyStart: PairPath [_paths=[[391, 396], []]]=3 PairPaths@BflyStart: PairPath [_paths=[[391, 396, 390], []]]=4 Start Vertex:390 PairPaths@BflyStart: PairPath [_paths=[[390, -2], []]]=1 Start Vertex:-1 PairPaths@BflyStart: PairPath [_paths=[[-1, 391], []]]=1 QUEUE IS: [:W2147483647(V-1_D-1)] #### getAllProbablePaths() The next node in the queue C is -1 butterfly pct done: 1 / 3 = 33.333336% pct done. ReadsStartingAtV_START_BFLY, Node: -1 read: PairPath [_paths=[[-1, 391], []]] Exploring extension of: 1 paths that end at vertex: -1 == Current Paths Constructed Up To Vertex: -1 : PathPartialReconstruction@[-1] : [-1] Adding the reads {PairPath [_paths=[[-1, 391], []]]=1} to the path [-1] ################################################ ###### Exploring extension of v: -1 by successor: 385 ################################################ component either lacks: 385 or at sink ################################################ ###### Exploring extension of v: -1 by successor: 391 ################################################ Count of paths ending at v: -1 = 1 path_ending_at_v: [-1] # [PathCounter(391)=0 Examining potential extension of path ending at node V: -1 by successor: 391, via path=[-1] path [-1] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] -checking if subPath has enough read support. Exploring sub path: [391] -readsOfPathUntilV: PairPath [_paths=[[-1, 391], []]] -checking if pp: PairPath [_paths=[[-1, 391], []]] supports extension of [-1, 391] => true examining subPath: [391] for reinforcement by read: [[-1, 391], []] :true the read PairPath [_paths=[[-1, 391], []]](1) enforces the sub-path ([391]) -found: 1 reads supporting subpath. the sub-path ([391]) has PASSED Successful extension of 391 to generate path [-1, 391] updateReadsOfPath: [-1, 391] read PairPath [_paths=[[-1, 391], []]] is consistent with 391 pct_contained_propagated: 0.0% 391 was added to the queue QUEUE IS: [GAAGTTCATG...GTTTGATGAA:W21(V391_0_D0)] #### getAllProbablePaths() The next node in the queue C is 391 butterfly pct done: 2 / 3 = 66.66667% pct done. ReadsStartingAtV_START_BFLY, Node: 391 read: PairPath [_paths=[[391, 396], []]] ReadsStartingAtV_START_BFLY, Node: 391 read: PairPath [_paths=[[391, 396, 390], []]] Exploring extension of: 1 paths that end at vertex: 391 == Current Paths Constructed Up To Vertex: 391 : PathPartialReconstruction@[391] : [-1, 391] ***** PairPath Counts ***** Node: 396 has 1 pairpaths stored: PairPath [_paths=[[396, 390], []]] has read support: 2 Node: 391 has 2 pairpaths stored: PairPath [_paths=[[391, 396, 390], []]] has read support: 4 PairPath [_paths=[[391, 396], []]] has read support: 3 ## Total number of pairpaths: 3 ***** PairPath Counts ***** Node: 396 has 1 pairpaths stored: PairPath [_paths=[[396, 390], []]] has read support: 2 Node: 391 has 2 pairpaths stored: PairPath [_paths=[[391, 396, 390], []]] has read support: 4 PairPath [_paths=[[391, 396], []]] has read support: 3 ## Total number of pairpaths: 3 Adding the reads {PairPath [_paths=[[391, 396], []]]=3, PairPath [_paths=[[391, 396, 390], []]]=4} to the path [-1, 391] ################################################ ###### Exploring extension of v: 391 by successor: 396 ################################################ Count of paths ending at v: 391 = 1 path_ending_at_v: [-1, 391] # [PathCounter(396)=0 Examining potential extension of path ending at node V: 391 by successor: 396, via path=[-1, 391] path [-1, 391] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1, 391] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 396], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] -checking if subPath has enough read support. Exploring sub path: [391, 396] -readsOfPathUntilV: PairPath [_paths=[[391, 396], []]] -checking if pp: PairPath [_paths=[[391, 396], []]] supports extension of [-1, 391, 396] => true examining subPath: [391, 396] for reinforcement by read: [[391, 396], []] :true the read PairPath [_paths=[[391, 396], []]](3) enforces the sub-path ([391, 396]) -found: 3 reads supporting subpath. the sub-path ([391, 396]) has PASSED Successful extension of 