0s autopkgtest [00:45:14]: starting date and time: 2024-04-19 00:45:14+0000 0s autopkgtest [00:45:14]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [00:45:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pgn43oce/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade augustus --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gsl/2.7.1+dfsg-6ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-6.secgroup --name adt-noble-arm64-augustus-20240419-004514-juju-7f2275-prod-proposed-migration-environment-2-a79366b1-670c-4fc1-a654-1dda5dc57ca6 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 110s autopkgtest [00:47:04]: testbed dpkg architecture: arm64 111s autopkgtest [00:47:05]: testbed apt version: 2.7.14build2 111s autopkgtest [00:47:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 111s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [54.2 kB] 112s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 112s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 112s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [376 kB] 112s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [130 kB] 112s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 112s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [92.9 kB] 112s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 112s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [563 kB] 112s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 112s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 114s Fetched 1360 kB in 1s (1108 kB/s) 114s Reading package lists... 115s sh: 4: dhclient: not found 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 117s The following packages will be upgraded: 117s apport apport-core-dump-handler base-passwd bind9-dnsutils bind9-host 117s bind9-libs cpio cryptsetup-bin dbus dbus-bin dbus-daemon 117s dbus-session-bus-common dbus-system-bus-common dbus-user-session dmidecode 117s e2fsprogs e2fsprogs-l10n ethtool fuse3 grep gzip iptables iputils-ping 117s iputils-tracepath kmod libargon2-1 libcap2 libcap2-bin libcom-err2 117s libcrypt-dev libcrypt1 libcryptsetup12 libdb5.3t64 libdbus-1-3 libext2fs2t64 117s libflashrom1 libfuse3-3 libgmp10 libicu74 libidn2-0 libinih1 libip4tc2 117s libip6tc2 libjbig0 libjson-c5 libkeyutils1 libkmod2 liblmdb0 liblz4-1 117s liblzo2-2 libmaxminddb0 libmd0 libmnl0 libmpfr6 libncurses6 libncursesw6 117s libnetfilter-conntrack3 libnfnetlink0 libnftables1 libnftnl11 libnghttp2-14 117s libnl-3-200 libnl-genl-3-200 libnl-route-3-200 libnspr4 libnuma1 libonig5 117s libp11-kit0 libpam-cap libpam-modules libpam-modules-bin libpam-runtime 117s libpam0g libpcre2-8-0 libpopt0 libsepol2 libsgutils2-1.46-2 libss2 117s libtasn1-6 libtinfo6 libubootenv-tool libubootenv0.1 libuchardet0 117s libunistring5 libunwind8 libutempter0 libx11-6 libx11-data libxau6 libxdmcp6 117s libxtables12 libxxhash0 libzstd1 login logrotate logsave make man-db mawk 117s ncurses-base ncurses-bin ncurses-term netcat-openbsd nftables numactl 117s os-prober passwd patch python-apt-common python3-apport python3-apt 117s python3-netifaces python3-problem-report python3-systemd rpcsvc-proto rsync 117s rsyslog screen sed sg3-utils sg3-utils-udev sudo sysvinit-utils tar time 117s usbutils xauth zstd 117s 128 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Need to get 30.8 MB of archives. 117s After this operation, 82.9 kB of additional disk space will be used. 117s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4build1 [159 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 gzip arm64 1.12-1ubuntu3 [97.2 kB] 117s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-4ubuntu3 [200 kB] 117s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu2 [186 kB] 117s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2build1 [191 kB] 118s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3build1 [248 kB] 118s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3build1 [51.1 kB] 118s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] 118s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-term all 6.4+20240113-1ubuntu2 [275 kB] 118s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-6ubuntu3 [33.8 kB] 118s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4build1 [118 kB] 118s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4build1 [85.9 kB] 118s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libpam0g arm64 1.5.3-5ubuntu5 [67.8 kB] 118s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules-bin arm64 1.5.3-5ubuntu5 [50.4 kB] 118s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules arm64 1.5.3-5ubuntu5 [278 kB] 118s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu4 [5998 B] 118s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 logsave arm64 1.47.0-2.4~exp1ubuntu4 [22.2 kB] 118s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libext2fs2t64 arm64 1.47.0-2.4~exp1ubuntu4 [225 kB] 118s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 e2fsprogs arm64 1.47.0-2.4~exp1ubuntu4 [594 kB] 118s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 liblz4-1 arm64 1.9.4-1build1 [64.1 kB] 118s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libpopt0 arm64 1.19+dfsg-1build1 [28.4 kB] 118s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2build1 [21.7 kB] 118s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2build1 [271 kB] 118s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 rsync arm64 3.2.7-1ubuntu1 [427 kB] 119s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python-apt-common all 2.7.7ubuntu1 [20.1 kB] 119s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 python3-apt arm64 2.7.7ubuntu1 [167 kB] 119s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 119s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 119s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 119s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 apport all 2.28.1-0ubuntu1 [83.5 kB] 119s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2 arm64 1:2.66-5ubuntu2 [30.2 kB] 119s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2ubuntu6 [243 kB] 119s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2build1 [24.6 kB] 119s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB] 119s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu2 [212 kB] 119s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2build1 [291 kB] 119s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses6 arm64 6.4+20240113-1ubuntu2 [110 kB] 119s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu2 [145 kB] 119s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu2 [104 kB] 119s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu3 [839 kB] 119s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2build1 [530 kB] 119s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2build1 [67.2 kB] 119s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu2 [276 kB] 119s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libtasn1-6 arm64 4.19.0-3build1 [43.1 kB] 119s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libcom-err2 arm64 1.47.0-2.4~exp1ubuntu4 [22.4 kB] 119s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libss2 arm64 1.47.0-2.4~exp1ubuntu4 [16.5 kB] 119s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1build1 [124 kB] 119s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-system-bus-common all 1.14.10-4ubuntu4 [81.6 kB] 119s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-session-bus-common all 1.14.10-4ubuntu4 [80.4 kB] 119s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-user-session arm64 1.14.10-4ubuntu4 [9960 B] 119s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-daemon arm64 1.14.10-4ubuntu4 [115 kB] 119s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-bin arm64 1.14.10-4ubuntu4 [38.8 kB] 119s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 dbus arm64 1.14.10-4ubuntu4 [23.9 kB] 119s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libdbus-1-3 arm64 1.14.10-4ubuntu4 [210 kB] 119s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-cap arm64 1:2.66-5ubuntu2 [12.5 kB] 119s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2-bin arm64 1:2.66-5ubuntu2 [33.5 kB] 119s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 iputils-ping arm64 3:20240117-1build1 [44.3 kB] 119s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 kmod arm64 31+20240202-2ubuntu6 [101 kB] 119s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 31+20240202-2ubuntu6 [51.7 kB] 119s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4build1 [20.5 kB] 119s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libjson-c5 arm64 0.17-1build1 [36.4 kB] 119s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu4 [262 kB] 119s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [732 kB] 120s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libicu74 arm64 74.2-1ubuntu3 [10.8 MB] 121s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] 121s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libmnl0 arm64 1.0.5-2build1 [12.4 kB] 121s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 iptables arm64 1.8.10-3ubuntu2 [388 kB] 121s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu2 [23.4 kB] 121s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libip6tc2 arm64 1.8.10-3ubuntu2 [23.7 kB] 121s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libnfnetlink0 arm64 1.0.2-2build1 [14.7 kB] 121s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libnetfilter-conntrack3 arm64 1.0.9-6build1 [45.6 kB] 121s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libnftnl11 arm64 1.2.6-2build1 [66.2 kB] 121s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libxtables12 arm64 1.8.10-3ubuntu2 [35.9 kB] 121s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 logrotate arm64 3.21.0-2build1 [50.9 kB] 121s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 netcat-openbsd arm64 1.226-1ubuntu2 [43.8 kB] 121s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 python3-netifaces arm64 0.11.0-2build3 [17.9 kB] 121s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 rsyslog arm64 8.2312.0-3ubuntu9 [511 kB] 121s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 sudo arm64 1.9.15p5-3ubuntu5 [929 kB] 121s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 liblmdb0 arm64 0.9.31-1build1 [48.1 kB] 121s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libmaxminddb0 arm64 1.9.1-1build1 [24.6 kB] 121s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libnghttp2-14 arm64 1.59.0-1build4 [74.1 kB] 121s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 bind9-dnsutils arm64 1:9.18.24-0ubuntu5 [155 kB] 121s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 bind9-host arm64 1:9.18.24-0ubuntu5 [50.2 kB] 121s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 bind9-libs arm64 1:9.18.24-0ubuntu5 [1197 kB] 121s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 cpio arm64 2.15+dfsg-1ubuntu2 [81.1 kB] 121s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 dmidecode arm64 3.5-3build1 [60.9 kB] 121s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 fuse3 arm64 3.14.0-5build1 [24.2 kB] 121s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libfuse3-3 arm64 3.14.0-5build1 [82.1 kB] 121s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 iputils-tracepath arm64 3:20240117-1build1 [13.2 kB] 121s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 nftables arm64 1.0.9-1build1 [70.0 kB] 121s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libnftables1 arm64 1.0.9-1build1 [352 kB] 121s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1build1 [23.6 kB] 121s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libuchardet0 arm64 0.0.8-1build1 [75.4 kB] 121s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-data all 2:1.8.7-1build1 [115 kB] 121s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-6 arm64 2:1.8.7-1build1 [649 kB] 121s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libxau6 arm64 1:1.0.9-1build6 [7264 B] 121s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu6 [10.4 kB] 121s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-4build2 [1232 kB] 121s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 time arm64 1.9-0.2build1 [45.0 kB] 121s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 usbutils arm64 1:017-3build1 [82.3 kB] 121s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 xauth arm64 1:1.1.2-1build1 [25.3 kB] 121s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 cryptsetup-bin arm64 2:2.7.0-1ubuntu4 [210 kB] 122s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 ethtool arm64 1:6.7-1build1 [227 kB] 122s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libflashrom1 arm64 1.3.0-2.1ubuntu2 [143 kB] 122s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 libinih1 arm64 55-1ubuntu2 [7216 B] 122s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 liblzo2-2 arm64 2.10-2build4 [50.6 kB] 122s Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 libmpfr6 arm64 4.2.1-1build1 [329 kB] 122s Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-genl-3-200 arm64 3.7.0-0.3build1 [12.2 kB] 122s Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-200 arm64 3.7.0-0.3build1 [183 kB] 122s Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-200 arm64 3.7.0-0.3build1 [57.5 kB] 122s Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 libnspr4 arm64 2:4.35-1.1build1 [114 kB] 122s Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libonig5 arm64 6.9.9-1build1 [172 kB] 122s Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 libsgutils2-1.46-2 arm64 1.46-3ubuntu4 [92.6 kB] 122s Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libubootenv-tool arm64 0.3.5-0.1build1 [7286 B] 122s Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 libubootenv0.1 arm64 0.3.5-0.1build1 [14.6 kB] 122s Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 libunwind8 arm64 1.6.2-3build1 [53.5 kB] 122s Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 libutempter0 arm64 1.2.1-3build1 [9590 B] 122s Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB] 122s Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1build1 [39.5 kB] 122s Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 os-prober arm64 1.81ubuntu4 [15.5 kB] 122s Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 patch arm64 2.7.6-7build3 [101 kB] 122s Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 python3-systemd arm64 235-1build4 [42.5 kB] 122s Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu7 [64.8 kB] 122s Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 screen arm64 4.9.1-1build1 [644 kB] 122s Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 sg3-utils arm64 1.46-3ubuntu4 [827 kB] 122s Get:126 http://ftpmaster.internal/ubuntu noble/main arm64 sg3-utils-udev all 1.46-3ubuntu4 [5922 B] 122s Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 zstd arm64 1.5.5+dfsg2-2build1 [575 kB] 122s Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 123s Preconfiguring packages ... 123s Fetched 30.8 MB in 6s (5426 kB/s) 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77747 files and directories currently installed.) 123s Preparing to unpack .../grep_3.11-4build1_arm64.deb ... 123s Unpacking grep (3.11-4build1) over (3.11-4) ... 123s Setting up grep (3.11-4build1) ... 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77747 files and directories currently installed.) 123s Preparing to unpack .../gzip_1.12-1ubuntu3_arm64.deb ... 123s Unpacking gzip (1.12-1ubuntu3) over (1.12-1ubuntu2) ... 123s Setting up gzip (1.12-1ubuntu3) ... 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77747 files and directories currently installed.) 123s Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu3_arm64.deb ... 123s Unpacking login (1:4.13+dfsg1-4ubuntu3) over (1:4.13+dfsg1-4ubuntu1) ... 123s Setting up login (1:4.13+dfsg1-4ubuntu3) ... 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77747 files and directories currently installed.) 123s Preparing to unpack .../ncurses-bin_6.4+20240113-1ubuntu2_arm64.deb ... 123s Unpacking ncurses-bin (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ... 123s Setting up ncurses-bin (6.4+20240113-1ubuntu2) ... 123s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77747 files and directories currently installed.) 125s Preparing to unpack .../e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu4_all.deb ... 125s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ... 125s Preparing to unpack .../logsave_1.47.0-2.4~exp1ubuntu4_arm64.deb ... 125s Unpacking logsave (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ... 125s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu4_arm64.deb ... 125s Leaving 'diversion of /lib/aarch64-linux-gnu/libe2p.so.2 to /lib/aarch64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' 125s Leaving 'diversion of /lib/aarch64-linux-gnu/libe2p.so.2.3 to /lib/aarch64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 125s Leaving 'diversion of /lib/aarch64-linux-gnu/libext2fs.so.2 to /lib/aarch64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' 125s Leaving 'diversion of /lib/aarch64-linux-gnu/libext2fs.so.2.4 to /lib/aarch64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 125s Unpacking libext2fs2t64:arm64 (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ... 125s Setting up libext2fs2t64:arm64 (1.47.0-2.4~exp1ubuntu4) ... 125s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77747 files and directories currently installed.) 125s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu4_arm64.deb ... 125s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ... 125s Preparing to unpack .../liblz4-1_1.9.4-1build1_arm64.deb ... 125s Unpacking liblz4-1:arm64 (1.9.4-1build1) over (1.9.4-1) ... 125s Setting up liblz4-1:arm64 (1.9.4-1build1) ... 125s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77746 files and directories currently installed.) 126s Preparing to unpack .../libmd0_1.1.0-2build1_arm64.deb ... 126s Unpacking libmd0:arm64 (1.1.0-2build1) over (1.1.0-2) ... 126s Setting up libmd0:arm64 (1.1.0-2build1) ... 126s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77746 files and directories currently installed.) 126s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu5_all.deb ... 126s Unpacking libpam-runtime (1.5.3-5ubuntu5) over (1.5.3-5ubuntu4) ... 126s Setting up libpam-runtime (1.5.3-5ubuntu5) ... 126s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77746 files and directories currently installed.) 126s Preparing to unpack .../libncurses6_6.4+20240113-1ubuntu2_arm64.deb ... 126s Unpacking libncurses6:arm64 (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ... 126s Preparing to unpack .../libncursesw6_6.4+20240113-1ubuntu2_arm64.deb ... 126s Unpacking libncursesw6:arm64 (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ... 126s Preparing to unpack .../libtinfo6_6.4+20240113-1ubuntu2_arm64.deb ... 126s Unpacking libtinfo6:arm64 (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ... 126s Setting up libtinfo6:arm64 (6.4+20240113-1ubuntu2) ... 