0s autopkgtest [11:39:37]: starting date: 2024-03-13 0s autopkgtest [11:39:37]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [11:39:37]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2aoisnlw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sqlite3,src:readline --apt-upgrade augustus --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sqlite3/3.45.1-1ubuntu1 readline/8.2-3.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-13.secgroup --name adt-noble-s390x-augustus-20240313-113937-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://ftpmaster.internal/ubuntu/ 323s autopkgtest [11:45:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 323s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 324s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [40.4 kB] 324s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2792 kB] 325s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 325s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [448 kB] 325s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [585 kB] 325s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 325s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 325s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 325s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3020 kB] 326s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 326s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [25.3 kB] 326s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 327s Fetched 7044 kB in 3s (2222 kB/s) 327s Reading package lists... 332s Reading package lists... 332s Building dependency tree... 332s Reading state information... 332s Calculating upgrade... 332s The following packages will be upgraded: 332s cloud-init gdisk libsqlite3-0 readline-common 332s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 332s Need to get 1662 kB of archives. 332s After this operation, 64.5 kB of additional disk space will be used. 332s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu1 [747 kB] 333s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-3.1 [56.4 kB] 333s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.1-0ubuntu1 [597 kB] 333s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x gdisk s390x 1.0.10-1 [262 kB] 333s Preconfiguring packages ... 333s Fetched 1662 kB in 1s (2219 kB/s) 333s (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 ... 52188 files and directories currently installed.) 333s Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu1_s390x.deb ... 333s Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu1) over (3.45.1-1) ... 333s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 333s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 333s Preparing to unpack .../cloud-init_24.1.1-0ubuntu1_all.deb ... 334s Unpacking cloud-init (24.1.1-0ubuntu1) over (24.1-0ubuntu1) ... 334s Preparing to unpack .../gdisk_1.0.10-1_s390x.deb ... 334s Unpacking gdisk (1.0.10-1) over (1.0.9-2.1) ... 334s Setting up cloud-init (24.1.1-0ubuntu1) ... 335s Setting up libsqlite3-0:s390x (3.45.1-1ubuntu1) ... 335s Setting up gdisk (1.0.10-1) ... 335s Setting up readline-common (8.2-3.1) ... 335s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 335s Processing triggers for man-db (2.12.0-3) ... 336s Processing triggers for install-info (7.1-3) ... 336s Processing triggers for libc-bin (2.39-0ubuntu2) ... 336s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 336s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 336s Reading package lists... 336s Building dependency tree... 336s Reading state information... 336s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 337s Unknown architecture, assuming PC-style ttyS0 337s sh: Attempting to set up Debian/Ubuntu apt sources automatically 337s sh: Distribution appears to be Ubuntu 340s Reading package lists... 340s Building dependency tree... 340s Reading state information... 340s eatmydata is already the newest version (131-1). 340s dbus is already the newest version (1.14.10-4ubuntu1). 340s dbus set to manually installed. 340s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 340s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s Reading package lists... 340s Building dependency tree... 340s Reading state information... 340s rng-tools-debian is already the newest version (2.4). 340s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 341s Reading package lists... 341s Building dependency tree... 341s Reading state information... 341s haveged is already the newest version (1.9.14-1ubuntu1). 341s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 341s Reading package lists... 341s Building dependency tree... 341s Reading state information... 341s The following packages will be REMOVED: 341s cloud-init* python3-configobj* python3-debconf* 342s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 342s After this operation, 3252 kB disk space will be freed. 342s (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 ... 52188 files and directories currently installed.) 342s Removing cloud-init (24.1.1-0ubuntu1) ... 342s Removing python3-configobj (5.0.8-3) ... 342s Removing python3-debconf (1.5.86) ... 342s Processing triggers for man-db (2.12.0-3) ... 342s (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 ... 51799 files and directories currently installed.) 342s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 343s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 343s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 343s Reading package lists... 344s Building dependency tree... 344s Reading state information... 344s linux-generic is already the newest version (6.8.0-11.11+1). 344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 344s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 344s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 344s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 345s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 345s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 348s Reading package lists... 348s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 348s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Reading package lists... 348s Building dependency tree...Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 348s 348s Reading state information... 348s Calculating upgrade... 348s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 348s Reading package lists... 348s Building dependency tree... 348s Reading state information... 349s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 349s autopkgtest [11:45:26]: rebooting testbed after setup commands that affected boot 364s autopkgtest [11:45:41]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 365s autopkgtest [11:45:42]: testbed dpkg architecture: s390x 366s autopkgtest [11:45:43]: @@@@@@@@@@@@@@@@@@@@ apt-source augustus 367s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 367s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 367s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s Get:1 http://ftpmaster.internal/ubuntu noble/universe augustus 3.5.0+dfsg-4build1 (dsc) [2371 B] 381s Get:2 http://ftpmaster.internal/ubuntu noble/universe augustus 3.5.0+dfsg-4build1 (tar) [152 MB] 381s Get:3 http://ftpmaster.internal/ubuntu noble/universe augustus 3.5.0+dfsg-4build1 (diff) [20.3 kB] 381s gpgv: Signature made Tue Dec 19 15:00:38 2023 UTC 381s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 381s gpgv: Can't check signature: No public key 381s dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-4build1.dsc: no acceptable signature found 395s autopkgtest [11:46:12]: testing package augustus version 3.5.0+dfsg-4build1 395s autopkgtest [11:46:12]: build not needed 1078s autopkgtest [11:57:35]: test test-example: preparing testbed 1080s Reading package lists... 1080s Building dependency tree... 1080s Reading state information... 