396 to generate path [-1, 391, 396] updateReadsOfPath: [-1, 391, 396] read PairPath [_paths=[[391, 396], []]] is consistent with 396 read PairPath [_paths=[[391, 396, 390], []]] is consistent with 396 pct_contained_propagated: 33.333336% 396 was added to the queue QUEUE IS: [TCAGAACAGTCATTGATATTCTTT:W5(V396_337_D1)] #### getAllProbablePaths() The next node in the queue C is 396 butterfly pct done: 3 / 3 = 100.0% pct done. ReadsStartingAtV_START_BFLY, Node: 396 read: PairPath [_paths=[[396, 390], []]] Exploring extension of: 1 paths that end at vertex: 396 == Current Paths Constructed Up To Vertex: 396 : PathPartialReconstruction@[396] : [-1, 391, 396] Adding the reads {PairPath [_paths=[[396, 390], []]]=2} to the path [-1, 391, 396] ################################################ ###### Exploring extension of v: 396 by successor: 390 ################################################ Count of paths ending at v: 396 = 1 path_ending_at_v: [-1, 391, 396] # [PathCounter(390)=0 Examining potential extension of path ending at node V: 396 by successor: 390, via path=[-1, 391, 396] TripletMapper doesnt contain node: 396 ReadsOfPathUntilV: PATH: [-1, 391, 396] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 396], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[396, 390], []]] -checking if subPath has enough read support. Exploring sub path: [390] -readsOfPathUntilV: PairPath [_paths=[[391, 396], []]] -checking if pp: PairPath [_paths=[[391, 396], []]] supports extension of [-1, 391, 396, 390] => false examining subPath: [390] for reinforcement by read: [[391, 396], []] :false the read PairPath [_paths=[[391, 396], []]](3) does not enforce the sub-path ([390]) -readsOfPathUntilV: PairPath [_paths=[[391, 396, 390], []]] -checking if pp: PairPath [_paths=[[391, 396, 390], []]] supports extension of [-1, 391, 396, 390] => true examining subPath: [390] for reinforcement by read: [[391, 396, 390], []] :true the read PairPath [_paths=[[391, 396, 390], []]](4) enforces the sub-path ([390]) -found: 4 reads supporting subpath. the sub-path ([390]) has PASSED Successful extension of 390 to generate path [-1, 391, 396, 390] updateReadsOfPath: [-1, 391, 396, 390] read PairPath [_paths=[[391, 396, 390], []]] is consistent with 390 read PairPath [_paths=[[396, 390], []]] is consistent with 390 pct_contained_propagated: 50.0% 390 was added to the queue QUEUE IS: [ATAAGCATAT...TATGCTTGTG:W20(V390_128_D2)] #### getAllProbablePaths() The next node in the queue C is 390 butterfly pct done: 4 / 3 = 133.33334% pct done. ReadsStartingAtV_START_BFLY, Node: 390 read: PairPath [_paths=[[390, -2], []]] Exploring extension of: 1 paths that end at vertex: 390 == Current Paths Constructed Up To Vertex: 390 : PathPartialReconstruction@[390] : [-1, 391, 396, 390] Adding the reads {PairPath [_paths=[[390, -2], []]]=1} to the path [-1, 391, 396, 390] ################################################ ###### Exploring extension of v: 390 by successor: -2 ################################################ Count of paths ending at v: 390 = 1 path_ending_at_v: [-1, 391, 396, 390] # [PathCounter(-2)=0 Examining potential extension of path ending at node V: 390 by successor: -2, via path=[-1, 391, 396, 390] TripletMapper doesnt contain node: 390 ReadsOfPathUntilV: PATH: [-1, 391, 396, 390] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 396], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[391, 396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 391], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[396, 390], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[390, -2], []]] -checking if subPath has enough read support. Exploring sub path: [390, -2] -readsOfPathUntilV: PairPath [_paths=[[391, 396], []]] -checking if pp: PairPath [_paths=[[391, 396], []]] supports extension of [-1, 391, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[391, 396], []] :false the read PairPath [_paths=[[391, 396], []]](3) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[391, 396, 390], []]] -checking if pp: PairPath [_paths=[[391, 396, 390], []]] supports extension of [-1, 391, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[391, 396, 390], []] :false the read PairPath [_paths=[[391, 396, 390], []]](4) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[-1, 391], []]] -checking if pp: PairPath [_paths=[[-1, 391], []]] supports extension of [-1, 391, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[-1, 391], []] :false the read PairPath [_paths=[[-1, 391], []]](1) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[396, 390], []]] -checking if pp: PairPath [_paths=[[396, 390], []]] supports extension of [-1, 391, 396, 390, -2] => false examining subPath: [390, -2] for reinforcement by read: [[396, 390], []] :false the read PairPath [_paths=[[396, 390], []]](2) does not enforce the sub-path ([390, -2]) -readsOfPathUntilV: PairPath [_paths=[[390, -2], []]] -checking if pp: PairPath [_paths=[[390, -2], []]] supports extension of [-1, 391, 396, 390, -2] => true examining subPath: [390, -2] for reinforcement by read: [[390, -2], []] :true the read PairPath [_paths=[[390, -2], []]](1) enforces the sub-path ([390, -2]) -found: 1 reads supporting subpath. the sub-path ([390, -2]) has PASSED Successful extension of -2 to generate path [-1, 391, 396, 390, -2] updateReadsOfPath: [-1, 391, 396, 390, -2] read PairPath [_paths=[[390, -2], []]] is consistent with -2 pct_contained_propagated: 80.0% -2 was added to the queue QUEUE IS: [:W-1(V-2_D-1)] #### getAllProbablePaths() The next node in the queue C is -2 butterfly pct done: 5 / 3 = 166.66666% pct done. ReadsStartingAtV_START_BFLY-2 EMPTY Exploring extension of: 1 paths that end at vertex: -2 == Current Paths Constructed Up To Vertex: -2 : PathPartialReconstruction@[-2] : [-1, 391, 396, 390, -2] the finished path: [-1, 391, 396, 390, -2] was added to the final paths, with 11 support FinalPath@BeforeFiltering: [-1, 391, 396, 390, -2] Grouping paths into genes IsoformClustering, number of clusters = 0 Sep Gene IDs:{[-1, 391, 396, 390, -2]=1} FinalPath@AfterFiltering: [-1, 391, 396, 390, -2] Final Paths: 1 Final path reported: comp0_g2_i1 len=360 path=[391:0-126 396:127-150 390:151-359] [-1, 391, 396, 390, -2] SECTION ============= Begin Assembly =============== Assembling subcomponent 2 Subcomponent: 2, adding pairpath: PairPath [_paths=[[393, 394, 395], []]] #### Component Read Summary BEFORE PairPath-per-node Reduction componentReadHash, start node: 393 has size: 1 #### Component Read Summary AFTER PairPath-per-node Reduction componentReadHash, start node: 393 has size: 1 ### Extracting triplets from reads. Setting initial triplet adjacency_path for central node: 394 => [393, 394, 395] ### 1 nodes have locked-in triplet paths: Triplet locks for: 394 : [[393, 394, 395]] ### Extracting complex path prefixes from reads. -capturing path prefixes -removing prefixes that are subpaths of other prefixes EXTENDED_TRIPLET_CAPTURED: [393, 394, 395] #### Extended triplets from reads: Complex prefix paths for: 395 : [[393, 394, 395]] SECTION ############### ## Starting Butterfly Assembly ## ################### PairPaths to assemble: Start Vertex:395 PairPaths@BflyStart: PairPath [_paths=[[395, -2], []]]=1 Start Vertex:393 PairPaths@BflyStart: PairPath [_paths=[[393, 394, 395], []]]=1 Start Vertex:-1 PairPaths@BflyStart: PairPath [_paths=[[-1, 393], []]]=1 QUEUE IS: [:W2147483647(V-1_D-1)] #### getAllProbablePaths() The next node in the queue C is -1 butterfly pct done: 1 / 3 = 33.333336% pct done. ReadsStartingAtV_START_BFLY, Node: -1 read: PairPath [_paths=[[-1, 393], []]] Exploring extension of: 1 paths that end at vertex: -1 == Current Paths Constructed Up To Vertex: -1 : PathPartialReconstruction@[-1] : [-1] Adding the reads {PairPath [_paths=[[-1, 393], []]]=1} to the path [-1] ################################################ ###### Exploring extension of v: -1 by successor: 393 ################################################ Count of paths ending at v: -1 = 1 path_ending_at_v: [-1] # [PathCounter(393)=0 Examining potential extension of path ending at node V: -1 by successor: 393, via path=[-1] path [-1] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 