126s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77746 files and directories currently installed.) 126s Preparing to unpack .../libidn2-0_2.3.7-2build1_arm64.deb ... 126s Unpacking libidn2-0:arm64 (2.3.7-2build1) over (2.3.7-2) ... 126s Setting up libidn2-0:arm64 (2.3.7-2build1) ... 127s (Reading database ... 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(1.14.10-4ubuntu4) ... 132s Setting up libpam-cap:arm64 (1:2.66-5ubuntu2) ... 132s Setting up iputils-ping (3:20240117-1build1) ... 132s Setting up libjson-c5:arm64 (0.17-1build1) ... 132s Setting up zstd (1.5.5+dfsg2-2build1) ... 132s Setting up dbus-bin (1.14.10-4ubuntu4) ... 132s Setting up libonig5:arm64 (6.9.9-1build1) ... 132s Setting up iputils-tracepath (3:20240117-1build1) ... 132s Setting up python3-systemd (235-1build4) ... 132s Setting up libkmod2:arm64 (31+20240202-2ubuntu6) ... 132s Setting up libpopt0:arm64 (1.19+dfsg-1build1) ... 132s Setting up ethtool (1:6.7-1build1) ... 132s Setting up sg3-utils (1.46-3ubuntu4) ... 132s Setting up ncurses-term (6.4+20240113-1ubuntu2) ... 132s Setting up libubootenv-tool (0.3.5-0.1build1) ... 132s Setting up logrotate (3.21.0-2build1) ... 132s logrotate.service is a disabled or a static unit not running, not starting it. 132s Setting up numactl (2.0.18-1build1) ... 132s Setting up bind9-libs:arm64 (1:9.18.24-0ubuntu5) ... 132s Setting up python3-apt (2.7.7ubuntu1) ... 133s Setting up screen (4.9.1-1build1) ... 133s Setting up libnftnl11:arm64 (1.2.6-2build1) ... 133s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... 133s update-initramfs: deferring update (trigger activated) 133s e2scrub_all.service is a disabled or a static unit not running, not starting it. 133s Setting up dbus-daemon (1.14.10-4ubuntu4) ... 133s Setting up kmod (31+20240202-2ubuntu6) ... 134s Setting up sg3-utils-udev (1.46-3ubuntu4) ... 134s update-initramfs: deferring update (trigger activated) 134s Setting up python3-apport (2.28.1-0ubuntu1) ... 134s Setting up libnl-route-3-200:arm64 (3.7.0-0.3build1) ... 134s Setting up fuse3 (3.14.0-5build1) ... 134s update-initramfs: deferring update (trigger activated) 134s Setting up dbus-user-session (1.14.10-4ubuntu4) ... 134s Setting up dbus (1.14.10-4ubuntu4) ... 134s A reboot is required to replace the running dbus-daemon. 134s Please reboot the system when convenient. 134s Setting up xauth (1:1.1.2-1build1) ... 134s Setting up libnetfilter-conntrack3:arm64 (1.0.9-6build1) ... 134s Setting up libnl-genl-3-200:arm64 (3.7.0-0.3build1) ... 134s Setting up libcryptsetup12:arm64 (2:2.7.0-1ubuntu4) ... 134s Setting up bind9-host (1:9.18.24-0ubuntu5) ... 134s Setting up rsync (3.2.7-1ubuntu1) ... 135s rsync.service is a disabled or a static unit not running, not starting it. 135s Setting up cryptsetup-bin (2:2.7.0-1ubuntu4) ... 135s Setting up libnftables1:arm64 (1.0.9-1build1) ... 135s Setting up nftables (1.0.9-1build1) ... 135s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu4) ... 135s Setting up iptables (1.8.10-3ubuntu2) ... 135s Setting up bind9-dnsutils (1:9.18.24-0ubuntu5) ... 135s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 136s Setting up apport (2.28.1-0ubuntu1) ... 136s Installing new version of config file /etc/apport/crashdb.conf ... 137s apport-autoreport.service is a disabled or a static unit not running, not starting it. 137s Processing triggers for debianutils (5.17build1) ... 137s Processing triggers for install-info (7.1-3build2) ... 137s Processing triggers for initramfs-tools (0.142ubuntu24) ... 137s update-initramfs: Generating /boot/initrd.img-6.8.0-22-generic 137s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 146s System running in EFI mode, skipping. 146s Processing triggers for libc-bin (2.39-0ubuntu8) ... 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 147s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 147s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 147s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 148s Reading package lists... 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [00:47:44]: rebooting testbed after setup commands that affected boot 301s autopkgtest [00:50:15]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP PREEMPT_DYNAMIC Fri Apr 5 02:52:09 UTC 2024 303s autopkgtest [00:50:17]: @@@@@@@@@@@@@@@@@@@@ apt-source augustus 313s Get:1 http://ftpmaster.internal/ubuntu noble/universe augustus 3.5.0+dfsg-4build5 (dsc) [2371 B] 313s Get:2 http://ftpmaster.internal/ubuntu noble/universe augustus 3.5.0+dfsg-4build5 (tar) [152 MB] 313s Get:3 http://ftpmaster.internal/ubuntu noble/universe augustus 3.5.0+dfsg-4build5 (diff) [20.5 kB] 313s gpgv: Signature made Tue Apr 16 08:51:45 2024 UTC 313s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 313s gpgv: Can't check signature: No public key 313s dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-4build5.dsc: no acceptable signature found 323s autopkgtest [00:50:37]: testing package augustus version 3.5.0+dfsg-4build5 323s autopkgtest [00:50:37]: build not needed 1335s autopkgtest [01:07:29]: test test-example: preparing testbed 1337s Reading package lists... 1337s Building dependency tree... 1337s Reading state information... 1337s Starting pkgProblemResolver with broken count: 0 1337s Starting 2 pkgProblemResolver with broken count: 0 1337s Done 1337s The following additional packages will be installed: 1337s augustus augustus-data augustus-doc libbamtools2.5.2 1337s libboost-iostreams1.83.0 libcolamd3 libgomp1 libgsl27 libgslcblas0 1337s libhts3t64 libhtscodecs2 libmysql++3t64 libmysqlclient21 1337s libsuitesparseconfig7 mysql-common 1337s Suggested packages: 1337s cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl 1337s libyaml-perl libdbd-mysql-perl python3-biopython gsl-ref-psdoc | gsl-doc-pdf 1337s | gsl-doc-info | gsl-ref-html 1337s Recommended packages: 1337s samtools 1337s The following NEW packages will be installed: 1337s augustus augustus-data augustus-doc autopkgtest-satdep libbamtools2.5.2 1337s libboost-iostreams1.83.0 libcolamd3 libgomp1 libgsl27 libgslcblas0 1337s libhts3t64 libhtscodecs2 libmysql++3t64 libmysqlclient21 1337s libsuitesparseconfig7 mysql-common 1337s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 1337s Need to get 51.4 MB/51.4 MB of archives. 1337s After this operation, 314 MB of additional disk space will be used. 1337s Get:1 /tmp/autopkgtest.3mwyiF/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 1338s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] 1338s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2.1ubuntu3 [258 kB] 1338s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] 1338s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libsuitesparseconfig7 arm64 1:7.6.1+dfsg-1build1 [12.5 kB] 1338s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libcolamd3 arm64 1:7.6.1+dfsg-1build1 [18.1 kB] 1338s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu2 [72.8 kB] 1338s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu2 [918 kB] 1338s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 1338s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3t64 arm64 1.19+ds-1.1build3 [429 kB] 1338s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 mysql-common all 5.8+1.1.0build1 [6746 B] 1338s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libmysqlclient21 arm64 8.0.36-2ubuntu3 [1245 kB] 1338s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libmysql++3t64 arm64 3.2.5-2.3 [97.2 kB] 1338s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 augustus-data all 3.5.0+dfsg-4build5 [22.8 MB] 1339s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 augustus arm64 3.5.0+dfsg-4build5 [1648 kB] 1339s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 augustus-doc all 3.5.0+dfsg-4build5 [23.5 MB] 1340s Fetched 51.4 MB in 2s (22.3 MB/s) 1340s Selecting previously unselected package libbamtools2.5.2:arm64. 1340s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77739 files and directories currently installed.) 1340s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ... 1340s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 1340s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 1340s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_arm64.deb ... 1340s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-2.1ubuntu3) ... 1340s Selecting previously unselected package libgomp1:arm64. 1340s Preparing to unpack .../02-libgomp1_14-20240412-0ubuntu1_arm64.deb ... 1340s Unpacking libgomp1:arm64 (14-20240412-0ubuntu1) ... 1340s Selecting previously unselected package libsuitesparseconfig7:arm64. 1340s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_arm64.deb ... 1340s Unpacking libsuitesparseconfig7:arm64 (1:7.6.1+dfsg-1build1) ... 1340s Selecting previously unselected package libcolamd3:arm64. 1340s Preparing to unpack .../04-libcolamd3_1%3a7.6.1+dfsg-1build1_arm64.deb ... 1340s Unpacking libcolamd3:arm64 (1:7.6.1+dfsg-1build1) ... 1340s Selecting previously unselected package libgslcblas0:arm64. 1340s Preparing to unpack .../05-libgslcblas0_2.7.1+dfsg-6ubuntu2_arm64.deb ... 1340s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 1340s Selecting previously unselected package libgsl27:arm64. 1340s Preparing to unpack .../06-libgsl27_2.7.1+dfsg-6ubuntu2_arm64.deb ... 1340s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 1340s Selecting previously unselected package libhtscodecs2:arm64. 1340s Preparing to unpack .../07-libhtscodecs2_1.6.0-1_arm64.deb ... 1340s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 1340s Selecting previously unselected package libhts3t64:arm64. 1340s Preparing to unpack .../08-libhts3t64_1.19+ds-1.1build3_arm64.deb ... 1340s Unpacking libhts3t64:arm64 (1.19+ds-1.1build3) ... 1340s Selecting previously unselected package mysql-common. 1340s Preparing to unpack .../09-mysql-common_5.8+1.1.0build1_all.deb ... 1340s Unpacking mysql-common (5.8+1.1.0build1) ... 1340s Selecting previously unselected package libmysqlclient21:arm64. 1340s Preparing to unpack .../10-libmysqlclient21_8.0.36-2ubuntu3_arm64.deb ... 1340s Unpacking libmysqlclient21:arm64 (8.0.36-2ubuntu3) ... 1340s Selecting previously unselected package libmysql++3t64:arm64. 1340s Preparing to unpack .../11-libmysql++3t64_3.2.5-2.3_arm64.deb ... 1340s Unpacking libmysql++3t64:arm64 (3.2.5-2.3) ... 1340s Selecting previously unselected package augustus-data. 1340s Preparing to unpack .../12-augustus-data_3.5.0+dfsg-4build5_all.deb ... 1340s Unpacking augustus-data (3.5.0+dfsg-4build5) ... 1341s Selecting previously unselected package augustus. 1341s Preparing to unpack .../13-augustus_3.5.0+dfsg-4build5_arm64.deb ... 1341s Unpacking augustus (3.5.0+dfsg-4build5) ... 1341s Selecting previously unselected package augustus-doc. 1341s Preparing to unpack .../14-augustus-doc_3.5.0+dfsg-4build5_all.deb ... 1341s Unpacking augustus-doc (3.5.0+dfsg-4build5) ... 1342s Selecting previously unselected package autopkgtest-satdep. 1342s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 1342s Unpacking autopkgtest-satdep (0) ... 1342s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 1342s Setting up mysql-common (5.8+1.1.0build1) ... 1342s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 1342s Setting up libmysqlclient21:arm64 (8.0.36-2ubuntu3) ... 1342s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 1342s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 1342s Setting up libgomp1:arm64 (14-20240412-0ubuntu1) ... 1342s Setting up augustus-data (3.5.0+dfsg-4build5) ... 1342s Setting up augustus-doc (3.5.0+dfsg-4build5) ... 1342s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-2.1ubuntu3) ... 1342s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... 1342s Setting up libhts3t64:arm64 (1.19+ds-1.1build3) ... 1342s Setting up libsuitesparseconfig7:arm64 (1:7.6.1+dfsg-1build1) ... 1342s Setting up libmysql++3t64:arm64 (3.2.5-2.3) ... 1342s Setting up libcolamd3:arm64 (1:7.6.1+dfsg-1build1) ... 1342s Setting up augustus (3.5.0+dfsg-4build5) ... 1342s Setting up autopkgtest-satdep (0) ... 1342s Processing triggers for man-db (2.12.0-4build2) ... 1343s Processing triggers for libc-bin (2.39-0ubuntu8) ... 1345s (Reading database ... 79996 files and directories currently installed.) 1345s Removing autopkgtest-satdep (0) ... 1346s autopkgtest [01:07:40]: test test-example: [----------------------- 1346s # This output was generated with AUGUSTUS (version 3.5.0). 1346s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 1346s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 1346s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 1346s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 1346s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 1346s # No extrinsic information on sequences given. 1346s # Sources of extrinsic information: M RM 1346s # Initializing the parameters using config directory /usr/share/augustus/config/ ... 1346s # human version. Using species specific transition matrix: /usr/share/augustus/config/species/human/human_trans_shadow_partial_utr.pbl 1346s # Looks like /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/example.fa is in fasta format. 1346s # We have hints for 0 sequences and for 0 of the sequences in the input set. 1346s # 1346s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 1346s # 1346s # Predicted genes for sequence number 1 on both strands 1347s # start gene g1 1347s HS04636 AUGUSTUS gene 836 8857 1 + . g1 1347s HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 1347s HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 1347s # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 1347s # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 1347s # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 1347s # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 1347s # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 1347s # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV 1347s # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] 1347s # Evidence for and against this transcript: 1347s # % of transcript supported by hints (any source): 0 1347s # CDS exons: 0/10 1347s # CDS introns: 0/9 1347s # 5'UTR exons and introns: 0/1 1347s # 3'UTR exons and introns: 0/1 1347s # hint groups fully obeyed: 0 1347s # incompatible hint groups: 0 1347s # end gene g1 1347s ### 1347s # 1347s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 1347s # 1347s # Predicted genes for sequence number 2 on both strands 1347s # start gene g2 1347s HS08198 AUGUSTUS gene 86 2344 1 + . g2 1347s HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1 1347s HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2"; 1347s # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC 1347s # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] 1347s # Evidence for and against this transcript: 1347s # % of transcript supported by hints (any source): 0 1347s # CDS exons: 0/5 1347s # CDS introns: 0/5 1347s # 5'UTR exons and introns: 0/1 1347s # 3'UTR exons and introns: 0/0 1347s # hint groups fully obeyed: 0 1347s # incompatible hint groups: 0 1347s # end gene g2 1347s ### 1347s # command line: 1347s # augustus --species=human --UTR=on /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/example.fa 1347s # This output was generated with AUGUSTUS (version 3.5.0). 1347s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 1347s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 1347s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 1347s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 1347s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 1347s # Sources of extrinsic information: M P E RM 1347s # Setting 1group1gene for E. 1347s # reading in the file /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/hints.gff ... 1347s # Have extrinsic information about 2 sequences (in the specified range). 1347s # Initializing the parameters using config directory /usr/share/augustus/config/ ... 1347s # human version. Using default transition matrix. 1347s # Looks like /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/example.fa is in fasta format. 1347s # We have hints for 2 sequences and for 2 of the sequences in the input set. 1347s # 1347s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 1347s # 1347s # Predicted genes for sequence number 1 on both strands 1347s # start gene g1 1347s HS04636 AUGUSTUS gene 966 7633 1 + . g1 1347s HS04636 AUGUSTUS transcript 966 7633 . + . g1.t1 1347s HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 6494 6554 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS CDS 7627 7633 . + 1 transcript_id "g1.t1"; gene_id "g1"; 1347s HS04636 AUGUSTUS stop_codon 7631 7633 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1347s # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 1347s # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 1347s # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 1347s # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 1347s # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 1347s # KEMSAELEALYGDIDAVELV] 1347s # Evidence for and against this transcript: 1347s # % of transcript supported by hints (any source): 4.76 1347s # CDS exons: 1/11 1347s # P: 1 1347s # CDS introns: 0/10 1347s # 5'UTR exons and introns: 0/0 1347s # 3'UTR exons and introns: 0/0 1347s # hint groups fully obeyed: 2 1347s # E: 1 1347s # P: 1 1347s # incompatible hint groups: 2 1347s # M: 1 1347s # P: 1 1347s # end gene g1 1347s ### 1347s # 1347s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 1347s # 1347s # Predicted genes for sequence number 2 on both strands 1347s # start gene g2 1347s HS08198 AUGUSTUS gene 445 2344 1 + . g2 1347s HS08198 AUGUSTUS transcript 445 2344 . + . g2.t1 1347s HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 758 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1347s HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1347s # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVA 1347s # PQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTE 1347s # DQIFYFPKY] 1347s # Evidence for and against this transcript: 1347s # % of transcript supported by hints (any source): 10 1347s # CDS exons: 0/5 1347s # CDS introns: 1/5 1347s # M: 1 1347s # 5'UTR exons and introns: 0/0 1347s # 3'UTR exons and introns: 0/0 1347s # hint groups fully obeyed: 2 1347s # E: 1 1347s # M: 1 1347s # incompatible hint groups: 1 1347s # M: 1 1347s # end gene g2 1347s ### 1347s # command line: 1347s # augustus --species=human --hintsfile=/tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/hints.gff --extrinsicCfgFile=/usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/example.fa 1348s autopkgtest [01:07:42]: test test-example: -----------------------] 1348s autopkgtest [01:07:42]: test test-example: - - - - - - - - - - results - - - - - - - - - - 1348s test-example PASS 1348s autopkgtest [01:07:42]: test test-example-with-training: preparing testbed 1350s Reading package lists... 