1080s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 1080s Starting 2 pkgProblemResolver with broken count: 0 1080s Done 1080s Done 1080s Starting pkgProblemResolver with broken count: 0 1080s Starting 2 pkgProblemResolver with broken count: 0 1080s Done 1081s The following additional packages will be installed: 1081s augustus augustus-data augustus-doc libbamtools2.5.2 1081s libboost-iostreams1.83.0 libcolamd3 libdeflate0 libgomp1 libgsl27 1081s libgslcblas0 libhts3 libhtscodecs2 libmysql++3v5 libmysqlclient21 1081s libsuitesparseconfig7 mysql-common 1081s Suggested packages: 1081s cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl 1081s libyaml-perl libdbd-mysql-perl python3-biopython gsl-ref-psdoc | gsl-doc-pdf 1081s | gsl-doc-info | gsl-ref-html 1081s Recommended packages: 1081s samtools 1081s The following NEW packages will be installed: 1081s augustus augustus-data augustus-doc libbamtools2.5.2 1081s libboost-iostreams1.83.0 libcolamd3 libdeflate0 libgomp1 libgsl27 1081s libgslcblas0 libhts3 libhtscodecs2 libmysql++3v5 libmysqlclient21 1081s libsuitesparseconfig7 mysql-common 1081s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 1081s 1 not fully installed or removed. 1081s Need to get 52.0 MB of archives. 1081s After this operation, 315 MB of additional disk space will be used. 1081s Get:1 http://ftpmaster.internal/ubuntu noble/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-4 [134 kB] 1082s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libboost-iostreams1.83.0 s390x 1.83.0-2ubuntu1 [340 kB] 1083s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 1083s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libsuitesparseconfig7 s390x 1:7.6.1+dfsg-1 [12.7 kB] 1083s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libcolamd3 s390x 1:7.6.1+dfsg-1 [23.4 kB] 1083s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu1 [147 kB] 1084s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu1 [1069 kB] 1086s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 1086s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 1086s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 1086s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x mysql-common all 5.8+1.1.0 [6626 B] 1086s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libmysqlclient21 s390x 8.0.36-1 [1325 kB] 1088s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x libmysql++3v5 s390x 3.2.5-2.1 [97.6 kB] 1088s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x augustus-data all 3.5.0+dfsg-4build1 [22.8 MB] 1094s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x augustus s390x 3.5.0+dfsg-4build1 [1853 kB] 1094s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x augustus-doc all 3.5.0+dfsg-4build1 [23.5 MB] 1096s Fetched 52.0 MB in 15s (3366 kB/s) 1096s Selecting previously unselected package libbamtools2.5.2:s390x. 1096s (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 ... 51744 files and directories currently installed.) 1096s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-4_s390x.deb ... 1096s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 1096s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 1096s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2ubuntu1_s390x.deb ... 1096s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 1096s Selecting previously unselected package libgomp1:s390x. 1096s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 1096s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 1096s Selecting previously unselected package libsuitesparseconfig7:s390x. 1096s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1_s390x.deb ... 1096s Unpacking libsuitesparseconfig7:s390x (1:7.6.1+dfsg-1) ... 1097s Selecting previously unselected package libcolamd3:s390x. 1097s Preparing to unpack .../04-libcolamd3_1%3a7.6.1+dfsg-1_s390x.deb ... 1097s Unpacking libcolamd3:s390x (1:7.6.1+dfsg-1) ... 1097s Selecting previously unselected package libgslcblas0:s390x. 1097s Preparing to unpack .../05-libgslcblas0_2.7.1+dfsg-6ubuntu1_s390x.deb ... 1097s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 1097s Selecting previously unselected package libgsl27:s390x. 1097s Preparing to unpack .../06-libgsl27_2.7.1+dfsg-6ubuntu1_s390x.deb ... 1097s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 1097s Selecting previously unselected package libdeflate0:s390x. 1097s Preparing to unpack .../07-libdeflate0_1.19-1_s390x.deb ... 1097s Unpacking libdeflate0:s390x (1.19-1) ... 1097s Selecting previously unselected package libhtscodecs2:s390x. 1097s Preparing to unpack .../08-libhtscodecs2_1.6.0-1_s390x.deb ... 1097s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 1097s Selecting previously unselected package libhts3:s390x. 1097s Preparing to unpack .../09-libhts3_1.18+ds-1_s390x.deb ... 1097s Unpacking libhts3:s390x (1.18+ds-1) ... 1097s Selecting previously unselected package mysql-common. 1097s Preparing to unpack .../10-mysql-common_5.8+1.1.0_all.deb ... 1097s Unpacking mysql-common (5.8+1.1.0) ... 1097s Selecting previously unselected package libmysqlclient21:s390x. 1097s Preparing to unpack .../11-libmysqlclient21_8.0.36-1_s390x.deb ... 1097s Unpacking libmysqlclient21:s390x (8.0.36-1) ... 1097s Selecting previously unselected package libmysql++3v5:s390x. 1097s Preparing to unpack .../12-libmysql++3v5_3.2.5-2.1_s390x.deb ... 1097s Unpacking libmysql++3v5:s390x (3.2.5-2.1) ... 1097s Selecting previously unselected package augustus-data. 1097s Preparing to unpack .../13-augustus-data_3.5.0+dfsg-4build1_all.deb ... 1097s Unpacking augustus-data (3.5.0+dfsg-4build1) ... 1098s Selecting previously unselected package augustus. 1098s Preparing to unpack .../14-augustus_3.5.0+dfsg-4build1_s390x.deb ... 1098s Unpacking augustus (3.5.0+dfsg-4build1) ... 1098s Selecting previously unselected package augustus-doc. 1098s Preparing to unpack .../15-augustus-doc_3.5.0+dfsg-4build1_all.deb ... 1098s Unpacking augustus-doc (3.5.0+dfsg-4build1) ... 1099s Setting up libhtscodecs2:s390x (1.6.0-1) ... 1099s Setting up mysql-common (5.8+1.1.0) ... 1099s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 1099s Setting up libmysqlclient21:s390x (8.0.36-1) ... 1099s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 1099s Setting up libdeflate0:s390x (1.19-1) ... 1099s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 1099s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 1099s Setting up augustus-data (3.5.0+dfsg-4build1) ... 1099s Setting up augustus-doc (3.5.0+dfsg-4build1) ... 1099s Setting up libboost-iostreams1.83.0:s390x (1.83.0-2ubuntu1) ... 1099s Setting up libmysql++3v5:s390x (3.2.5-2.1) ... 1099s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-4) ... 1099s Setting up libsuitesparseconfig7:s390x (1:7.6.1+dfsg-1) ... 1099s Setting up libhts3:s390x (1.18+ds-1) ... 1099s Setting up libcolamd3:s390x (1:7.6.1+dfsg-1) ... 1099s Setting up augustus (3.5.0+dfsg-4build1) ... 1099s Setting up autopkgtest-satdep (0) ... 1099s Processing triggers for man-db (2.12.0-3) ... 1100s Processing triggers for libc-bin (2.39-0ubuntu2) ... 1102s (Reading database ... 54004 files and directories currently installed.) 1102s Removing autopkgtest-satdep (0) ... 1103s autopkgtest [11:58:00]: test test-example: [----------------------- 1104s # This output was generated with AUGUSTUS (version 3.5.0). 1104s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 1104s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 1104s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 1104s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 1104s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 1104s # No extrinsic information on sequences given. 1104s # Sources of extrinsic information: M RM 1104s # Initializing the parameters using config directory /usr/share/augustus/config/ ... 1104s # human version. Using species specific transition matrix: /usr/share/augustus/config/species/human/human_trans_shadow_partial_utr.pbl 1104s # Looks like /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/example.fa is in fasta format. 