393], []]] -checking if subPath has enough read support. Exploring sub path: [-1, 393] -readsOfPathUntilV: PairPath [_paths=[[-1, 393], []]] -checking if pp: PairPath [_paths=[[-1, 393], []]] supports extension of [-1, 393] => true examining subPath: [-1, 393] for reinforcement by read: [[-1, 393], []] :true the read PairPath [_paths=[[-1, 393], []]](1) enforces the sub-path ([-1, 393]) -found: 1 reads supporting subpath. the sub-path ([-1, 393]) has PASSED Successful extension of 393 to generate path [-1, 393] updateReadsOfPath: [-1, 393] ***** PairPath Counts ***** Node: 393 has 1 pairpaths stored: PairPath [_paths=[[393, 394, 395], []]] has read support: 1 ## Total number of pairpaths: 1 ***** PairPath Counts ***** Node: 393 has 1 pairpaths stored: PairPath [_paths=[[393, 394, 395], []]] has read support: 1 ## Total number of pairpaths: 1 read PairPath [_paths=[[-1, 393], []]] is consistent with 393 pct_contained_propagated: 0.0% 393 was added to the queue ################################################ ###### Exploring extension of v: -1 by successor: 385 ################################################ component either lacks: 385 or at sink ################################################ ###### Exploring extension of v: -1 by successor: 391 ################################################ component either lacks: 391 or at sink QUEUE IS: [GTGGTTTGATGAACCAGAACAGTC:W2(V393_361_D0)] #### getAllProbablePaths() The next node in the queue C is 393 butterfly pct done: 2 / 3 = 66.66667% pct done. ReadsStartingAtV_START_BFLY, Node: 393 read: PairPath [_paths=[[393, 394, 395], []]] Exploring extension of: 1 paths that end at vertex: 393 == Current Paths Constructed Up To Vertex: 393 : PathPartialReconstruction@[393] : [-1, 393] Adding the reads {PairPath [_paths=[[393, 394, 395], []]]=1} to the path [-1, 393] ################################################ ###### Exploring extension of v: 393 by successor: 394 ################################################ Count of paths ending at v: 393 = 1 path_ending_at_v: [-1, 393] # [PathCounter(394)=0 Examining potential extension of path ending at node V: 393 by successor: 394, via path=[-1, 393] path [-1, 393] is too short to check for triplet support. ReadsOfPathUntilV: PATH: [-1, 393] ReadsOfPathUntiV: READ: PairPath [_paths=[[393, 394, 395], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 393], []]] -checking if subPath has enough read support. Exploring sub path: [-1, 393, 394] -readsOfPathUntilV: PairPath [_paths=[[393, 394, 395], []]] -checking if pp: PairPath [_paths=[[393, 394, 395], []]] supports extension of [-1, 393, 394] => true examining subPath: [-1, 393, 394] for reinforcement by read: [[393, 394, 395], []] :true the read PairPath [_paths=[[393, 394, 395], []]](1) enforces the sub-path ([-1, 393, 394]) -found: 1 reads supporting subpath. the sub-path ([-1, 393, 394]) has PASSED Successful extension of 394 to generate path [-1, 393, 394] updateReadsOfPath: [-1, 393, 394] read PairPath [_paths=[[393, 394, 395], []]] is consistent with 394 pct_contained_propagated: 50.0% 394 was added to the queue QUEUE IS: [ATTGATATTCTTT:W17(V394_115_D1)] #### getAllProbablePaths() The next node in the queue C is 394 butterfly pct done: 3 / 3 = 100.0% pct done. ReadsStartingAtV_START_BFLY394 EMPTY Exploring extension of: 1 paths that end at vertex: 394 == Current Paths Constructed Up To Vertex: 394 : PathPartialReconstruction@[394] : [-1, 393, 394] ################################################ ###### Exploring extension of v: 394 by successor: 395 ################################################ Count of paths ending at v: 394 = 1 path_ending_at_v: [-1, 393, 394] # [PathCounter(395)=0 Examining potential extension of path ending at node V: 394 by successor: 395, via path=[-1, 393, 394] TripletMapper doesnt contain node: 394 ReadsOfPathUntilV: PATH: [-1, 393, 394] ReadsOfPathUntiV: READ: PairPath [_paths=[[393, 394, 395], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 393], []]] -checking if subPath has enough read support. Exploring sub path: [395] -readsOfPathUntilV: PairPath [_paths=[[393, 