1350s Building dependency tree... 1350s Reading state information... 1350s Starting pkgProblemResolver with broken count: 0 1350s Starting 2 pkgProblemResolver with broken count: 0 1350s Done 1350s The following NEW packages will be installed: 1350s autopkgtest-satdep 1350s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1350s Need to get 0 B/712 B of archives. 1350s After this operation, 0 B of additional disk space will be used. 1350s Get:1 /tmp/autopkgtest.3mwyiF/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 1351s Selecting previously unselected package autopkgtest-satdep. 1351s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79996 files and directories currently installed.) 1351s Preparing to unpack .../2-autopkgtest-satdep.deb ... 1351s Unpacking autopkgtest-satdep (0) ... 1351s Setting up autopkgtest-satdep (0) ... 1353s (Reading database ... 79996 files and directories currently installed.) 1353s Removing autopkgtest-satdep (0) ... 1353s autopkgtest [01:07:47]: test test-example-with-training: [----------------------- 1354s '/usr/share/augustus/config' -> './config' 1354s '/usr/share/augustus/config/cgp' -> './config/cgp' 1354s '/usr/share/augustus/config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg' -> './config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg' 1354s '/usr/share/augustus/config/cgp/log_reg_parameters_arabidopsis.cfg' -> './config/cgp/log_reg_parameters_arabidopsis.cfg' 1354s '/usr/share/augustus/config/cgp/log_reg_parameters_default.cfg' -> './config/cgp/log_reg_parameters_default.cfg' 1354s '/usr/share/augustus/config/cgp/log_reg_parameters_fly.cfg' -> './config/cgp/log_reg_parameters_fly.cfg' 1354s '/usr/share/augustus/config/cgp/log_reg_parameters_human.cfg' -> './config/cgp/log_reg_parameters_human.cfg' 1354s '/usr/share/augustus/config/cgp/log_reg_parameters_primates.cfg' -> './config/cgp/log_reg_parameters_primates.cfg' 1354s '/usr/share/augustus/config/cgp/log_reg_parameters_s_aureus.cfg' -> './config/cgp/log_reg_parameters_s_aureus.cfg' 1354s '/usr/share/augustus/config/extrinsic' -> './config/extrinsic' 1354s '/usr/share/augustus/config/extrinsic/extrinsic-cgp.cfg' -> './config/extrinsic/extrinsic-cgp.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.E.XNT.cfg' -> './config/extrinsic/extrinsic.E.XNT.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.E.cfg' -> './config/extrinsic/extrinsic.E.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg' -> './config/extrinsic/extrinsic.M.RM.E.W.P.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg' -> './config/extrinsic/extrinsic.M.RM.E.W.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.PB.cfg' -> './config/extrinsic/extrinsic.M.RM.PB.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.ME.cfg' -> './config/extrinsic/extrinsic.ME.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.MEMS.cfg' -> './config/extrinsic/extrinsic.MEMS.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.MP.cfg' -> './config/extrinsic/extrinsic.MP.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg' -> './config/extrinsic/extrinsic.MPE.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.MT.cfg' -> './config/extrinsic/extrinsic.MT.cfg' 1354s '/usr/share/augustus/config/extrinsic/extrinsic.cfg' -> './config/extrinsic/extrinsic.cfg' 1354s '/usr/share/augustus/config/model' -> './config/model' 1354s '/usr/share/augustus/config/model/constraints_shadow_partial.txt' -> './config/model/constraints_shadow_partial.txt' 1354s '/usr/share/augustus/config/model/constraints_shadow_partial_utr.txt' -> './config/model/constraints_shadow_partial_utr.txt' 1354s '/usr/share/augustus/config/model/ovlp_len.pbl' -> './config/model/ovlp_len.pbl' 1354s '/usr/share/augustus/config/model/ovlp_len_archaea.pbl' -> './config/model/ovlp_len_archaea.pbl' 1354s '/usr/share/augustus/config/model/states_shadow.cfg' -> './config/model/states_shadow.cfg' 1354s '/usr/share/augustus/config/model/states_shadow_2igenic.cfg' -> './config/model/states_shadow_2igenic.cfg' 1354s '/usr/share/augustus/config/model/states_shadow_bacterium.cfg' -> './config/model/states_shadow_bacterium.cfg' 1354s '/usr/share/augustus/config/model/states_shadow_intronless.cfg' -> './config/model/states_shadow_intronless.cfg' 1354s '/usr/share/augustus/config/model/states_shadow_utr.cfg' -> './config/model/states_shadow_utr.cfg' 1354s '/usr/share/augustus/config/model/states_shadow_utr_nc.cfg' -> './config/model/states_shadow_utr_nc.cfg' 1354s '/usr/share/augustus/config/model/states_singlestrand.cfg' -> './config/model/states_singlestrand.cfg' 1354s '/usr/share/augustus/config/model/states_singlestrand_2igenic.cfg' -> './config/model/states_singlestrand_2igenic.cfg' 1354s '/usr/share/augustus/config/model/trans_shadow_atleastone.pbl' -> './config/model/trans_shadow_atleastone.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_bacterium.pbl' -> './config/model/trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_complete.pbl' -> './config/model/trans_shadow_complete.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_complete_utr.pbl' -> './config/model/trans_shadow_complete_utr.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_exactlyone.pbl' -> './config/model/trans_shadow_exactlyone.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_intronless.pbl' -> './config/model/trans_shadow_intronless.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_partial.pbl' -> './config/model/trans_shadow_partial.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_partial_utr.pbl' -> './config/model/trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/model/trans_shadow_partial_utr_nc.pbl' -> './config/model/trans_shadow_partial_utr_nc.pbl' 1354s '/usr/share/augustus/config/model/trans_singlestrand_atleastone.pbl' -> './config/model/trans_singlestrand_atleastone.pbl' 1354s '/usr/share/augustus/config/model/trans_singlestrand_complete.pbl' -> './config/model/trans_singlestrand_complete.pbl' 1354s '/usr/share/augustus/config/model/trans_singlestrand_exactlyone.pbl' -> './config/model/trans_singlestrand_exactlyone.pbl' 1354s '/usr/share/augustus/config/model/trans_singlestrand_partial.pbl' -> './config/model/trans_singlestrand_partial.pbl' 1354s '/usr/share/augustus/config/parameters' -> './config/parameters' 1354s '/usr/share/augustus/config/parameters/AUG_CMDLN_PARAMETERS.md' -> './config/parameters/AUG_CMDLN_PARAMETERS.md' 1354s '/usr/share/augustus/config/parameters/aug_cmdln_parameters.json' -> './config/parameters/aug_cmdln_parameters.json' 1354s '/usr/share/augustus/config/profile' -> './config/profile' 1354s '/usr/share/augustus/config/profile/blosum55.qij' -> './config/profile/blosum55.qij' 1354s '/usr/share/augustus/config/profile/blosum62.qij' -> './config/profile/blosum62.qij' 1354s '/usr/share/augustus/config/profile/default.qij' -> './config/profile/default.qij' 1354s '/usr/share/augustus/config/species' -> './config/species' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae' -> './config/species/Anopheles_gambiae' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Anopheles_gambiae/README.txt' -> './config/species/Anopheles_gambiae/README.txt' 1354s '/usr/share/augustus/config/species/Argopecten_irradians' -> './config/species/Argopecten_irradians' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt' -> './config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Argopecten_irradians/README.txt' -> './config/species/Argopecten_irradians/README.txt' 1354s '/usr/share/augustus/config/species/Aurelia_aurita' -> './config/species/Aurelia_aurita' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt' -> './config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Aurelia_aurita/README.txt' -> './config/species/Aurelia_aurita/README.txt' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos' -> './config/species/Bathycoccus_prasinos' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Bathycoccus_prasinos/README.txt' -> './config/species/Bathycoccus_prasinos/README.txt' 1354s '/usr/share/augustus/config/species/Berviolum_minutum' -> './config/species/Berviolum_minutum' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt' -> './config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Berviolum_minutum/README.txt' -> './config/species/Berviolum_minutum/README.txt' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae' -> './config/species/Branchiostoma_floridae' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Branchiostoma_floridae/README.txt' -> './config/species/Branchiostoma_floridae/README.txt' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana' -> './config/species/Cassiopea_xamachana' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg' 1354s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma' -> './config/species/Chlamydomonas_eustigma' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/README.txt' -> './config/species/Chlamydomonas_eustigma/README.txt' 1354s '/usr/share/augustus/config/species/Chloropicon_primus' -> './config/species/Chloropicon_primus' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt' -> './config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Chloropicon_primus/README.txt' -> './config/species/Chloropicon_primus/README.txt' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei' -> './config/species/Chrysaora_chesapeakei' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/README.txt' -> './config/species/Chrysaora_chesapeakei/README.txt' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus' -> './config/species/Conidiobolus_coronatus' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis' -> './config/species/Cryptosporidium_hominis' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Cryptosporidium_hominis/README.txt' -> './config/species/Cryptosporidium_hominis/README.txt' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica' -> './config/species/Cyclotella_cryptica' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Cyclotella_cryptica/README.txt' -> './config/species/Cyclotella_cryptica/README.txt' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata' -> './config/species/Dermasterias_imbricata' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Dermasterias_imbricata/README.txt' -> './config/species/Dermasterias_imbricata/README.txt' 1354s '/usr/share/augustus/config/species/Dunaliella_salina' -> './config/species/Dunaliella_salina' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_intron_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_weightmatrix.txt' -> './config/species/Dunaliella_salina/Dunaliella_salina_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Dunaliella_salina/README.txt' -> './config/species/Dunaliella_salina/README.txt' 1354s '/usr/share/augustus/config/species/E_coli_K12' -> './config/species/E_coli_K12' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_exon_probs.pbl' -> './config/species/E_coli_K12/E_coli_K12_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_igenic_probs.pbl' -> './config/species/E_coli_K12/E_coli_K12_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_metapars.cfg' -> './config/species/E_coli_K12/E_coli_K12_metapars.cfg' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_metapars.utr.cfg' -> './config/species/E_coli_K12/E_coli_K12_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_ovlp_len.pbl' -> './config/species/E_coli_K12/E_coli_K12_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_parameters.cfg' -> './config/species/E_coli_K12/E_coli_K12_parameters.cfg' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl' -> './config/species/E_coli_K12/E_coli_K12_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_weightmatrix.txt' -> './config/species/E_coli_K12/E_coli_K12_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus' -> './config/species/Ectocarpus_siliculosus' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_exon_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_igenic_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_intron_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_weightmatrix.txt' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/README.txt' -> './config/species/Ectocarpus_siliculosus/README.txt' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi' -> './config/species/Encephalitozoon_cuniculi' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_exon_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_igenic_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_intron_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_weightmatrix.txt' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/README.txt' -> './config/species/Encephalitozoon_cuniculi/README.txt' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris' -> './config/species/Fistulifera_solaris' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_exon_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_igenic_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_intron_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_weightmatrix.txt' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Fistulifera_solaris/README.txt' -> './config/species/Fistulifera_solaris/README.txt' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102' -> './config/species/Fragilariopsis_cylindrus_CCMP1102' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_exon_probs.pbl' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_igenic_probs.pbl' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_intron_probs.pbl' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cgp.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.utr.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_weightmatrix.txt' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/README.txt' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/README.txt' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera' -> './config/species/Gonapodya_prolifera' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_exon_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_igenic_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_intron_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_weightmatrix.txt' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Gonapodya_prolifera/README.txt' -> './config/species/Gonapodya_prolifera/README.txt' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris' -> './config/species/Hydra_vulgaris' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Hydra_vulgaris/README.txt' -> './config/species/Hydra_vulgaris/README.txt' 1354s '/usr/share/augustus/config/species/Leptasterias_sp' -> './config/species/Leptasterias_sp' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt' -> './config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Leptasterias_sp/README.txt' -> './config/species/Leptasterias_sp/README.txt' 1354s '/usr/share/augustus/config/species/Loa_loa' -> './config/species/Loa_loa' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_exon_probs.pbl' -> './config/species/Loa_loa/Loa_loa_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_igenic_probs.pbl' -> './config/species/Loa_loa/Loa_loa_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_intron_probs.pbl' -> './config/species/Loa_loa/Loa_loa_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.cfg' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.cgp.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.utr.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_parameters.cfg' -> './config/species/Loa_loa/Loa_loa_parameters.cfg' 1354s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_weightmatrix.txt' -> './config/species/Loa_loa/Loa_loa_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Loa_loa/README.txt' -> './config/species/Loa_loa/README.txt' 1354s '/usr/share/augustus/config/species/Micromonas_commoda' -> './config/species/Micromonas_commoda' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_exon_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_igenic_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_intron_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_weightmatrix.txt' -> './config/species/Micromonas_commoda/Micromonas_commoda_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Micromonas_commoda/README.txt' -> './config/species/Micromonas_commoda/README.txt' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla' -> './config/species/Micromonas_pusilla' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_exon_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_igenic_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_intron_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_weightmatrix.txt' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Micromonas_pusilla/README.txt' -> './config/species/Micromonas_pusilla/README.txt' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum' -> './config/species/Monoraphidium_neglectum' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_exon_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_igenic_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_intron_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_weightmatrix.txt' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Monoraphidium_neglectum/README.txt' -> './config/species/Monoraphidium_neglectum/README.txt' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis' -> './config/species/Monosiga_brevicollis' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Monosiga_brevicollis/README.txt' -> './config/species/Monosiga_brevicollis/README.txt' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi' -> './config/species/Naegleria_gruberi' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Naegleria_gruberi/README.txt' -> './config/species/Naegleria_gruberi/README.txt' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai' -> './config/species/Nemopilema_nomurai' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_weightmatrix.txt' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Nemopilema_nomurai/README.txt' -> './config/species/Nemopilema_nomurai/README.txt' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus' -> './config/species/Notospermus_geniculatus' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_weightmatrix.txt' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Notospermus_geniculatus/README.txt' -> './config/species/Notospermus_geniculatus/README.txt' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus' -> './config/species/Ostreococcus_sp_lucimarinus' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_exon_probs.pbl' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_igenic_probs.pbl' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_intron_probs.pbl' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cgp.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.utr.