1104s # We have hints for 0 sequences and for 0 of the sequences in the input set. 1104s # 1104s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 1104s # 1104s # Predicted genes for sequence number 1 on both strands 1104s # start gene g1 1104s HS04636 AUGUSTUS gene 836 8857 1 + . g1 1104s HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 1104s HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1"; 1104s # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 1104s # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 1104s # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 1104s # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 1104s # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 1104s # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV 1104s # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] 1104s # Evidence for and against this transcript: 1104s # % of transcript supported by hints (any source): 0 1104s # CDS exons: 0/10 1104s # CDS introns: 0/9 1104s # 5'UTR exons and introns: 0/1 1104s # 3'UTR exons and introns: 0/1 1104s # hint groups fully obeyed: 0 1104s # incompatible hint groups: 0 1104s # end gene g1 1104s ### 1104s # 1104s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 1104s # 1104s # Predicted genes for sequence number 2 on both strands 1104s # start gene g2 1104s HS08198 AUGUSTUS gene 86 2344 1 + . g2 1104s HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1 1104s HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1104s HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2"; 1104s # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC 1104s # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] 1104s # Evidence for and against this transcript: 1104s # % of transcript supported by hints (any source): 0 1104s # CDS exons: 0/5 1104s # CDS introns: 0/5 1104s # 5'UTR exons and introns: 0/1 1104s # 3'UTR exons and introns: 0/0 1104s # hint groups fully obeyed: 0 1104s # incompatible hint groups: 0 1104s # end gene g2 1104s ### 1104s # command line: 1104s # augustus --species=human --UTR=on /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/example.fa 1104s # This output was generated with AUGUSTUS (version 3.5.0). 1104s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 1104s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 1104s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 1104s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 1104s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 1104s # Sources of extrinsic information: M P E RM 1104s # Setting 1group1gene for E. 1104s # reading in the file /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/hints.gff ... 1104s # Have extrinsic information about 2 sequences (in the specified range). 1104s # Initializing the parameters using config directory /usr/share/augustus/config/ ... 1104s # human version. Using default transition matrix. 1104s # Looks like /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/example.fa is in fasta format. 1104s # We have hints for 2 sequences and for 2 of the sequences in the input set. 1104s # 1104s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 1104s # 1104s # Predicted genes for sequence number 1 on both strands 1104s # start gene g1 1104s HS04636 AUGUSTUS gene 966 7633 1 + . g1 1104s HS04636 AUGUSTUS transcript 966 7633 . + . g1.t1 1104s HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 6494 6554 . + 2 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS CDS 7627 7633 . + 1 transcript_id "g1.t1"; gene_id "g1"; 1104s HS04636 AUGUSTUS stop_codon 7631 7633 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1104s # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL 1104s # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD 1104s # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG 1104s # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH 1104s # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE 1104s # KEMSAELEALYGDIDAVELV] 1104s # Evidence for and against this transcript: 1104s # % of transcript supported by hints (any source): 4.76 1104s # CDS exons: 1/11 1104s # P: 1 1104s # CDS introns: 0/10 1104s # 5'UTR exons and introns: 0/0 1104s # 3'UTR exons and introns: 0/0 1104s # hint groups fully obeyed: 2 1104s # E: 1 1104s # P: 1 1104s # incompatible hint groups: 2 1104s # M: 1 1104s # P: 1 1104s # end gene g1 1104s ### 1104s # 1104s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 1104s # 1104s # Predicted genes for sequence number 2 on both strands 1105s # start gene g2 1105s HS08198 AUGUSTUS gene 445 2344 1 + . g2 1105s HS08198 AUGUSTUS transcript 445 2344 . + . g2.t1 1105s HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1105s HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1105s HS08198 AUGUSTUS CDS 758 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; 1105s HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; 1105s HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1105s HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; 1105s # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVA 1105s # PQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTE 1105s # DQIFYFPKY] 1105s # Evidence for and against this transcript: 1105s # % of transcript supported by hints (any source): 10 1105s # CDS exons: 0/5 1105s # CDS introns: 1/5 1105s # M: 1 1105s # 5'UTR exons and introns: 0/0 1105s # 3'UTR exons and introns: 0/0 1105s # hint groups fully obeyed: 2 1105s # E: 1 1105s # M: 1 1105s # incompatible hint groups: 1 1105s # M: 1 1105s # end gene g2 1105s ### 1105s # command line: 1105s # augustus --species=human --hintsfile=/tmp/autopkgtest.vkTNZz/build.LDj/src/examples/hints.gff --extrinsicCfgFile=/usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/example.fa 1105s autopkgtest [11:58:02]: test test-example: -----------------------] 1105s autopkgtest [11:58:02]: test test-example: - - - - - - - - - - results - - - - - - - - - - 1105s test-example PASS 1106s autopkgtest [11:58:03]: test test-example-with-training: preparing testbed 1108s Reading package lists... 1108s Building dependency tree... 1108s Reading state information... 1108s Starting pkgProblemResolver with broken count: 0 1108s Starting 2 pkgProblemResolver with broken count: 0 1108s Done 1108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1108s 1 not fully installed or removed. 1108s After this operation, 0 B of additional disk space will be used. 1108s Setting up autopkgtest-satdep (0) ... 1111s (Reading database ... 54004 files and directories currently installed.) 1111s Removing autopkgtest-satdep (0) ... 1112s autopkgtest [11:58:09]: test test-example-with-training: [----------------------- 1112s '/usr/share/augustus/config' -> './config' 1112s '/usr/share/augustus/config/cgp' -> './config/cgp' 1112s '/usr/share/augustus/config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg' -> './config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg' 1112s '/usr/share/augustus/config/cgp/log_reg_parameters_arabidopsis.cfg' -> './config/cgp/log_reg_parameters_arabidopsis.cfg' 1112s '/usr/share/augustus/config/cgp/log_reg_parameters_default.cfg' -> './config/cgp/log_reg_parameters_default.cfg' 1112s '/usr/share/augustus/config/cgp/log_reg_parameters_fly.cfg' -> './config/cgp/log_reg_parameters_fly.cfg' 1112s '/usr/share/augustus/config/cgp/log_reg_parameters_human.cfg' -> './config/cgp/log_reg_parameters_human.cfg' 1112s '/usr/share/augustus/config/cgp/log_reg_parameters_primates.cfg' -> './config/cgp/log_reg_parameters_primates.cfg' 1112s '/usr/share/augustus/config/cgp/log_reg_parameters_s_aureus.cfg' -> './config/cgp/log_reg_parameters_s_aureus.cfg' 1112s '/usr/share/augustus/config/extrinsic' -> './config/extrinsic' 1112s '/usr/share/augustus/config/extrinsic/extrinsic-cgp.cfg' -> './config/extrinsic/extrinsic-cgp.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.E.XNT.cfg' -> './config/extrinsic/extrinsic.E.XNT.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.E.cfg' -> './config/extrinsic/extrinsic.E.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg' -> './config/extrinsic/extrinsic.M.RM.E.W.P.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg' -> './config/extrinsic/extrinsic.M.RM.E.W.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.M.RM.PB.cfg' -> './config/extrinsic/extrinsic.M.RM.PB.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.ME.cfg' -> './config/extrinsic/extrinsic.ME.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.MEMS.cfg' -> './config/extrinsic/extrinsic.MEMS.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.MP.cfg' -> './config/extrinsic/extrinsic.MP.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg' -> './config/extrinsic/extrinsic.MPE.