394, 395], []]] -checking if pp: PairPath [_paths=[[393, 394, 395], []]] supports extension of [-1, 393, 394, 395] => true examining subPath: [395] for reinforcement by read: [[393, 394, 395], []] :true the read PairPath [_paths=[[393, 394, 395], []]](1) enforces the sub-path ([395]) -found: 1 reads supporting subpath. the sub-path ([395]) has PASSED Successful extension of 395 to generate path [-1, 393, 394, 395] updateReadsOfPath: [-1, 393, 394, 395] read PairPath [_paths=[[393, 394, 395], []]] is consistent with 395 pct_contained_propagated: 50.0% 395 was added to the queue QUEUE IS: [ATAAGCATAT...TATGCTTGTG:W20(V395_128_D2)] #### getAllProbablePaths() The next node in the queue C is 395 butterfly pct done: 4 / 3 = 133.33334% pct done. ReadsStartingAtV_START_BFLY, Node: 395 read: PairPath [_paths=[[395, -2], []]] Exploring extension of: 1 paths that end at vertex: 395 == Current Paths Constructed Up To Vertex: 395 : PathPartialReconstruction@[395] : [-1, 393, 394, 395] Adding the reads {PairPath [_paths=[[395, -2], []]]=1} to the path [-1, 393, 394, 395] ################################################ ###### Exploring extension of v: 395 by successor: -2 ################################################ Count of paths ending at v: 395 = 1 path_ending_at_v: [-1, 393, 394, 395] # [PathCounter(-2)=0 Examining potential extension of path ending at node V: 395 by successor: -2, via path=[-1, 393, 394, 395] TripletMapper doesnt contain node: 395 ReadsOfPathUntilV: PATH: [-1, 393, 394, 395] ReadsOfPathUntiV: READ: PairPath [_paths=[[393, 394, 395], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[-1, 393], []]] ReadsOfPathUntiV: READ: PairPath [_paths=[[395, -2], []]] -checking if subPath has enough read support. Exploring sub path: [395, -2] -readsOfPathUntilV: PairPath [_paths=[[393, 394, 395], []]] -checking if pp: PairPath [_paths=[[393, 394, 395], []]] supports extension of [-1, 393, 394, 395, -2] => false examining subPath: [395, -2] for reinforcement by read: [[393, 394, 395], []] :false the read PairPath [_paths=[[393, 394, 395], []]](1) does not enforce the sub-path ([395, -2]) -readsOfPathUntilV: PairPath [_paths=[[-1, 393], []]] -checking if pp: PairPath [_paths=[[-1, 393], []]] supports extension of [-1, 393, 394, 395, -2] => false examining subPath: [395, -2] for reinforcement by read: [[-1, 393], []] :false the read PairPath [_paths=[[-1, 393], []]](1) does not enforce the sub-path ([395, -2]) -readsOfPathUntilV: PairPath [_paths=[[395, -2], []]] -checking if pp: PairPath [_paths=[[395, -2], []]] supports extension of [-1, 393, 394, 395, -2] => true examining subPath: [395, -2] for reinforcement by read: [[395, -2], []] :true the read PairPath [_paths=[[395, -2], []]](1) enforces the sub-path ([395, -2]) -found: 1 reads supporting subpath. the sub-path ([395, -2]) has PASSED Successful extension of -2 to generate path [-1, 393, 394, 395, -2] updateReadsOfPath: [-1, 393, 394, 395, -2] read PairPath [_paths=[[395, -2], []]] is consistent with -2 pct_contained_propagated: 66.66667% -2 was added to the queue QUEUE IS: [:W-1(V-2_D-1)] #### getAllProbablePaths() The next node in the queue C is -2 butterfly pct done: 5 / 3 = 166.66666% pct done. ReadsStartingAtV_START_BFLY-2 EMPTY Exploring extension of: 1 paths that end at vertex: -2 == Current Paths Constructed Up To Vertex: -2 : PathPartialReconstruction@[-2] : [-1, 393, 394, 395, -2] the finished path: [-1, 393, 394, 395, -2] was added to the final paths, with 3 support FinalPath@BeforeFiltering: [-1, 393, 394, 395, -2] Grouping paths into genes IsoformClustering, number of clusters = 0 Sep Gene IDs:{[-1, 393, 394, 395, -2]=1} FinalPath@AfterFiltering: [-1, 393, 394, 395, -2] Final Paths: 1 Final path reported: comp0_g3_i1 len=269 path=[393:0-46 394:47-59 395:60-268] [-1, 393, 394, 395, -2] total number of paths reported = 3 from 3 components Done make[1]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' fakeroot debian/rules binary dh binary --parallel --with javahelper dh_testroot -O--parallel dh_prep -O--parallel debian/rules override_dh_auto_install