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_weightmatrix.txt' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/README.txt' -> './config/species/Ostreococcus_sp_lucimarinus/README.txt' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri' -> './config/species/Ostreococcus_tauri' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_exon_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_igenic_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_intron_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_weightmatrix.txt' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Ostreococcus_tauri/README.txt' -> './config/species/Ostreococcus_tauri/README.txt' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia' -> './config/species/Paramecium_tetraurelia' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Paramecium_tetraurelia/README.txt' -> './config/species/Paramecium_tetraurelia/README.txt' 1354s '/usr/share/augustus/config/species/Pediculus_humanus' -> './config/species/Pediculus_humanus' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt' -> './config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Pediculus_humanus/README.txt' -> './config/species/Pediculus_humanus/README.txt' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus' -> './config/species/Perkinsus_marinus' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Perkinsus_marinus/README.txt' -> './config/species/Perkinsus_marinus/README.txt' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum' -> './config/species/Phaeodactylum_tricornutum' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_exon_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_igenic_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_intron_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_weightmatrix.txt' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/README.txt' -> './config/species/Phaeodactylum_tricornutum/README.txt' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens' -> './config/species/Physcomitrium_patens' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Physcomitrium_patens/README.txt' -> './config/species/Physcomitrium_patens/README.txt' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa' -> './config/species/Populus_trichocarpa' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg' 1354s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata' -> './config/species/Pseudo-nitzschia_multistriata' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_exon_probs.pbl' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_igenic_probs.pbl' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_intron_probs.pbl' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cgp.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.utr.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_weightmatrix.txt' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/README.txt' -> './config/species/Pseudo-nitzschia_multistriata/README.txt' 1354s '/usr/share/augustus/config/species/Ptychodera_flava' -> './config/species/Ptychodera_flava' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_exon_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_igenic_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_intron_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_weightmatrix.txt' -> './config/species/Ptychodera_flava/Ptychodera_flava_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Ptychodera_flava/README.txt' -> './config/species/Ptychodera_flava/README.txt' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides' -> './config/species/Pycnopodia_helianthoides' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/README.txt' -> './config/species/Pycnopodia_helianthoides/README.txt' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata' -> './config/species/Raphidocelis_subcapitata' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/README.txt' -> './config/species/Raphidocelis_subcapitata/README.txt' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg' 1354s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum' -> './config/species/Rhopilema_esculentum' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/README.txt' -> './config/species/Rhopilema_esculentum/README.txt' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg' 1354s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Ricinus_communis' -> './config/species/Ricinus_communis' 1354s '/usr/share/augustus/config/species/Ricinus_communis/README.txt' -> './config/species/Ricinus_communis/README.txt' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.cfg' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_parameters.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_parameters.cfg' 1354s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt' -> './config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum' -> './config/species/Sclerotinia_sclerotiorum' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/README.txt' -> './config/species/Sclerotinia_sclerotiorum/README.txt' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg' 1354s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum' -> './config/species/Skeletonema_costatum' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/README.txt' -> './config/species/Skeletonema_costatum/README.txt' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg' 1354s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora' -> './config/species/Sordaria_macrospora' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/README.txt' -> './config/species/Sordaria_macrospora/README.txt' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg' 1354s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae' -> './config/species/Sphaceloma_murrayae' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/README.txt' -> './config/species/Sphaceloma_murrayae/README.txt' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg' 1354s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata' -> './config/species/Taeniopygia_guttata' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/README.txt' -> './config/species/Taeniopygia_guttata/README.txt' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg' 1354s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335' -> './config/species/Thalassiosira_pseudonana_CCMP1335' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/README.txt' -> './config/species/Thalassiosira_pseudonana_CCMP1335/README.txt' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_exon_probs.pbl' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_igenic_probs.pbl' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_intron_probs.pbl' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cgp.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.utr.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg' 1354s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens' -> './config/species/Trichoplax_adhaerens' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/README.txt' -> './config/species/Trichoplax_adhaerens/README.txt' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg' 1354s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi' -> './config/species/Trypanosoma_cruzi' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/README.txt' -> './config/species/Trypanosoma_cruzi/README.txt' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg' 1354s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Vitis_vinifera' -> './config/species/Vitis_vinifera' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/README.txt' -> './config/species/Vitis_vinifera/README.txt' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg' 1354s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt' -> './config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis' -> './config/species/Vitrella_brassicaformis' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/README.txt' -> './config/species/Vitrella_brassicaformis/README.txt' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg' 1354s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis' -> './config/species/Xenopus_tropicalis' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg' 1354s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus' -> './config/species/Xiphophorus_maculatus' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/README.txt' -> './config/species/Xiphophorus_maculatus/README.txt' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_exon_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_igenic_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_intron_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_utr_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_weightmatrix.txt' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus' -> './config/species/Xipophorus_maculatus' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_exon_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_igenic_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_intron_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_utr_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_weightmatrix.txt' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/adorsata' -> './config/species/adorsata' 1354s '/usr/share/augustus/config/species/adorsata/adorsata_parameters.cfg' -> './config/species/adorsata/adorsata_parameters.cfg' 1354s '/usr/share/augustus/config/species/adorsata/adorsata_weightmatrix.txt' -> './config/species/adorsata/adorsata_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/adorsata/generic_exon_probs.pbl' -> './config/species/adorsata/generic_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/adorsata/generic_igenic_probs.pbl' -> './config/species/adorsata/generic_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/adorsata/generic_intron_probs.pbl' -> './config/species/adorsata/generic_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/adorsata/generic_weightmatrix.txt' -> './config/species/adorsata/generic_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/aedes' -> './config/species/aedes' 1354s '/usr/share/augustus/config/species/aedes/aedes_exon_probs.pbl' -> './config/species/aedes/aedes_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/aedes/aedes_igenic_probs.pbl' -> './config/species/aedes/aedes_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/aedes/aedes_intron_probs.pbl' -> './config/species/aedes/aedes_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/aedes/aedes_parameters.cfg' -> './config/species/aedes/aedes_parameters.cfg' 1354s '/usr/share/augustus/config/species/aedes/aedes_weightmatrix.txt' -> './config/species/aedes/aedes_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/amphimedon' -> './config/species/amphimedon' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_exon_probs.pbl' -> './config/species/amphimedon/amphimedon_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_igenic_probs.pbl' -> './config/species/amphimedon/amphimedon_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_intron_probs.pbl' -> './config/species/amphimedon/amphimedon_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_metapars.cfg' -> './config/species/amphimedon/amphimedon_metapars.cfg' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_parameters.cfg' -> './config/species/amphimedon/amphimedon_parameters.cfg' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_utr_probs.pbl' -> './config/species/amphimedon/amphimedon_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/amphimedon/amphimedon_weightmatrix.txt' -> './config/species/amphimedon/amphimedon_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum' -> './config/species/ancylostoma_ceylanicum' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/README.TXT' -> './config/species/ancylostoma_ceylanicum/README.TXT' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg' 1354s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/anidulans' -> './config/species/anidulans' 1354s '/usr/share/augustus/config/species/anidulans/anidulans_exon_probs.pbl' -> './config/species/anidulans/anidulans_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/anidulans/anidulans_igenic_probs.pbl' -> './config/species/anidulans/anidulans_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/anidulans/anidulans_intron_probs.pbl' -> './config/species/anidulans/anidulans_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/anidulans/anidulans_parameters.cfg' -> './config/species/anidulans/anidulans_parameters.cfg' 1354s '/usr/share/augustus/config/species/anidulans/anidulans_weightmatrix.txt' -> './config/species/anidulans/anidulans_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/arabidopsis' -> './config/species/arabidopsis' 1354s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_exon_probs.pbl' -> './config/species/arabidopsis/arabidopsis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_igenic_probs.pbl' -> './config/species/arabidopsis/arabidopsis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_intron_probs.pbl' -> './config/species/arabidopsis/arabidopsis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_parameters.cfg' -> './config/species/arabidopsis/arabidopsis_parameters.cfg' 1354s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_utr_probs.pbl' -> './config/species/arabidopsis/arabidopsis_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_weightmatrix.txt' -> './config/species/arabidopsis/arabidopsis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus' -> './config/species/aspergillus_fumigatus' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans' -> './config/species/aspergillus_nidulans' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_weightmatrix.txt' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae' -> './config/species/aspergillus_oryzae' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_exon_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_igenic_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_intron_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_metapars.cfg' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_metapars.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_weightmatrix.txt' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/aspergillus_terreus' -> './config/species/aspergillus_terreus' 1354s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg' -> './config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg' -> './config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg' 1354s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt' -> './config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/b_pseudomallei' -> './config/species/b_pseudomallei' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_exon_probs.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_igenic_probs.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_metapars.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_metapars.cfg' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_metapars.utr.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_ovlp_len.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt' -> './config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/bombus_impatiens1' -> './config/species/bombus_impatiens1' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5' 1354s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt' -> './config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/bombus_terrestris2' -> './config/species/bombus_terrestris2' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt' -> './config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/botrytis_cinerea' -> './config/species/botrytis_cinerea' 1354s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg' -> './config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg' 1354s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg' -> './config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg' 1354s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt' -> './config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/brugia' -> './config/species/brugia' 1354s '/usr/share/augustus/config/species/brugia/brugia_exon_probs.pbl' -> './config/species/brugia/brugia_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/brugia/brugia_igenic_probs.pbl' -> './config/species/brugia/brugia_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/brugia/brugia_intron_probs.pbl' -> './config/species/brugia/brugia_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/brugia/brugia_parameters.cfg' -> './config/species/brugia/brugia_parameters.cfg' 1354s '/usr/share/augustus/config/species/brugia/brugia_splicefile' -> './config/species/brugia/brugia_splicefile' 1354s '/usr/share/augustus/config/species/brugia/brugia_weightmatrix.txt' -> './config/species/brugia/brugia_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/c_elegans_trsk' -> './config/species/c_elegans_trsk' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF' -> './config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF' -> './config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF' -> './config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.utr.