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.MT.cfg' -> './config/extrinsic/extrinsic.MT.cfg' 1112s '/usr/share/augustus/config/extrinsic/extrinsic.cfg' -> './config/extrinsic/extrinsic.cfg' 1112s '/usr/share/augustus/config/model' -> './config/model' 1112s '/usr/share/augustus/config/model/constraints_shadow_partial.txt' -> './config/model/constraints_shadow_partial.txt' 1112s '/usr/share/augustus/config/model/constraints_shadow_partial_utr.txt' -> './config/model/constraints_shadow_partial_utr.txt' 1112s '/usr/share/augustus/config/model/ovlp_len.pbl' -> './config/model/ovlp_len.pbl' 1112s '/usr/share/augustus/config/model/ovlp_len_archaea.pbl' -> './config/model/ovlp_len_archaea.pbl' 1112s '/usr/share/augustus/config/model/states_shadow.cfg' -> './config/model/states_shadow.cfg' 1112s '/usr/share/augustus/config/model/states_shadow_2igenic.cfg' -> './config/model/states_shadow_2igenic.cfg' 1112s '/usr/share/augustus/config/model/states_shadow_bacterium.cfg' -> './config/model/states_shadow_bacterium.cfg' 1112s '/usr/share/augustus/config/model/states_shadow_intronless.cfg' -> './config/model/states_shadow_intronless.cfg' 1112s '/usr/share/augustus/config/model/states_shadow_utr.cfg' -> './config/model/states_shadow_utr.cfg' 1112s '/usr/share/augustus/config/model/states_shadow_utr_nc.cfg' -> './config/model/states_shadow_utr_nc.cfg' 1112s '/usr/share/augustus/config/model/states_singlestrand.cfg' -> './config/model/states_singlestrand.cfg' 1112s '/usr/share/augustus/config/model/states_singlestrand_2igenic.cfg' -> './config/model/states_singlestrand_2igenic.cfg' 1112s '/usr/share/augustus/config/model/trans_shadow_atleastone.pbl' -> './config/model/trans_shadow_atleastone.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_bacterium.pbl' -> './config/model/trans_shadow_bacterium.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_complete.pbl' -> './config/model/trans_shadow_complete.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_complete_utr.pbl' -> './config/model/trans_shadow_complete_utr.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_exactlyone.pbl' -> './config/model/trans_shadow_exactlyone.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_intronless.pbl' -> './config/model/trans_shadow_intronless.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_partial.pbl' -> './config/model/trans_shadow_partial.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_partial_utr.pbl' -> './config/model/trans_shadow_partial_utr.pbl' 1112s '/usr/share/augustus/config/model/trans_shadow_partial_utr_nc.pbl' -> './config/model/trans_shadow_partial_utr_nc.pbl' 1112s '/usr/share/augustus/config/model/trans_singlestrand_atleastone.pbl' -> './config/model/trans_singlestrand_atleastone.pbl' 1112s '/usr/share/augustus/config/model/trans_singlestrand_complete.pbl' -> './config/model/trans_singlestrand_complete.pbl' 1112s '/usr/share/augustus/config/model/trans_singlestrand_exactlyone.pbl' -> './config/model/trans_singlestrand_exactlyone.pbl' 1112s '/usr/share/augustus/config/model/trans_singlestrand_partial.pbl' -> './config/model/trans_singlestrand_partial.pbl' 1112s '/usr/share/augustus/config/parameters' -> './config/parameters' 1112s '/usr/share/augustus/config/parameters/AUG_CMDLN_PARAMETERS.md' -> './config/parameters/AUG_CMDLN_PARAMETERS.md' 1112s '/usr/share/augustus/config/parameters/aug_cmdln_parameters.json' -> './config/parameters/aug_cmdln_parameters.json' 1112s '/usr/share/augustus/config/profile' -> './config/profile' 1112s '/usr/share/augustus/config/profile/blosum55.qij' -> './config/profile/blosum55.qij' 1112s '/usr/share/augustus/config/profile/blosum62.qij' -> './config/profile/blosum62.qij' 1112s '/usr/share/augustus/config/profile/default.qij' -> './config/profile/default.qij' 1112s '/usr/share/augustus/config/species' -> './config/species' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae' -> './config/species/Anopheles_gambiae' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt' -> './config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Anopheles_gambiae/README.txt' -> './config/species/Anopheles_gambiae/README.txt' 1112s '/usr/share/augustus/config/species/Argopecten_irradians' -> './config/species/Argopecten_irradians' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl' -> './config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg' -> './config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt' -> './config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Argopecten_irradians/README.txt' -> './config/species/Argopecten_irradians/README.txt' 1112s '/usr/share/augustus/config/species/Aurelia_aurita' -> './config/species/Aurelia_aurita' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl' -> './config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg' -> './config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt' -> './config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Aurelia_aurita/README.txt' -> './config/species/Aurelia_aurita/README.txt' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos' -> './config/species/Bathycoccus_prasinos' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt' -> './config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Bathycoccus_prasinos/README.txt' -> './config/species/Bathycoccus_prasinos/README.txt' 1112s '/usr/share/augustus/config/species/Berviolum_minutum' -> './config/species/Berviolum_minutum' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl' -> './config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg' -> './config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt' -> './config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Berviolum_minutum/README.txt' -> './config/species/Berviolum_minutum/README.txt' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae' -> './config/species/Branchiostoma_floridae' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt' -> './config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Branchiostoma_floridae/README.txt' -> './config/species/Branchiostoma_floridae/README.txt' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana' -> './config/species/Cassiopea_xamachana' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg' 1112s '/usr/share/augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt' -> './config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma' -> './config/species/Chlamydomonas_eustigma' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt' -> './config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Chlamydomonas_eustigma/README.txt' -> './config/species/Chlamydomonas_eustigma/README.txt' 1112s '/usr/share/augustus/config/species/Chloropicon_primus' -> './config/species/Chloropicon_primus' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl' -> './config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg' -> './config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt' -> './config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt' 1112s '/usr/share/augustus/config/species/Chloropicon_primus/README.txt' -> './config/species/Chloropicon_primus/README.txt' 1112s '/usr/share/augustus/config/species/Chrysaora_chesapeakei' -> './config/species/Chrysaora_chesapeakei' 1112s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl' 1112s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl' 1112s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg' 1113s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg' 1113s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt' -> './config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Chrysaora_chesapeakei/README.txt' -> './config/species/Chrysaora_chesapeakei/README.txt' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus' -> './config/species/Conidiobolus_coronatus' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt' -> './config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis' -> './config/species/Cryptosporidium_hominis' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt' -> './config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Cryptosporidium_hominis/README.txt' -> './config/species/Cryptosporidium_hominis/README.txt' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica' -> './config/species/Cyclotella_cryptica' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt' -> './config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Cyclotella_cryptica/README.txt' -> './config/species/Cyclotella_cryptica/README.txt' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata' -> './config/species/Dermasterias_imbricata' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt' -> './config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Dermasterias_imbricata/README.txt' -> './config/species/Dermasterias_imbricata/README.txt' 1113s '/usr/share/augustus/config/species/Dunaliella_salina' -> './config/species/Dunaliella_salina' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_intron_probs.pbl' -> './config/species/Dunaliella_salina/Dunaliella_salina_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg' -> './config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/Dunaliella_salina_weightmatrix.txt' -> './config/species/Dunaliella_salina/Dunaliella_salina_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Dunaliella_salina/README.txt' -> './config/species/Dunaliella_salina/README.txt' 1113s '/usr/share/augustus/config/species/E_coli_K12' -> './config/species/E_coli_K12' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_metapars.cfg' -> './config/species/E_coli_K12/E_coli_K12_metapars.cfg' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_parameters.cfg' -> './config/species/E_coli_K12/E_coli_K12_parameters.