make[1]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust; do dh_auto_install \ -O--sourcedirectory=${target}; done make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' Making install in src make[3]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm/src' make[4]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm/src' make[4]: Nothing to be done for `install-data-am'. test -z "/usr/lib/trinityrnaseq/Inchworm/bin" || /bin/mkdir -p "/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/debian/tmp/usr/lib/trinityrnaseq/Inchworm/bin" /usr/bin/install -c inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats '/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/debian/tmp/usr/lib/trinityrnaseq/Inchworm/bin' make[4]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm/src' make[3]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm/src' make[3]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[4]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[3]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/Inchworm' make[2]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make install; done <<< src >>> make[3]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust/src' mv slclust ../bin/ make[3]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg/trinity-plugins/slclust' make[1]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' debian/rules override_dh_install make[1]: Entering directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' dh_install --fail-missing find debian/trinityrnaseq -name '*.p?' | xargs sed -i \ 's=^#!/usr/local/bin/perl=#!/usr/bin/perl=' chmod u+x \ debian/trinityrnaseq/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl \ debian/trinityrnaseq/usr/lib/trinityrnaseq/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl \ debian/trinityrnaseq/usr/lib/trinityrnaseq/util/misc/capture_orig_n_unmapped_reads.pl \ debian/trinityrnaseq/usr/lib/trinityrnaseq/util/support_scripts/plugin_install_tests.sh \ debian/trinityrnaseq/usr/lib/trinityrnaseq/util/support_scripts/trinity_install_tests.sh make[1]: Leaving directory `/«BUILDDIR»/trinityrnaseq-2.0.6+dfsg' jh_installjavadoc -O--parallel dh_installdocs -O--parallel dh_installchangelogs -O--parallel dh_installman -O--parallel dh_lintian -O--parallel dh_perl -O--parallel dh_link -O--parallel jh_installlibs -O--parallel jh_classpath -O--parallel jh_manifest -O--parallel jh_exec -O--parallel jh_depends -O--parallel dh_compress -O--parallel dh_fixperms -O--parallel dh_strip -O--parallel dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_makeshlibs -O--parallel dh_shlibdeps -O--parallel dh_installdeb -O--parallel dh_gencontrol -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package trinityrnaseq-sampledata: unused substitution variable ${perl:Depends} dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform amd64: trinityrnaseq dh_gencontrol debug symbol wrapper: packages to act on: trinityrnaseq dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/trinityrnaseq-dbgsym, skipping package trinityrnaseq dh_md5sums -O--parallel dh_builddeb -O--parallel INFO: pkgstriptranslations version 121 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `trinityrnaseq' in `../trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.deb'. INFO: pkgstriptranslations version 121 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `trinityrnaseq-sampledata' in `../trinityrnaseq-sampledata_2.0.6+dfsg-0biolinux3_all.deb'. dpkg-genchanges -b -mLaunchpad Build Daemon >../trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build trinityrnaseq-2.0.6+dfsg dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151029-1003 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.changes: ────────────────────────────────────────────────── Format: 1.8 Date: Fri, 11 Sep 2015 15:53:32 +0100 Source: trinityrnaseq Binary: trinityrnaseq trinityrnaseq-sampledata Architecture: amd64 all Version: 2.0.6+dfsg-0biolinux3 Distribution: trusty Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Tim Booth Description: trinityrnaseq - RNA-Seq De novo Assembly trinityrnaseq-sampledata - RNA-Seq De