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_utr_probs.pbl' -> './config/species/c_elegans_trsk/c_elegans_trsk_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt' -> './config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/cacao' -> './config/species/cacao' 1354s '/usr/share/augustus/config/species/cacao/cacao_exon_probs.pbl' -> './config/species/cacao/cacao_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/cacao/cacao_igenic_probs.pbl' -> './config/species/cacao/cacao_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/cacao/cacao_intron_probs.pbl' -> './config/species/cacao/cacao_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/cacao/cacao_metapars.cfg' -> './config/species/cacao/cacao_metapars.cfg' 1354s '/usr/share/augustus/config/species/cacao/cacao_metapars.utr.cfg' -> './config/species/cacao/cacao_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/cacao/cacao_parameters.cfg' -> './config/species/cacao/cacao_parameters.cfg' 1354s '/usr/share/augustus/config/species/cacao/cacao_utr_probs.pbl' -> './config/species/cacao/cacao_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/cacao/cacao_weightmatrix.txt' -> './config/species/cacao/cacao_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/caenorhabditis' -> './config/species/caenorhabditis' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_exon_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_intron_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_metapars.cfg' -> './config/species/caenorhabditis/caenorhabditis_metapars.cfg' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_parameters.cfg' -> './config/species/caenorhabditis/caenorhabditis_parameters.cfg' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl' -> './config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_utr_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_weightmatrix.txt' -> './config/species/caenorhabditis/caenorhabditis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/camponotus_floridanus' -> './config/species/camponotus_floridanus' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/README.TXT' -> './config/species/camponotus_floridanus/README.TXT' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg' 1354s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt' -> './config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/candida_albicans' -> './config/species/candida_albicans' 1354s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_exon_probs.pbl' -> './config/species/candida_albicans/candida_albicans_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_igenic_probs.pbl' -> './config/species/candida_albicans/candida_albicans_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_intron_probs.pbl' -> './config/species/candida_albicans/candida_albicans_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_metapars.cfg' -> './config/species/candida_albicans/candida_albicans_metapars.cfg' 1354s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_parameters.cfg' -> './config/species/candida_albicans/candida_albicans_parameters.cfg' 1354s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_weightmatrix.txt' -> './config/species/candida_albicans/candida_albicans_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/candida_guilliermondii' -> './config/species/candida_guilliermondii' 1354s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg' -> './config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg' 1354s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg' -> './config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg' 1354s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt' -> './config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/candida_tropicalis' -> './config/species/candida_tropicalis' 1354s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_metapars.cfg' -> './config/species/candida_tropicalis/candida_tropicalis_metapars.cfg' 1354s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg' -> './config/species/candida_tropicalis/candida_tropicalis_parameters.cfg' 1354s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt' -> './config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/chaetomium_globosum' -> './config/species/chaetomium_globosum' 1354s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg' -> './config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg' 1354s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg' -> './config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg' 1354s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt' -> './config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/chicken' -> './config/species/chicken' 1354s '/usr/share/augustus/config/species/chicken/README.TXT' -> './config/species/chicken/README.TXT' 1354s '/usr/share/augustus/config/species/chicken/chicken_exon_probs.pbl' -> './config/species/chicken/chicken_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/chicken/chicken_igenic_probs.pbl' -> './config/species/chicken/chicken_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/chicken/chicken_intron_probs.pbl' -> './config/species/chicken/chicken_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/chicken/chicken_metapars.cfg' -> './config/species/chicken/chicken_metapars.cfg' 1354s '/usr/share/augustus/config/species/chicken/chicken_metapars.utr.cfg' -> './config/species/chicken/chicken_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/chicken/chicken_parameters.cfg' -> './config/species/chicken/chicken_parameters.cfg' 1354s '/usr/share/augustus/config/species/chicken/chicken_weightmatrix.txt' -> './config/species/chicken/chicken_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/chiloscyllium' -> './config/species/chiloscyllium' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_exon_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_intron_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.cfg' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg' -> './config/species/chiloscyllium/chiloscyllium_parameters.cfg' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1' -> './config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_weightmatrix.txt' -> './config/species/chiloscyllium/chiloscyllium_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/chlamy2011' -> './config/species/chlamy2011' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_exon_probs.pbl' -> './config/species/chlamy2011/chlamy2011_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_igenic_probs.pbl' -> './config/species/chlamy2011/chlamy2011_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_intron_probs.pbl' -> './config/species/chlamy2011/chlamy2011_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.cfg' -> './config/species/chlamy2011/chlamy2011_metapars.cfg' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.utr.cfg' -> './config/species/chlamy2011/chlamy2011_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_parameters.cfg' -> './config/species/chlamy2011/chlamy2011_parameters.cfg' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl' -> './config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl' -> './config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_utr_probs.pbl' -> './config/species/chlamy2011/chlamy2011_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_weightmatrix.txt' -> './config/species/chlamy2011/chlamy2011_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/chlamydomonas' -> './config/species/chlamydomonas' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_exon_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_igenic_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_intron_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_metapars.cfg' -> './config/species/chlamydomonas/chlamydomonas_metapars.cfg' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_parameters.cfg' -> './config/species/chlamydomonas/chlamydomonas_parameters.cfg' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl' -> './config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl' -> './config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_utr_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_weightmatrix.txt' -> './config/species/chlamydomonas/chlamydomonas_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/chlorella' -> './config/species/chlorella' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_exon_probs.pbl' -> './config/species/chlorella/chlorella_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_igenic_probs.pbl' -> './config/species/chlorella/chlorella_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_intron_probs.pbl' -> './config/species/chlorella/chlorella_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_metapars.cfg' -> './config/species/chlorella/chlorella_metapars.cfg' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_metapars.utr.cfg' -> './config/species/chlorella/chlorella_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_parameters.cfg' -> './config/species/chlorella/chlorella_parameters.cfg' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_utr_probs.pbl' -> './config/species/chlorella/chlorella_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/chlorella/chlorella_weightmatrix.txt' -> './config/species/chlorella/chlorella_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/ciona' -> './config/species/ciona' 1354s '/usr/share/augustus/config/species/ciona/README.TXT' -> './config/species/ciona/README.TXT' 1354s '/usr/share/augustus/config/species/ciona/ciona_exon_probs.pbl' -> './config/species/ciona/ciona_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/ciona/ciona_igenic_probs.pbl' -> './config/species/ciona/ciona_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/ciona/ciona_intron_probs.pbl' -> './config/species/ciona/ciona_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/ciona/ciona_metapars.cfg' -> './config/species/ciona/ciona_metapars.cfg' 1354s '/usr/share/augustus/config/species/ciona/ciona_metapars.cgp.cfg' -> './config/species/ciona/ciona_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/ciona/ciona_metapars.utr.cfg' -> './config/species/ciona/ciona_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/ciona/ciona_parameters.cfg' -> './config/species/ciona/ciona_parameters.cfg' 1354s '/usr/share/augustus/config/species/ciona/ciona_parameters.cfg.orig1' -> './config/species/ciona/ciona_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/ciona/ciona_weightmatrix.txt' -> './config/species/ciona/ciona_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/coccidioides_immitis' -> './config/species/coccidioides_immitis' 1354s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_exon_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_igenic_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_intron_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_metapars.cfg' -> './config/species/coccidioides_immitis/coccidioides_immitis_metapars.cfg' 1354s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg' -> './config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg' 1354s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_weightmatrix.txt' -> './config/species/coccidioides_immitis/coccidioides_immitis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/coprinus' -> './config/species/coprinus' 1354s '/usr/share/augustus/config/species/coprinus/coprinus_exon_probs.pbl' -> './config/species/coprinus/coprinus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/coprinus/coprinus_igenic_probs.pbl' -> './config/species/coprinus/coprinus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/coprinus/coprinus_intron_probs.pbl' -> './config/species/coprinus/coprinus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/coprinus/coprinus_parameters.cfg' -> './config/species/coprinus/coprinus_parameters.cfg' 1354s '/usr/share/augustus/config/species/coprinus/coprinus_weightmatrix.txt' -> './config/species/coprinus/coprinus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/coprinus_cinereus' -> './config/species/coprinus_cinereus' 1354s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_exon_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_igenic_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_intron_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_metapars.cfg' -> './config/species/coprinus_cinereus/coprinus_cinereus_metapars.cfg' 1354s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg' -> './config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg' 1354s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_weightmatrix.txt' -> './config/species/coprinus_cinereus/coprinus_cinereus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/coyote_tobacco' -> './config/species/coyote_tobacco' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_metapars.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_metapars.cfg' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_parameters.cfg' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_weightmatrix.txt' -> './config/species/coyote_tobacco/coyote_tobacco_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/cryptococcus' -> './config/species/cryptococcus' 1354s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_exon_probs.pbl' -> './config/species/cryptococcus/cryptococcus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_igenic_probs.pbl' -> './config/species/cryptococcus/cryptococcus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_intron_probs.pbl' -> './config/species/cryptococcus/cryptococcus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_parameters.cfg' -> './config/species/cryptococcus/cryptococcus_parameters.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_weightmatrix.txt' -> './config/species/cryptococcus/cryptococcus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii' -> './config/species/cryptococcus_neoformans_gattii' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_exon_probs.pbl' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_igenic_probs.pbl' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_intron_probs.pbl' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_metapars.cfg' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_metapars.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B' -> './config/species/cryptococcus_neoformans_neoformans_B' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_exon_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_igenic_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_intron_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_metapars.cfg' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_metapars.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21' -> './config/species/cryptococcus_neoformans_neoformans_JEC21' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_exon_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_igenic_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_intron_probs.pbl' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_metapars.cfg' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_metapars.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_parameters.cfg' 1354s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/culex' -> './config/species/culex' 1354s '/usr/share/augustus/config/species/culex/culex_exon_probs.pbl' -> './config/species/culex/culex_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/culex/culex_exon_probs.pbl.wech' -> './config/species/culex/culex_exon_probs.pbl.wech' 1354s '/usr/share/augustus/config/species/culex/culex_igenic_probs.pbl' -> './config/species/culex/culex_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/culex/culex_igenic_probs.pbl.wech' -> './config/species/culex/culex_igenic_probs.pbl.wech' 1354s '/usr/share/augustus/config/species/culex/culex_intron_probs.pbl' -> './config/species/culex/culex_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/culex/culex_intron_probs.pbl.wech' -> './config/species/culex/culex_intron_probs.pbl.wech' 1354s '/usr/share/augustus/config/species/culex/culex_metapars.cfg' -> './config/species/culex/culex_metapars.cfg' 1354s '/usr/share/augustus/config/species/culex/culex_parameters.cfg' -> './config/species/culex/culex_parameters.cfg' 1354s '/usr/share/augustus/config/species/culex/culex_parameters.old.cfg' -> './config/species/culex/culex_parameters.old.cfg' 1354s '/usr/share/augustus/config/species/culex/culex_trans_shadow_partial_utr.pbl' -> './config/species/culex/culex_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/culex/culex_utr_probs.pbl' -> './config/species/culex/culex_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/culex/culex_weightmatrix.txt' -> './config/species/culex/culex_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii' -> './config/species/debaryomyces_hansenii' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_exon_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_igenic_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_intron_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_metapars.cfg' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_metapars.cfg' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg' 1354s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_weightmatrix.txt' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/elephant_shark' -> './config/species/elephant_shark' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_exon_probs.pbl' -> './config/species/elephant_shark/elephant_shark_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_igenic_probs.pbl' -> './config/species/elephant_shark/elephant_shark_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_intron_probs.pbl' -> './config/species/elephant_shark/elephant_shark_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_metapars.cfg' -> './config/species/elephant_shark/elephant_shark_metapars.cfg' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_metapars.utr.cfg' -> './config/species/elephant_shark/elephant_shark_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_parameters.cfg' -> './config/species/elephant_shark/elephant_shark_parameters.cfg' 1354s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_weightmatrix.txt' -> './config/species/elephant_shark/elephant_shark_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB' -> './config/species/encephalitozoon_cuniculi_GB' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_exon_probs.pbl' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_igenic_probs.pbl' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_intron_probs.pbl' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_metapars.cfg' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_metapars.cfg' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg' 1354s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_weightmatrix.txt' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii' -> './config/species/eremothecium_gossypii' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_exon_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_igenic_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_intron_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_metapars.cfg' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_metapars.cfg' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg' 1354s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_weightmatrix.txt' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/fly' -> './config/species/fly' 1354s '/usr/share/augustus/config/species/fly/fly_exon_probs.pbl' -> './config/species/fly/fly_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/fly/fly_igenic_probs.pbl' -> './config/species/fly/fly_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/fly/fly_intron_probs.pbl' -> './config/species/fly/fly_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/fly/fly_metapars.cfg' -> './config/species/fly/fly_metapars.cfg' 1354s '/usr/share/augustus/config/species/fly/fly_metapars.utr.cfg' -> './config/species/fly/fly_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/fly/fly_parameters.cfg' -> './config/species/fly/fly_parameters.cfg' 1354s '/usr/share/augustus/config/species/fly/fly_utr_probs.pbl' -> './config/species/fly/fly_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/fly/fly_weightmatrix.txt' -> './config/species/fly/fly_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/fly_exp' -> './config/species/fly_exp' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_exon_probs.pbl' -> './config/species/fly_exp/fly_exp_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_igenic_probs.pbl' -> './config/species/fly_exp/fly_exp_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_intron_probs.pbl' -> './config/species/fly_exp/fly_exp_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_metapars.cfg' -> './config/species/fly_exp/fly_exp_metapars.cfg' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_metapars.utr.cfg' -> './config/species/fly_exp/fly_exp_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_parameters.cfg' -> './config/species/fly_exp/fly_exp_parameters.cfg' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_utr_probs.pbl' -> './config/species/fly_exp/fly_exp_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/fly_exp/fly_exp_weightmatrix.txt' -> './config/species/fly_exp/fly_exp_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/fusarium' -> './config/species/fusarium' 