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/E_coli_K12/E_coli_K12_weightmatrix.txt' -> './config/species/E_coli_K12/E_coli_K12_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus' -> './config/species/Ectocarpus_siliculosus' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_exon_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_igenic_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_intron_probs.pbl' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_weightmatrix.txt' -> './config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Ectocarpus_siliculosus/README.txt' -> './config/species/Ectocarpus_siliculosus/README.txt' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi' -> './config/species/Encephalitozoon_cuniculi' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_exon_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_igenic_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_intron_probs.pbl' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_weightmatrix.txt' -> './config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Encephalitozoon_cuniculi/README.txt' -> './config/species/Encephalitozoon_cuniculi/README.txt' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris' -> './config/species/Fistulifera_solaris' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_exon_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_igenic_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_intron_probs.pbl' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/Fistulifera_solaris_weightmatrix.txt' -> './config/species/Fistulifera_solaris/Fistulifera_solaris_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Fistulifera_solaris/README.txt' -> './config/species/Fistulifera_solaris/README.txt' 1113s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102' -> './config/species/Fragilariopsis_cylindrus_CCMP1102' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg' 1113s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_weightmatrix.txt' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Fragilariopsis_cylindrus_CCMP1102/README.txt' -> './config/species/Fragilariopsis_cylindrus_CCMP1102/README.txt' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera' -> './config/species/Gonapodya_prolifera' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_exon_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_igenic_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_intron_probs.pbl' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/Gonapodya_prolifera_weightmatrix.txt' -> './config/species/Gonapodya_prolifera/Gonapodya_prolifera_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Gonapodya_prolifera/README.txt' -> './config/species/Gonapodya_prolifera/README.txt' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris' -> './config/species/Hydra_vulgaris' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt' -> './config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Hydra_vulgaris/README.txt' -> './config/species/Hydra_vulgaris/README.txt' 1113s '/usr/share/augustus/config/species/Leptasterias_sp' -> './config/species/Leptasterias_sp' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl' -> './config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg' -> './config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt' -> './config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Leptasterias_sp/README.txt' -> './config/species/Leptasterias_sp/README.txt' 1113s '/usr/share/augustus/config/species/Loa_loa' -> './config/species/Loa_loa' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_exon_probs.pbl' -> './config/species/Loa_loa/Loa_loa_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_igenic_probs.pbl' -> './config/species/Loa_loa/Loa_loa_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_intron_probs.pbl' -> './config/species/Loa_loa/Loa_loa_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.cfg' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.cgp.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_metapars.utr.cfg' -> './config/species/Loa_loa/Loa_loa_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_parameters.cfg' -> './config/species/Loa_loa/Loa_loa_parameters.cfg' 1113s '/usr/share/augustus/config/species/Loa_loa/Loa_loa_weightmatrix.txt' -> './config/species/Loa_loa/Loa_loa_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Loa_loa/README.txt' -> './config/species/Loa_loa/README.txt' 1113s '/usr/share/augustus/config/species/Micromonas_commoda' -> './config/species/Micromonas_commoda' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_exon_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_igenic_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_intron_probs.pbl' -> './config/species/Micromonas_commoda/Micromonas_commoda_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg' -> './config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/Micromonas_commoda_weightmatrix.txt' -> './config/species/Micromonas_commoda/Micromonas_commoda_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Micromonas_commoda/README.txt' -> './config/species/Micromonas_commoda/README.txt' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla' -> './config/species/Micromonas_pusilla' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_exon_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_igenic_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_intron_probs.pbl' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/Micromonas_pusilla_weightmatrix.txt' -> './config/species/Micromonas_pusilla/Micromonas_pusilla_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Micromonas_pusilla/README.txt' -> './config/species/Micromonas_pusilla/README.txt' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum' -> './config/species/Monoraphidium_neglectum' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_exon_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_igenic_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_intron_probs.pbl' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_weightmatrix.txt' -> './config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Monoraphidium_neglectum/README.txt' -> './config/species/Monoraphidium_neglectum/README.txt' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis' -> './config/species/Monosiga_brevicollis' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt' -> './config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Monosiga_brevicollis/README.txt' -> './config/species/Monosiga_brevicollis/README.txt' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi' -> './config/species/Naegleria_gruberi' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt' -> './config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Naegleria_gruberi/README.txt' -> './config/species/Naegleria_gruberi/README.txt' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai' -> './config/species/Nemopilema_nomurai' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_weightmatrix.txt' -> './config/species/Nemopilema_nomurai/Nemopilema_nomurai_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Nemopilema_nomurai/README.txt' -> './config/species/Nemopilema_nomurai/README.txt' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus' -> './config/species/Notospermus_geniculatus' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/Notospermus_geniculatus_weightmatrix.txt' -> './config/species/Notospermus_geniculatus/Notospermus_geniculatus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Notospermus_geniculatus/README.txt' -> './config/species/Notospermus_geniculatus/README.txt' 