novo Assembly Changes: trinityrnaseq (2.0.6+dfsg-0biolinux3) trusty; urgency=medium . * Split out sample data into an arch:all package * Build only for amd64 because jellyfish does not work on i386 * Ensure nothing gets left in debian/tmp Checksums-Sha1: b1c54677409d1beeef7b78a36ff7282d568e145f 1635654 trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.deb 43945e9a3bf5c4d470ce1d0e68ed800f08047375 114422574 trinityrnaseq-sampledata_2.0.6+dfsg-0biolinux3_all.deb Checksums-Sha256: b36567fbe806d45e8eee2a5fe20addc39429bbd4387b62d671f7c199305a8b9b 1635654 trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.deb fe4c18fb0ed4051be0f37ca679e643abde33ed88c5e5cb1b1dd110b6f2c8ffbb 114422574 trinityrnaseq-sampledata_2.0.6+dfsg-0biolinux3_all.deb Files: 3e94c7c37c6256389f062ad4e545248b 1635654 science optional trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.deb e5883c986e4e4dc2ec3e6eb951c81ae2 114422574 science optional trinityrnaseq-sampledata_2.0.6+dfsg-0biolinux3_all.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ trinityrnaseq_2.0.6+dfsg-0biolinux3_amd64.deb ───────────────────────────────────────────── new debian package, version 2.0. size 1635654 bytes: control archive=15705 bytes. 1266 bytes, 19 lines control 43739 bytes, 443 lines md5sums Package: trinityrnaseq Version: 2.0.6+dfsg-0biolinux3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8271 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.4.0), perl, jaligner, libcommons-collections4-java, libgetopt-java, libjung-java, bowtie, python, libwww-perl, default-jre-headless, samtools, jellyfish (>= 2.1.4), r-base-core, r-bioc-edger, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl Suggests: collectl, trinityrnaseq-sampledata Section: science Priority: optional Homepage: http://trinityrnaseq.github.io/ Description: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. drwxr-xr-x root/root 0 2015-10-29 10:01 ./ drwxr-xr-x root/root 0 2015-10-29 10:01 ./usr/ drwxr-xr-x root/root 0 2015-10-29 10:01 ./usr/bin/ -rwxr-xr-x root/root 148 2015-06-25 13:52 ./usr/bin/Trinity drwxr-xr-x root/root 0 2015-10-29 10:01 ./usr/lib/ drwxr-xr-x root/root 0 2015-10-29 10:01 ./usr/lib/trinityrnaseq/ drwxr-xr-x root/root 0 2015-03-02 18:08 ./usr/lib/trinityrnaseq/Analysis/ drwxr-xr-x root/root 0 2015-10-29 10:01 ./usr/lib/trinityrnaseq/Analysis/DifferentialExpression/ -rwxr-xr-x root/root 82890 2015-03-02 18:08 ./usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR drwxr-xr-x root/root 0 2015-03-02 18:08 ./usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/ -rw-r--r-- 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./usr/share/man/man1/Trinity.1.gz trinityrnaseq-sampledata_2.0.6+dfsg-0biolinux3_all.deb ────────────────────────────────────────────────────── new debian package, version 2.0. size 114422574 bytes: control archive=6201 bytes. 487 bytes, 13 lines control 24338 bytes, 189 lines md5sums Package: trinityrnaseq-sampledata Source: trinityrnaseq Version: 2.0.6+dfsg-0biolinux3 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 175076 Recommends: trinityrnaseq Section: science Priority: optional Homepage: http://trinityrnaseq.github.io/ Description: RNA-Seq De novo Assembly This package provides the example data that is bundled with Trinity. 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└──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 607844 Build-Time: 200 Distribution: trusty Host Architecture: amd64 Install-Time: 42 Job: trinityrnaseq_2.0.6+dfsg-0biolinux3.dsc Machine Architecture: amd64 Package: trinityrnaseq Package-Time: 246 Source-Version: 2.0.6+dfsg-0biolinux3 Space: 607844 Status: successful Version: 2.0.6+dfsg-0biolinux3 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151029-1003 Build needed 00:04:06, 607844k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8217040'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8217040/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8217040'] Unmounting chroot for build PACKAGEBUILD-8217040... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8217040'] Removing build PACKAGEBUILD-8217040