1354s '/usr/share/augustus/config/species/fusarium/fusarium_exon_probs.pbl' -> './config/species/fusarium/fusarium_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/fusarium/fusarium_igenic_probs.pbl' -> './config/species/fusarium/fusarium_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/fusarium/fusarium_intron_probs.pbl' -> './config/species/fusarium/fusarium_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/fusarium/fusarium_parameters.cfg' -> './config/species/fusarium/fusarium_parameters.cfg' 1354s '/usr/share/augustus/config/species/fusarium/fusarium_weightmatrix.txt' -> './config/species/fusarium/fusarium_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/fusarium_graminearum' -> './config/species/fusarium_graminearum' 1354s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_exon_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_igenic_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_intron_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_metapars.cfg' -> './config/species/fusarium_graminearum/fusarium_graminearum_metapars.cfg' 1354s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg' -> './config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg' 1354s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_weightmatrix.txt' -> './config/species/fusarium_graminearum/fusarium_graminearum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/galdieria' -> './config/species/galdieria' 1354s '/usr/share/augustus/config/species/galdieria/extrinsic.PE.cfg' -> './config/species/galdieria/extrinsic.PE.cfg' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_exon_probs.pbl' -> './config/species/galdieria/galdieria_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_igenic_probs.pbl' -> './config/species/galdieria/galdieria_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_intron_probs.pbl' -> './config/species/galdieria/galdieria_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_metapars.cfg' -> './config/species/galdieria/galdieria_metapars.cfg' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_parameters.cfg' -> './config/species/galdieria/galdieria_parameters.cfg' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_splicefile' -> './config/species/galdieria/galdieria_splicefile' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl' -> './config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_utr_probs.pbl' -> './config/species/galdieria/galdieria_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/galdieria/galdieria_weightmatrix.txt' -> './config/species/galdieria/galdieria_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/generic' -> './config/species/generic' 1354s '/usr/share/augustus/config/species/generic/generic_metapars.cfg' -> './config/species/generic/generic_metapars.cfg' 1354s '/usr/share/augustus/config/species/generic/generic_metapars.cgp.cfg' -> './config/species/generic/generic_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/generic/generic_metapars.utr.cfg' -> './config/species/generic/generic_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/generic/generic_parameters.cfg' -> './config/species/generic/generic_parameters.cfg' 1354s '/usr/share/augustus/config/species/generic/generic_weightmatrix.txt' -> './config/species/generic/generic_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/gigaspora_margarita' -> './config/species/gigaspora_margarita' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/README.TXT' -> './config/species/gigaspora_margarita/README.TXT' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_exon_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_igenic_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_intron_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_weightmatrix.txt' -> './config/species/gigaspora_margarita/gigaspora_margarita_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/gigaspora_margarita/gth.cfg' -> './config/species/gigaspora_margarita/gth.cfg' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1' -> './config/species/heliconius_melpomene1' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_exon_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_igenic_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_intron_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.cfg' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.utr.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg' 1354s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_weightmatrix.txt' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/histoplasma' -> './config/species/histoplasma' 1354s '/usr/share/augustus/config/species/histoplasma/histoplasma_exon_probs.pbl' -> './config/species/histoplasma/histoplasma_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/histoplasma/histoplasma_igenic_probs.pbl' -> './config/species/histoplasma/histoplasma_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/histoplasma/histoplasma_intron_probs.pbl' -> './config/species/histoplasma/histoplasma_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/histoplasma/histoplasma_parameters.cfg' -> './config/species/histoplasma/histoplasma_parameters.cfg' 1354s '/usr/share/augustus/config/species/histoplasma/histoplasma_weightmatrix.txt' -> './config/species/histoplasma/histoplasma_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum' -> './config/species/histoplasma_capsulatum' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_exon_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_igenic_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_intron_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_metapars.cfg' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_metapars.cfg' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg' 1354s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_weightmatrix.txt' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/honeybee1' -> './config/species/honeybee1' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_exon_probs.pbl' -> './config/species/honeybee1/honeybee1_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_igenic_probs.pbl' -> './config/species/honeybee1/honeybee1_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_intron_probs.pbl' -> './config/species/honeybee1/honeybee1_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_metapars.cfg' -> './config/species/honeybee1/honeybee1_metapars.cfg' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_metapars.utr.cfg' -> './config/species/honeybee1/honeybee1_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_parameters.cfg' -> './config/species/honeybee1/honeybee1_parameters.cfg' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_parameters.cfg.orig1' -> './config/species/honeybee1/honeybee1_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_utr_probs.pbl' -> './config/species/honeybee1/honeybee1_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/honeybee1/honeybee1_weightmatrix.txt' -> './config/species/honeybee1/honeybee1_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/human' -> './config/species/human' 1354s '/usr/share/augustus/config/species/human/README.TXT' -> './config/species/human/README.TXT' 1354s '/usr/share/augustus/config/species/human/human_exon_probs.pbl' -> './config/species/human/human_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/human/human_igenic_probs.pbl' -> './config/species/human/human_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/human/human_intron_probs.pbl' -> './config/species/human/human_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/human/human_parameters.cfg' -> './config/species/human/human_parameters.cfg' 1354s '/usr/share/augustus/config/species/human/human_trans_shadow_partial_utr.pbl' -> './config/species/human/human_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/human/human_utr_probs.pbl' -> './config/species/human/human_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/human/human_weightmatrix.txt' -> './config/species/human/human_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma' -> './config/species/hymenolepis_microstoma' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_exon_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_igenic_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_intron_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_weightmatrix.txt' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/hymenolepis_microstoma/make.doc' -> './config/species/hymenolepis_microstoma/make.doc' 1354s '/usr/share/augustus/config/species/japaneselamprey' -> './config/species/japaneselamprey' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_exon_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_intron_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_metapars.cfg' -> './config/species/japaneselamprey/japaneselamprey_metapars.cfg' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_metapars.utr.cfg' -> './config/species/japaneselamprey/japaneselamprey_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_parameters.cfg' -> './config/species/japaneselamprey/japaneselamprey_parameters.cfg' 1354s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_weightmatrix.txt' -> './config/species/japaneselamprey/japaneselamprey_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis' -> './config/species/kluyveromyces_lactis' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_exon_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_igenic_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_intron_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_metapars.cfg' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_metapars.cfg' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg' 1354s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_weightmatrix.txt' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/laccaria_bicolor' -> './config/species/laccaria_bicolor' 1354s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_exon_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_igenic_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_intron_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_metapars.cfg' -> './config/species/laccaria_bicolor/laccaria_bicolor_metapars.cfg' 1354s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg' -> './config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg' 1354s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_weightmatrix.txt' -> './config/species/laccaria_bicolor/laccaria_bicolor_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae' -> './config/species/leishmania_tarentolae' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_exon_probs.pbl' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_igenic_probs.pbl' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.cfg' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.utr.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg' 1354s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_weightmatrix.txt' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus' -> './config/species/lodderomyces_elongisporus' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg' 1354s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea' -> './config/species/magnaporthe_grisea' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg' 1354s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/maize' -> './config/species/maize' 1354s '/usr/share/augustus/config/species/maize/maize_exon_probs.pbl' -> './config/species/maize/maize_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/maize/maize_igenic_probs.pbl' -> './config/species/maize/maize_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/maize/maize_intron_probs.pbl' -> './config/species/maize/maize_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/maize/maize_metapars.cfg' -> './config/species/maize/maize_metapars.cfg' 1354s '/usr/share/augustus/config/species/maize/maize_parameters.cfg' -> './config/species/maize/maize_parameters.cfg' 1354s '/usr/share/augustus/config/species/maize/maize_splicefile.txt.gz' -> './config/species/maize/maize_splicefile.txt.gz' 1354s '/usr/share/augustus/config/species/maize/maize_weightmatrix.txt' -> './config/species/maize/maize_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/maize5' -> './config/species/maize5' 1354s '/usr/share/augustus/config/species/maize5/maize5_exon_probs.pbl' -> './config/species/maize5/maize5_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/maize5/maize5_igenic_probs.pbl' -> './config/species/maize5/maize5_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/maize5/maize5_intron_probs.pbl' -> './config/species/maize5/maize5_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/maize5/maize5_metapars.cfg' -> './config/species/maize5/maize5_metapars.cfg' 1354s '/usr/share/augustus/config/species/maize5/maize5_metapars.utr.cfg' -> './config/species/maize5/maize5_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/maize5/maize5_parameters.cfg' -> './config/species/maize5/maize5_parameters.cfg' 1354s '/usr/share/augustus/config/species/maize5/maize5_utr_probs.pbl' -> './config/species/maize5/maize5_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/maize5/maize5_weightmatrix.txt' -> './config/species/maize5/maize5_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi' -> './config/species/mnemiopsis_leidyi' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/README.TXT' -> './config/species/mnemiopsis_leidyi/README.TXT' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/nasonia' -> './config/species/nasonia' 1354s '/usr/share/augustus/config/species/nasonia/nasonia_exon_probs.pbl' -> './config/species/nasonia/nasonia_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/nasonia/nasonia_igenic_probs.pbl' -> './config/species/nasonia/nasonia_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/nasonia/nasonia_intron_probs.pbl' -> './config/species/nasonia/nasonia_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/nasonia/nasonia_metapars.cfg' -> './config/species/nasonia/nasonia_metapars.cfg' 1354s '/usr/share/augustus/config/species/nasonia/nasonia_parameters.cfg' -> './config/species/nasonia/nasonia_parameters.cfg' 1354s '/usr/share/augustus/config/species/nasonia/nasonia_weightmatrix.txt' -> './config/species/nasonia/nasonia_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/nematostella_vectensis' -> './config/species/nematostella_vectensis' 1354s '/usr/share/augustus/config/species/nematostella_vectensis/README.TXT' -> './config/species/nematostella_vectensis/README.TXT' 1354s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg' -> './config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg' 1354s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt' -> './config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/neurospora' -> './config/species/neurospora' 1354s '/usr/share/augustus/config/species/neurospora/neurospora_exon_probs.pbl' -> './config/species/neurospora/neurospora_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/neurospora/neurospora_igenic_probs.pbl' -> './config/species/neurospora/neurospora_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/neurospora/neurospora_intron_probs.pbl' -> './config/species/neurospora/neurospora_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/neurospora/neurospora_parameters.cfg' -> './config/species/neurospora/neurospora_parameters.cfg' 1354s '/usr/share/augustus/config/species/neurospora/neurospora_weightmatrix.txt' -> './config/species/neurospora/neurospora_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/neurospora_crassa' -> './config/species/neurospora_crassa' 1354s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_exon_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_igenic_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_intron_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_metapars.cfg' -> './config/species/neurospora_crassa/neurospora_crassa_metapars.cfg' 1354s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg' -> './config/species/neurospora_crassa/neurospora_crassa_parameters.cfg' 1354s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_weightmatrix.txt' -> './config/species/neurospora_crassa/neurospora_crassa_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/parasteatoda' -> './config/species/parasteatoda' 1354s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_exon_probs.pbl' -> './config/species/parasteatoda/parasteatoda_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_igenic_probs.pbl' -> './config/species/parasteatoda/parasteatoda_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_intron_probs.pbl' -> './config/species/parasteatoda/parasteatoda_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_parameters.cfg' -> './config/species/parasteatoda/parasteatoda_parameters.cfg' 1354s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_utr_probs.pbl' -> './config/species/parasteatoda/parasteatoda_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_weightmatrix.txt' -> './config/species/parasteatoda/parasteatoda_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/pchrysosporium' -> './config/species/pchrysosporium' 1354s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_exon_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_igenic_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_intron_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_parameters.cfg' -> './config/species/pchrysosporium/pchrysosporium_parameters.cfg' 1354s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt' -> './config/species/pchrysosporium/pchrysosporium_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/pea_aphid' -> './config/species/pea_aphid' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_exon_probs.pbl' -> './config/species/pea_aphid/pea_aphid_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_igenic_probs.pbl' -> './config/species/pea_aphid/pea_aphid_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_intron_probs.pbl' -> './config/species/pea_aphid/pea_aphid_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_metapars.cfg' -> './config/species/pea_aphid/pea_aphid_metapars.cfg' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_parameters.cfg' -> './config/species/pea_aphid/pea_aphid_parameters.cfg' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl' -> './config/species/pea_aphid/pea_aphid_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_utr_probs.pbl' -> './config/species/pea_aphid/pea_aphid_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_weightmatrix.txt' -> './config/species/pea_aphid/pea_aphid_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/pfalciparum' -> './config/species/pfalciparum' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_exon_probs.pbl' -> './config/species/pfalciparum/pfalciparum_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_igenic_probs.pbl' -> './config/species/pfalciparum/pfalciparum_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_intron_probs.pbl' -> './config/species/pfalciparum/pfalciparum_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_metapars.cfg' -> './config/species/pfalciparum/pfalciparum_metapars.cfg' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_parameters.cfg' -> './config/species/pfalciparum/pfalciparum_parameters.cfg' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl' -> './config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl' 