1113s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus' -> './config/species/Ostreococcus_sp_lucimarinus' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_weightmatrix.txt' -> './config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Ostreococcus_sp_lucimarinus/README.txt' -> './config/species/Ostreococcus_sp_lucimarinus/README.txt' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri' -> './config/species/Ostreococcus_tauri' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_exon_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_igenic_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_intron_probs.pbl' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/Ostreococcus_tauri_weightmatrix.txt' -> './config/species/Ostreococcus_tauri/Ostreococcus_tauri_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Ostreococcus_tauri/README.txt' -> './config/species/Ostreococcus_tauri/README.txt' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia' -> './config/species/Paramecium_tetraurelia' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt' -> './config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Paramecium_tetraurelia/README.txt' -> './config/species/Paramecium_tetraurelia/README.txt' 1113s '/usr/share/augustus/config/species/Pediculus_humanus' -> './config/species/Pediculus_humanus' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl' -> './config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg' -> './config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt' -> './config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Pediculus_humanus/README.txt' -> './config/species/Pediculus_humanus/README.txt' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus' -> './config/species/Perkinsus_marinus' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt' -> './config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Perkinsus_marinus/README.txt' -> './config/species/Perkinsus_marinus/README.txt' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum' -> './config/species/Phaeodactylum_tricornutum' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_exon_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_igenic_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_intron_probs.pbl' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_weightmatrix.txt' -> './config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Phaeodactylum_tricornutum/README.txt' -> './config/species/Phaeodactylum_tricornutum/README.txt' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens' -> './config/species/Physcomitrium_patens' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt' -> './config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Physcomitrium_patens/README.txt' -> './config/species/Physcomitrium_patens/README.txt' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa' -> './config/species/Populus_trichocarpa' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg' 1113s '/usr/share/augustus/config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt' -> './config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata' -> './config/species/Pseudo-nitzschia_multistriata' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg' 1113s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_weightmatrix.txt' -> './config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Pseudo-nitzschia_multistriata/README.txt' -> './config/species/Pseudo-nitzschia_multistriata/README.txt' 1113s '/usr/share/augustus/config/species/Ptychodera_flava' -> './config/species/Ptychodera_flava' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_exon_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_igenic_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_intron_probs.pbl' -> './config/species/Ptychodera_flava/Ptychodera_flava_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg' -> './config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/Ptychodera_flava_weightmatrix.txt' -> './config/species/Ptychodera_flava/Ptychodera_flava_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Ptychodera_flava/README.txt' -> './config/species/Ptychodera_flava/README.txt' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides' -> './config/species/Pycnopodia_helianthoides' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt' -> './config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Pycnopodia_helianthoides/README.txt' -> './config/species/Pycnopodia_helianthoides/README.txt' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata' -> './config/species/Raphidocelis_subcapitata' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/README.txt' -> './config/species/Raphidocelis_subcapitata/README.txt' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg' 1113s '/usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt' -> './config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum' -> './config/species/Rhopilema_esculentum' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/README.txt' -> './config/species/Rhopilema_esculentum/README.txt' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg' 1113s '/usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt' -> './config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Ricinus_communis' -> './config/species/Ricinus_communis' 1113s '/usr/share/augustus/config/species/Ricinus_communis/README.txt' -> './config/species/Ricinus_communis/README.txt' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl' -> './config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.cfg' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_parameters.cfg' -> './config/species/Ricinus_communis/Ricinus_communis_parameters.cfg' 1113s '/usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt' -> './config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum' -> './config/species/Sclerotinia_sclerotiorum' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/README.txt' -> './config/species/Sclerotinia_sclerotiorum/README.txt' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg' 1113s '/usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt' -> './config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum' -> './config/species/Skeletonema_costatum' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/README.txt' -> './config/species/Skeletonema_costatum/README.txt' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg' 1113s '/usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt' -> './config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora' -> './config/species/Sordaria_macrospora' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/README.txt' -> './config/species/Sordaria_macrospora/README.txt' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg' 1113s '/usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt' -> './config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae' -> './config/species/Sphaceloma_murrayae' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/README.txt' -> './config/species/Sphaceloma_murrayae/README.txt' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg' 1113s '/usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt' -> './config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata' -> './config/species/Taeniopygia_guttata' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/README.txt' -> './config/species/Taeniopygia_guttata/README.txt' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg' 1113s '/usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt' -> './config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335' -> './config/species/Thalassiosira_pseudonana_CCMP1335' 1113s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/README.txt' -> './config/species/Thalassiosira_pseudonana_CCMP1335/README.txt' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg' 1113s '/usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt' -> './config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens' -> './config/species/Trichoplax_adhaerens' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/README.txt' -> './config/species/Trichoplax_adhaerens/README.txt' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg' 1113s '/usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt' -> './config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi' -> './config/species/Trypanosoma_cruzi' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/README.txt' -> './config/species/Trypanosoma_cruzi/README.txt' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg' 