1354s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_weightmatrix.txt' -> './config/species/pfalciparum/pfalciparum_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium' -> './config/species/phanerochaete_chrysosporium' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_exon_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_igenic_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_intron_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_metapars.cfg' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_metapars.cfg' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg' 1354s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_weightmatrix.txt' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/pichia_stipitis' -> './config/species/pichia_stipitis' 1354s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_exon_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_igenic_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_intron_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_metapars.cfg' -> './config/species/pichia_stipitis/pichia_stipitis_metapars.cfg' 1354s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg' -> './config/species/pichia_stipitis/pichia_stipitis_parameters.cfg' 1354s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_weightmatrix.txt' -> './config/species/pichia_stipitis/pichia_stipitis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/pisaster' -> './config/species/pisaster' 1354s '/usr/share/augustus/config/species/pisaster/extrinsic.pisaster.cfg' -> './config/species/pisaster/extrinsic.pisaster.cfg' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_exon_probs.pbl' -> './config/species/pisaster/pisaster_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_igenic_probs.pbl' -> './config/species/pisaster/pisaster_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_intron_probs.pbl' -> './config/species/pisaster/pisaster_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.cfg' -> './config/species/pisaster/pisaster_metapars.cfg' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.cgp.cfg' -> './config/species/pisaster/pisaster_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.utr.cfg' -> './config/species/pisaster/pisaster_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_parameters.cfg' -> './config/species/pisaster/pisaster_parameters.cfg' 1354s '/usr/share/augustus/config/species/pisaster/pisaster_weightmatrix.txt' -> './config/species/pisaster/pisaster_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/pneumocystis' -> './config/species/pneumocystis' 1354s '/usr/share/augustus/config/species/pneumocystis/README.TXT' -> './config/species/pneumocystis/README.TXT' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_exon_probs.pbl' -> './config/species/pneumocystis/pneumocystis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_igenic_probs.pbl' -> './config/species/pneumocystis/pneumocystis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_intron_probs.pbl' -> './config/species/pneumocystis/pneumocystis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_metapars.cfg' -> './config/species/pneumocystis/pneumocystis_metapars.cfg' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_metaparsBAK.cfg' -> './config/species/pneumocystis/pneumocystis_metaparsBAK.cfg' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_parameters.cfg' -> './config/species/pneumocystis/pneumocystis_parameters.cfg' 1354s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_weightmatrix.txt' -> './config/species/pneumocystis/pneumocystis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/rhincodon' -> './config/species/rhincodon' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_exon_probs.pbl' -> './config/species/rhincodon/rhincodon_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_igenic_probs.pbl' -> './config/species/rhincodon/rhincodon_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_intron_probs.pbl' -> './config/species/rhincodon/rhincodon_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.cfg' -> './config/species/rhincodon/rhincodon_metapars.cfg' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.cgp.cfg' -> './config/species/rhincodon/rhincodon_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.utr.cfg' -> './config/species/rhincodon/rhincodon_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_parameters.cfg' -> './config/species/rhincodon/rhincodon_parameters.cfg' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_parameters.cfg.orig1' -> './config/species/rhincodon/rhincodon_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/rhincodon/rhincodon_weightmatrix.txt' -> './config/species/rhincodon/rhincodon_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae' -> './config/species/rhizopus_oryzae' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_exon_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_igenic_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_intron_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_metapars.cfg' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_metapars.cfg' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg' 1354s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_weightmatrix.txt' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/rhodnius' -> './config/species/rhodnius' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_exon_probs.pbl' -> './config/species/rhodnius/rhodnius_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_igenic_probs.pbl' -> './config/species/rhodnius/rhodnius_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_intron_probs.pbl' -> './config/species/rhodnius/rhodnius_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_metapars.cfg' -> './config/species/rhodnius/rhodnius_metapars.cfg' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_metapars.utr.cfg' -> './config/species/rhodnius/rhodnius_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_parameters.cfg' -> './config/species/rhodnius/rhodnius_parameters.cfg' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_utr_probs.pbl' -> './config/species/rhodnius/rhodnius_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/rhodnius/rhodnius_weightmatrix.txt' -> './config/species/rhodnius/rhodnius_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/rice' -> './config/species/rice' 1354s '/usr/share/augustus/config/species/rice/README.TXT' -> './config/species/rice/README.TXT' 1354s '/usr/share/augustus/config/species/rice/rice_exon_probs.pbl' -> './config/species/rice/rice_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/rice/rice_igenic_probs.pbl' -> './config/species/rice/rice_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/rice/rice_intron_probs.pbl' -> './config/species/rice/rice_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/rice/rice_metapars.cfg' -> './config/species/rice/rice_metapars.cfg' 1354s '/usr/share/augustus/config/species/rice/rice_metapars.utr.cfg' -> './config/species/rice/rice_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/rice/rice_parameters.cfg' -> './config/species/rice/rice_parameters.cfg' 1354s '/usr/share/augustus/config/species/rice/rice_utr_probs.pbl' -> './config/species/rice/rice_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/rice/rice_weightmatrix.txt' -> './config/species/rice/rice_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/s_aureus' -> './config/species/s_aureus' 1354s '/usr/share/augustus/config/species/s_aureus/README.TXT' -> './config/species/s_aureus/README.TXT' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_exon_probs.pbl' -> './config/species/s_aureus/s_aureus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_igenic_probs.pbl' -> './config/species/s_aureus/s_aureus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_metapars.cfg' -> './config/species/s_aureus/s_aureus_metapars.cfg' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_metapars.utr.cfg' -> './config/species/s_aureus/s_aureus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_ovlp_len.pbl' -> './config/species/s_aureus/s_aureus_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_parameters.cfg' -> './config/species/s_aureus/s_aureus_parameters.cfg' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_parameters.cgp.cfg' -> './config/species/s_aureus/s_aureus_parameters.cgp.cfg' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl' -> './config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/s_aureus/s_aureus_weightmatrix.txt' -> './config/species/s_aureus/s_aureus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/s_pneumoniae' -> './config/species/s_pneumoniae' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_exon_probs.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_igenic_probs.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_metapars.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_metapars.cfg' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_metapars.utr.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_ovlp_len.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_weightmatrix.txt' -> './config/species/s_pneumoniae/s_pneumoniae_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/saccharomyces' -> './config/species/saccharomyces' 1354s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_exon_probs.pbl' -> './config/species/saccharomyces/saccharomyces_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_igenic_probs.pbl' -> './config/species/saccharomyces/saccharomyces_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_intron_probs.pbl' -> './config/species/saccharomyces/saccharomyces_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_parameters.cfg' -> './config/species/saccharomyces/saccharomyces_parameters.cfg' 1354s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_weightmatrix.txt' -> './config/species/saccharomyces/saccharomyces_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C' -> './config/species/saccharomyces_cerevisiae_S288C' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_exon_probs.pbl' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_igenic_probs.pbl' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_intron_probs.pbl' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_metapars.cfg' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_metapars.cfg' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_weightmatrix.txt' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_exon_probs.pbl' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_igenic_probs.pbl' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_intron_probs.pbl' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_metapars.cfg' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_metapars.cfg' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg' 1354s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_weightmatrix.txt' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/schistosoma' -> './config/species/schistosoma' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_exon_probs.pbl' -> './config/species/schistosoma/schistosoma_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_igenic_probs.pbl' -> './config/species/schistosoma/schistosoma_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_intron_probs.pbl' -> './config/species/schistosoma/schistosoma_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_metapars.cfg' -> './config/species/schistosoma/schistosoma_metapars.cfg' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_parameters.cfg' -> './config/species/schistosoma/schistosoma_parameters.cfg' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_parameters.cfg.opt' -> './config/species/schistosoma/schistosoma_parameters.cfg.opt' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_splicefile.txt' -> './config/species/schistosoma/schistosoma_splicefile.txt' 1354s '/usr/share/augustus/config/species/schistosoma/schistosoma_weightmatrix.txt' -> './config/species/schistosoma/schistosoma_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/schistosoma2' -> './config/species/schistosoma2' 1354s '/usr/share/augustus/config/species/schistosoma2/README.TXT' -> './config/species/schistosoma2/README.TXT' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_exon_probs.pbl' -> './config/species/schistosoma2/schistosoma2_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_igenic_probs.pbl' -> './config/species/schistosoma2/schistosoma2_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_intron_probs.pbl' -> './config/species/schistosoma2/schistosoma2_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.cfg' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.cgp.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.utr.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_parameters.cfg' -> './config/species/schistosoma2/schistosoma2_parameters.cfg' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_utr_probs.pbl' -> './config/species/schistosoma2/schistosoma2_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_weightmatrix.txt' -> './config/species/schistosoma2/schistosoma2_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe' -> './config/species/schizosaccharomyces_pombe' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg' 1354s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/scyliorhinus' -> './config/species/scyliorhinus' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_exon_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_igenic_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_intron_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.cfg' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.cgp.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.utr.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_parameters.cfg' -> './config/species/scyliorhinus/scyliorhinus_parameters.cfg' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1' -> './config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_weightmatrix.txt' -> './config/species/scyliorhinus/scyliorhinus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/sealamprey' -> './config/species/sealamprey' 1354s '/usr/share/augustus/config/species/sealamprey/sealamprey_exon_probs.pbl' -> './config/species/sealamprey/sealamprey_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/sealamprey/sealamprey_igenic_probs.pbl' -> './config/species/sealamprey/sealamprey_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/sealamprey/sealamprey_intron_probs.pbl' -> './config/species/sealamprey/sealamprey_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/sealamprey/sealamprey_metapars.cfg' -> './config/species/sealamprey/sealamprey_metapars.cfg' 1354s '/usr/share/augustus/config/species/sealamprey/sealamprey_parameters.cfg' -> './config/species/sealamprey/sealamprey_parameters.cfg' 1354s '/usr/share/augustus/config/species/sealamprey/sealamprey_weightmatrix.txt' -> './config/species/sealamprey/sealamprey_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus' -> './config/species/strongylocentrotus_purpuratus' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/README.TXT' -> './config/species/strongylocentrotus_purpuratus/README.TXT' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus' -> './config/species/sulfolobus_solfataricus' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_exon_probs.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_igenic_probs.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.cfg' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.utr.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_ovlp_len.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_weightmatrix.txt' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/sunflower' -> './config/species/sunflower' 1354s '/usr/share/augustus/config/species/sunflower/README.TXT' -> './config/species/sunflower/README.TXT' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_exon_probs.pbl' -> './config/species/sunflower/sunflower_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_igenic_probs.pbl' -> './config/species/sunflower/sunflower_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_intron_probs.pbl' -> './config/species/sunflower/sunflower_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.cfg' -> './config/species/sunflower/sunflower_metapars.cfg' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.cgp.cfg' -> './config/species/sunflower/sunflower_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.utr.cfg' -> './config/species/sunflower/sunflower_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_parameters.cfg' -> './config/species/sunflower/sunflower_parameters.cfg' 1354s '/usr/share/augustus/config/species/sunflower/sunflower_weightmatrix.txt' -> './config/species/sunflower/sunflower_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/template_prokaryotic' -> './config/species/template_prokaryotic' 1354s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_metapars.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_metapars.cfg' 1354s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl' -> './config/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_parameters.cfg' 1354s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl' -> './config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt' -> './config/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/tetrahymena' -> './config/species/tetrahymena' 1354s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_exon_probs.pbl' -> './config/species/tetrahymena/tetrahymena_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_igenic_probs.pbl' -> './config/species/tetrahymena/tetrahymena_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_intron_probs.pbl' -> './config/species/tetrahymena/tetrahymena_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_metapars.cfg' -> './config/species/tetrahymena/tetrahymena_metapars.cfg' 1354s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_parameters.cfg' -> './config/species/tetrahymena/tetrahymena_parameters.cfg' 1354s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_weightmatrix.txt' -> './config/species/tetrahymena/tetrahymena_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis' -> './config/species/thermoanaerobacter_tengcongensis' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_exon_probs.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_igenic_probs.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.cfg' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.utr.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_ovlp_len.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_ovlp_len.pbl' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl' 1354s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_weightmatrix.txt' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/tomato' -> './config/species/tomato' 1354s '/usr/share/augustus/config/species/tomato/tomato_exon_probs.pbl' -> './config/species/tomato/tomato_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/tomato/tomato_igenic_probs.pbl' -> './config/species/tomato/tomato_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/tomato/tomato_intron_probs.pbl' -> './config/species/tomato/tomato_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/tomato/tomato_metapars.cfg' -> './config/species/tomato/tomato_metapars.cfg' 1354s '/usr/share/augustus/config/species/tomato/tomato_metapars.utr.cfg' -> './config/species/tomato/tomato_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/tomato/tomato_parameters.cfg' -> './config/species/tomato/tomato_parameters.cfg' 1354s '/usr/share/augustus/config/species/tomato/tomato_utr_probs.pbl' -> './config/species/tomato/tomato_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/tomato/tomato_weightmatrix.txt' -> './config/species/tomato/tomato_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/toxoplasma' -> './config/species/toxoplasma' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_exon_probs.pbl' -> './config/species/toxoplasma/toxoplasma_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_igenic_probs.pbl' -> './config/species/toxoplasma/toxoplasma_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_intron_probs.pbl' -> './config/species/toxoplasma/toxoplasma_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_metaparameters.cfg' -> './config/species/toxoplasma/toxoplasma_metaparameters.cfg' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_parameters.cfg' -> './config/species/toxoplasma/toxoplasma_parameters.cfg' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl' -> './config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_utr_probs.pbl' -> './config/species/toxoplasma/toxoplasma_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_weightmatrix.txt' -> './config/species/toxoplasma/toxoplasma_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/tribolium2012' -> './config/species/tribolium2012' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl1' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl2' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl3' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl4' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl1' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl2' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl3' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl4' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl1' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl2' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl3' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl4' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_metapars.cfg' -> './config/species/tribolium2012/tribolium2012_metapars.cfg' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_metapars.utr.cfg' -> './config/species/tribolium2012/tribolium2012_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg' -> './config/species/tribolium2012/tribolium2012_parameters.cfg' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig2' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig3' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig4' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig5' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig6' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig7' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl' -> './config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_utr_probs.pbl' -> './config/species/tribolium2012/tribolium2012_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_weightmatrix.txt' -> './config/species/tribolium2012/tribolium2012_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/trichinella' -> './config/species/trichinella' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_exon_probs.pbl' -> './config/species/trichinella/trichinella_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_igenic_probs.pbl' -> './config/species/trichinella/trichinella_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_intron_probs.pbl' -> './config/species/trichinella/trichinella_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_metapars.cfg' -> './config/species/trichinella/trichinella_metapars.cfg' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_metapars.utr.cfg' -> './config/species/trichinella/trichinella_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_parameters.cfg' -> './config/species/trichinella/trichinella_parameters.cfg' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_utr_probs.pbl' -> './config/species/trichinella/trichinella_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/trichinella/trichinella_weightmatrix.txt' -> './config/species/trichinella/trichinella_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/ustilago' -> './config/species/ustilago' 1354s '/usr/share/augustus/config/species/ustilago/ustilago_exon_probs.pbl' -> './config/species/ustilago/ustilago_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/ustilago/ustilago_igenic_probs.pbl' -> './config/species/ustilago/ustilago_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/ustilago/ustilago_intron_probs.pbl' -> './config/species/ustilago/ustilago_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/ustilago/ustilago_parameters.cfg' -> './config/species/ustilago/ustilago_parameters.cfg' 1354s '/usr/share/augustus/config/species/ustilago/ustilago_weightmatrix.txt' -> './config/species/ustilago/ustilago_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/ustilago_maydis' -> './config/species/ustilago_maydis' 1354s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_exon_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_igenic_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_intron_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_metapars.cfg' -> './config/species/ustilago_maydis/ustilago_maydis_metapars.cfg' 1354s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg' -> './config/species/ustilago_maydis/ustilago_maydis_parameters.cfg' 1354s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_weightmatrix.txt' -> './config/species/ustilago_maydis/ustilago_maydis_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1' -> './config/species/verticillium_albo_atrum1' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_exon_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_igenic_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_intron_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.cfg' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.utr.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_utr_probs.pbl' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_weightmatrix.txt' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1' -> './config/species/verticillium_longisporum1' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_exon_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_igenic_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_intron_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.cfg' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.utr.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_utr_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_weightmatrix.txt' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/volvox' -> './config/species/volvox' 1354s '/usr/share/augustus/config/species/volvox/volvox_exon_probs.pbl' -> './config/species/volvox/volvox_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/volvox/volvox_igenic_probs.pbl' -> './config/species/volvox/volvox_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/volvox/volvox_intron_probs.pbl' -> './config/species/volvox/volvox_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/volvox/volvox_metapars.cfg' -> './config/species/volvox/volvox_metapars.cfg' 1354s '/usr/share/augustus/config/species/volvox/volvox_metapars.cgp.cfg' -> './config/species/volvox/volvox_metapars.cgp.cfg' 1354s '/usr/share/augustus/config/species/volvox/volvox_metapars.utr.cfg' -> './config/species/volvox/volvox_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/volvox/volvox_parameters.cfg' -> './config/species/volvox/volvox_parameters.cfg' 1354s '/usr/share/augustus/config/species/volvox/volvox_utr_probs.pbl' -> './config/species/volvox/volvox_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/volvox/volvox_weightmatrix.txt' -> './config/species/volvox/volvox_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/wheat' -> './config/species/wheat' 1354s '/usr/share/augustus/config/species/wheat/README.txt' -> './config/species/wheat/README.txt' 1354s '/usr/share/augustus/config/species/wheat/wheat_exon_probs.pbl' -> './config/species/wheat/wheat_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/wheat/wheat_igenic_probs.pbl' -> './config/species/wheat/wheat_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/wheat/wheat_intron_probs.pbl' -> './config/species/wheat/wheat_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/wheat/wheat_parameters.cfg' -> './config/species/wheat/wheat_parameters.cfg' 1354s '/usr/share/augustus/config/species/wheat/wheat_utr_probs.pbl' -> './config/species/wheat/wheat_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/wheat/wheat_weightmatrix.txt' -> './config/species/wheat/wheat_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica' -> './config/species/yarrowia_lipolytica' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_exon_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_igenic_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_intron_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.cfg' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.utr.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_utr_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_utr_probs.pbl' 1354s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_weightmatrix.txt' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_weightmatrix.txt' 1354s '/usr/share/augustus/config/species/zebrafish' -> './config/species/zebrafish' 1354s '/usr/share/augustus/config/species/zebrafish/README.TXT' -> './config/species/zebrafish/README.TXT' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_exon_probs.pbl' -> './config/species/zebrafish/zebrafish_exon_probs.pbl' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_exon_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_exon_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_igenic_probs.pbl' -> './config/species/zebrafish/zebrafish_igenic_probs.pbl' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_intron_probs.pbl' -> './config/species/zebrafish/zebrafish_intron_probs.pbl' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_intron_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_intron_probs.pbl.HMM' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_metapars.cfg' -> './config/species/zebrafish/zebrafish_metapars.cfg' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_metapars.utr.cfg' -> './config/species/zebrafish/zebrafish_metapars.utr.cfg' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_parameters.cfg' -> './config/species/zebrafish/zebrafish_parameters.cfg' 1354s '/usr/share/augustus/config/species/zebrafish/zebrafish_weightmatrix.txt' -> './config/species/zebrafish/zebrafish_weightmatrix.txt' 1354s Will create parameters for a EUKARYOTIC species! 1354s creating directory /tmp/tmp.GacanNxJov/config/species/test/ ... 1354s creating /tmp/tmp.GacanNxJov/config/species/test/test_parameters.cfg ... 1354s creating /tmp/tmp.GacanNxJov/config/species/test/test_weightmatrix.txt ... 1354s creating /tmp/tmp.GacanNxJov/config/species/test/test_metapars.cfg ... 1354s The necessary files for training test have been created. 1354s Now, either run etraining or optimize_parameters.pl with --species=test. 1354s etraining quickly estimates the parameters from a file with training genes. 1354s optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters. 1354s 1354s # Read in 1 genbank sequences. 1354s Quantiles of the GC contents in the training set: 1354s 0% 0.402 1354s 5% 0.402 10% 0.402 1354s 15% 0.402 20% 0.402 1354s 25% 0.402 30% 0.402 1354s 35% 0.402 40% 0.402 1354s 45% 0.402 50% 0.402 1354s 55% 0.402 60% 0.402 1354s 65% 0.402 70% 0.402 1354s 75% 0.402 80% 0.402 1354s 85% 0.402 90% 0.402 1354s 95% 0.402 100% 0.402 1354s HMM-training the parameters... 1354s i= 0 bc= (0.237, 0.263, 0.263, 0.237) 1354s ** building model for exons *EXON* 1354s start codon frequencies: ATG(1) 1354s # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) 1354s number of bases in the reading frames: 570 571 570 1354s --- frame = 0 --- minPatSum = 233 1354s --- frame = 1 --- minPatSum = 233 1354s --- frame = 2 --- minPatSum = 233 1354s --- initial frame = 0 --- minPatSum = 233 1354s --- initial frame = 1 --- minPatSum = 233 1354s --- initial frame = 2 --- minPatSum = 233 1354s --- internal exon terminal frame = 0 --- minPatSum = 233 1354s --- internal exon terminal frame = 1 --- minPatSum = 233 1354s --- internal exon terminal frame = 2 --- minPatSum = 233 1354s single, initial, internal, terminal mean exon lengths : 1354s n.a. 627 191 7 1354s single exon : 0 1354s initial exon 0 : 1 1354s initial exon 1 : 0 1354s initial exon 2 : 0 1354s internal exon 0 : 3 1354s internal exon 1 : 0 1354s internal exon 2 : 3 1354s terminal exon : 1 1354s Frequency of stop codons: 1354s tag: 0 (0) 1354s taa: 1 (1) 1354s tga: 0 (0) 1354s end *EXON* 1354s Storing parameters to file... 1354s Writing exon model parameters [1] to file /tmp/tmp.GacanNxJov/config/species/test/test_exon_probs.pbl. 1354s # This output was generated with AUGUSTUS (version 3.5.0). 1354s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 1354s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 1354s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 1354s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 1354s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 1354s # No extrinsic information on sequences given. 1354s # Sources of extrinsic information: M RM 1354s # Initializing the parameters using config directory /tmp/tmp.GacanNxJov/config/ ... 1354s # test version. Using default transition matrix. 1354s # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) 1354s # Looks like /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/example.fa is in fasta format. 1354s # We have hints for 0 sequences and for 0 of the sequences in the input set. 1354s # 1354s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 1354s # 1354s # Predicted genes for sequence number 1 on both strands 1354s # start gene g1 1354s HS04636 AUGUSTUS gene 1 1163 0.06 + . g1 1354s HS04636 AUGUSTUS transcript 1 1163 0.06 + . g1.t1 1354s HS04636 AUGUSTUS intron 1 350 0.36 + . transcript_id "g1.t1"; gene_id "g1"; 1354s HS04636 AUGUSTUS intron 673 856 0.17 + . transcript_id "g1.t1"; gene_id "g1"; 1354s HS04636 AUGUSTUS CDS 351 672 0.11 + 2 transcript_id "g1.t1"; gene_id "g1"; 1354s HS04636 AUGUSTUS CDS 857 1163 0.32 + 1 transcript_id "g1.t1"; gene_id "g1"; 1354s HS04636 AUGUSTUS stop_codon 1161 1163 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1354s # protein sequence = [VQTRHGGGGGRGDSLRPRTSGPLRFLERKPSVLLPSPGIPSKAISPELALGSARAKTAKKKRHLAETCAPGAVELGEE 1354s # REGSDRRVGTTPSAPKLGQLPGFPIFSFPVRSTSRNSSAAPPSAPQPDALRQQSLPPRRALPAARMLARALLLCAVLALSHTGEYLAPRTGDSGSTHP 1354s # GRVSALTSWVYPSTPTSLRIEKLRDLGKSLDR] 1354s # Evidence for and against this transcript: 1354s # % of transcript supported by hints (any source): 0 1354s # CDS exons: 0/2 1354s # CDS introns: 0/2 1354s # 5'UTR exons and introns: 0/0 1354s # 3'UTR exons and introns: 0/0 1354s # hint groups fully obeyed: 0 1354s # incompatible hint groups: 0 1354s # end gene g1 1354s ### 1354s # 1354s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 1354s # 1354s # Predicted genes for sequence number 2 on both strands 1354s # start gene g2 1354s HS08198 AUGUSTUS gene 1 2271 0.02 - . g2 1354s HS08198 AUGUSTUS transcript 1 2271 0.02 - . g2.t1 1354s HS08198 AUGUSTUS intron 1 112 0.38 - . transcript_id "g2.t1"; gene_id "g2"; 1354s HS08198 AUGUSTUS intron 950 1314 0.05 - . transcript_id "g2.t1"; gene_id "g2"; 1354s HS08198 AUGUSTUS intron 2041 2116 0.39 - . transcript_id "g2.t1"; gene_id "g2"; 1354s HS08198 AUGUSTUS CDS 113 949 0.16 - 1 transcript_id "g2.t1"; gene_id "g2"; 1354s HS08198 AUGUSTUS CDS 1315 2040 0.26 - 1 transcript_id "g2.t1"; gene_id "g2"; 1355s HS08198 AUGUSTUS CDS 2117 2271 0.39 - 0 transcript_id "g2.t1"; gene_id "g2"; 1355s HS08198 AUGUSTUS start_codon 2269 2271 . - 0 transcript_id "g2.t1"; gene_id "g2"; 1355s # protein sequence = [MAYAREDLPSQIPRAEIGPVTLRGLQPTGSAGLLKRRGGGREGLGGTGAGPDRQKIPCPGWQGPDLRLVSRRTGSGHP 1355s # TGGVVSRGTDFSALELCAGLTSSLLQQRRDSAGASGPPHHAAMLAPAVHSPSRTWNWSAASQKPGAPRQGSGWTSAREWGWLSWGPAGDTHRTWGSRR 1355s # SGPQSGGPPGPAAQTHSGPSRSQGASGLQGRQGSWGPGTRRRGGLWERGLCVPCPSGPSSLLPHQACLSLLPGPLLSRRIRMGERKCVPMAHPAPRGG 1355s # PVSVQSLSACLVTEAGPHIPPGAERRVGVRVQGCSGTHSFRKVLTAMAVPWGATCSVVASARWPCSCRKRQAEPTATRSQVPANWGQTMGELEGTVGG 1355s # PLTCFPLHPPQLHLLPSPPQQLLPVSLYPSHNFYLPPSTPPNFYLLRIKIGLGLDGADGGCGPAWPLRLLAQRASCQEQSQEGRSPRGQHGGGSRVAG 1355s # LWEAKGSTTKSQDRVYSAVTEPSPGSPCPSVASPPPTSSLLVSLASICTSWQGLAPCPMYKVRVDLWLFIHFSCTPDFHRQSLALYTLSSLNHHPVVL 1355s # SPWP] 1355s # Evidence for and against this transcript: 1355s # % of transcript supported by hints (any source): 0 1355s # CDS exons: 0/3 1355s # CDS introns: 0/3 1355s # 5'UTR exons and introns: 0/0 1355s # 3'UTR exons and introns: 0/0 1355s # hint groups fully obeyed: 0 1355s # incompatible hint groups: 0 1355s # end gene g2 1355s ### 1355s # command line: 1355s # augustus --species=test /tmp/autopkgtest.3mwyiF/build.uZ0/src/examples/example.fa 1355s autopkgtest [01:07:49]: test test-example-with-training: -----------------------] 1356s autopkgtest [01:07:50]: test test-example-with-training: - - - - - - - - - - results - - - - - - - - - - 1356s test-example-with-training PASS 1356s autopkgtest [01:07:50]: @@@@@@@@@@@@@@@@@@@@ summary 1356s test-example PASS 1356s test-example-with-training PASS 1371s Creating nova instance adt-noble-arm64-augustus-20240419-004514-juju-7f2275-prod-proposed-migration-environment-2-a79366b1-670c-4fc1-a654-1dda5dc57ca6 from image adt/ubuntu-noble-arm64-server-20240417.img (UUID 95ae19fe-c66c-4497-b9b8-2fcb73a387ab)...