1113s '/usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt' -> './config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Vitis_vinifera' -> './config/species/Vitis_vinifera' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/README.txt' -> './config/species/Vitis_vinifera/README.txt' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl' -> './config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg' -> './config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg' 1113s '/usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt' -> './config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis' -> './config/species/Vitrella_brassicaformis' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/README.txt' -> './config/species/Vitrella_brassicaformis/README.txt' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg' 1113s '/usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt' -> './config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis' -> './config/species/Xenopus_tropicalis' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg' 1113s '/usr/share/augustus/config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt' -> './config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus' -> './config/species/Xiphophorus_maculatus' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/README.txt' -> './config/species/Xiphophorus_maculatus/README.txt' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_exon_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_igenic_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_intron_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_utr_probs.pbl' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_weightmatrix.txt' -> './config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus' -> './config/species/Xipophorus_maculatus' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_exon_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_igenic_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_intron_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_parameters.cfg' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_utr_probs.pbl' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/Xipophorus_maculatus/Xipophorus_maculatus_weightmatrix.txt' -> './config/species/Xipophorus_maculatus/Xipophorus_maculatus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/adorsata' -> './config/species/adorsata' 1113s '/usr/share/augustus/config/species/adorsata/adorsata_parameters.cfg' -> './config/species/adorsata/adorsata_parameters.cfg' 1113s '/usr/share/augustus/config/species/adorsata/adorsata_weightmatrix.txt' -> './config/species/adorsata/adorsata_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/adorsata/generic_exon_probs.pbl' -> './config/species/adorsata/generic_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/adorsata/generic_igenic_probs.pbl' -> './config/species/adorsata/generic_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/adorsata/generic_intron_probs.pbl' -> './config/species/adorsata/generic_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/adorsata/generic_weightmatrix.txt' -> './config/species/adorsata/generic_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/aedes' -> './config/species/aedes' 1113s '/usr/share/augustus/config/species/aedes/aedes_exon_probs.pbl' -> './config/species/aedes/aedes_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/aedes/aedes_igenic_probs.pbl' -> './config/species/aedes/aedes_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/aedes/aedes_intron_probs.pbl' -> './config/species/aedes/aedes_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/aedes/aedes_parameters.cfg' -> './config/species/aedes/aedes_parameters.cfg' 1113s '/usr/share/augustus/config/species/aedes/aedes_weightmatrix.txt' -> './config/species/aedes/aedes_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/amphimedon' -> './config/species/amphimedon' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_exon_probs.pbl' -> './config/species/amphimedon/amphimedon_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_igenic_probs.pbl' -> './config/species/amphimedon/amphimedon_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_intron_probs.pbl' -> './config/species/amphimedon/amphimedon_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_metapars.cfg' -> './config/species/amphimedon/amphimedon_metapars.cfg' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_parameters.cfg' -> './config/species/amphimedon/amphimedon_parameters.cfg' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_utr_probs.pbl' -> './config/species/amphimedon/amphimedon_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/amphimedon/amphimedon_weightmatrix.txt' -> './config/species/amphimedon/amphimedon_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum' -> './config/species/ancylostoma_ceylanicum' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/README.TXT' -> './config/species/ancylostoma_ceylanicum/README.TXT' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg' 1113s '/usr/share/augustus/config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt' -> './config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/anidulans' -> './config/species/anidulans' 1113s '/usr/share/augustus/config/species/anidulans/anidulans_exon_probs.pbl' -> './config/species/anidulans/anidulans_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/anidulans/anidulans_igenic_probs.pbl' -> './config/species/anidulans/anidulans_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/anidulans/anidulans_intron_probs.pbl' -> './config/species/anidulans/anidulans_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/anidulans/anidulans_parameters.cfg' -> './config/species/anidulans/anidulans_parameters.cfg' 1113s '/usr/share/augustus/config/species/anidulans/anidulans_weightmatrix.txt' -> './config/species/anidulans/anidulans_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/arabidopsis' -> './config/species/arabidopsis' 1113s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_exon_probs.pbl' -> './config/species/arabidopsis/arabidopsis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_igenic_probs.pbl' -> './config/species/arabidopsis/arabidopsis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_intron_probs.pbl' -> './config/species/arabidopsis/arabidopsis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_parameters.cfg' -> './config/species/arabidopsis/arabidopsis_parameters.cfg' 1113s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_utr_probs.pbl' -> './config/species/arabidopsis/arabidopsis_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/arabidopsis/arabidopsis_weightmatrix.txt' -> './config/species/arabidopsis/arabidopsis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus' -> './config/species/aspergillus_fumigatus' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt' -> './config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans' -> './config/species/aspergillus_nidulans' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_nidulans/aspergillus_nidulans_weightmatrix.txt' -> './config/species/aspergillus_nidulans/aspergillus_nidulans_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae' -> './config/species/aspergillus_oryzae' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_exon_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_igenic_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_intron_probs.pbl' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_metapars.cfg' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_metapars.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_oryzae/aspergillus_oryzae_weightmatrix.txt' -> './config/species/aspergillus_oryzae/aspergillus_oryzae_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/aspergillus_terreus' -> './config/species/aspergillus_terreus' 1113s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl' -> './config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg' -> './config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg' -> './config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg' 1113s '/usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt' -> './config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/b_pseudomallei' -> './config/species/b_pseudomallei' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_exon_probs.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_igenic_probs.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_metapars.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_metapars.cfg' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_metapars.utr.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_ovlp_len.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_ovlp_len.pbl' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2' -> './config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl' -> './config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl' 1113s '/usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt' -> './config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/bombus_impatiens1' -> './config/species/bombus_impatiens1' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl' -> './config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF' -> './config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5' -> './config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5' 1113s '/usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt' -> './config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/bombus_terrestris2' -> './config/species/bombus_terrestris2' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF' -> './config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4' -> './config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl' -> './config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt' -> './config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/botrytis_cinerea' -> './config/species/botrytis_cinerea' 1113s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl' -> './config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg' -> './config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg' 1113s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg' -> './config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg' 1113s '/usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt' -> './config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/brugia' -> './config/species/brugia' 1113s '/usr/share/augustus/config/species/brugia/brugia_exon_probs.pbl' -> './config/species/brugia/brugia_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/brugia/brugia_igenic_probs.pbl' -> './config/species/brugia/brugia_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/brugia/brugia_intron_probs.pbl' -> './config/species/brugia/brugia_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/brugia/brugia_parameters.cfg' -> './config/species/brugia/brugia_parameters.cfg' 1113s '/usr/share/augustus/config/species/brugia/brugia_splicefile' -> './config/species/brugia/brugia_splicefile' 1113s '/usr/share/augustus/config/species/brugia/brugia_weightmatrix.txt' -> './config/species/brugia/brugia_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/c_elegans_trsk' -> './config/species/c_elegans_trsk' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg' -> './config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt' -> './config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/cacao' -> './config/species/cacao' 1113s '/usr/share/augustus/config/species/cacao/cacao_exon_probs.pbl' -> './config/species/cacao/cacao_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/cacao/cacao_igenic_probs.pbl' -> './config/species/cacao/cacao_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/cacao/cacao_intron_probs.pbl' -> './config/species/cacao/cacao_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/cacao/cacao_metapars.cfg' -> './config/species/cacao/cacao_metapars.cfg' 1113s '/usr/share/augustus/config/species/cacao/cacao_metapars.utr.cfg' -> './config/species/cacao/cacao_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/cacao/cacao_parameters.cfg' -> './config/species/cacao/cacao_parameters.cfg' 1113s '/usr/share/augustus/config/species/cacao/cacao_utr_probs.pbl' -> './config/species/cacao/cacao_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/cacao/cacao_weightmatrix.txt' -> './config/species/cacao/cacao_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/caenorhabditis' -> './config/species/caenorhabditis' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_exon_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_intron_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_metapars.cfg' -> './config/species/caenorhabditis/caenorhabditis_metapars.cfg' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_parameters.cfg' -> './config/species/caenorhabditis/caenorhabditis_parameters.cfg' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl' -> './config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_utr_probs.pbl' -> './config/species/caenorhabditis/caenorhabditis_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/caenorhabditis/caenorhabditis_weightmatrix.txt' -> './config/species/caenorhabditis/caenorhabditis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/camponotus_floridanus' -> './config/species/camponotus_floridanus' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/README.TXT' -> './config/species/camponotus_floridanus/README.TXT' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl' -> './config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg' -> './config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg' 1113s '/usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt' -> './config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/candida_albicans' -> './config/species/candida_albicans' 1113s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_exon_probs.pbl' -> './config/species/candida_albicans/candida_albicans_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_igenic_probs.pbl' -> './config/species/candida_albicans/candida_albicans_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_intron_probs.pbl' -> './config/species/candida_albicans/candida_albicans_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_metapars.cfg' -> './config/species/candida_albicans/candida_albicans_metapars.cfg' 1113s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_parameters.cfg' -> './config/species/candida_albicans/candida_albicans_parameters.cfg' 1113s '/usr/share/augustus/config/species/candida_albicans/candida_albicans_weightmatrix.txt' -> './config/species/candida_albicans/candida_albicans_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/candida_guilliermondii' -> './config/species/candida_guilliermondii' 1113s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl' -> './config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg' -> './config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg' 1113s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg' -> './config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg' 1113s '/usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt' -> './config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/candida_tropicalis' -> './config/species/candida_tropicalis' 1113s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl' -> './config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_metapars.cfg' -> './config/species/candida_tropicalis/candida_tropicalis_metapars.cfg' 1113s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg' -> './config/species/candida_tropicalis/candida_tropicalis_parameters.cfg' 1113s '/usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt' -> './config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/chaetomium_globosum' -> './config/species/chaetomium_globosum' 1113s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl' -> './config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg' -> './config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg' 1113s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg' -> './config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg' 1113s '/usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt' -> './config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/chicken' -> './config/species/chicken' 1113s '/usr/share/augustus/config/species/chicken/README.TXT' -> './config/species/chicken/README.TXT' 1113s '/usr/share/augustus/config/species/chicken/chicken_exon_probs.pbl' -> './config/species/chicken/chicken_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/chicken/chicken_igenic_probs.pbl' -> './config/species/chicken/chicken_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/chicken/chicken_intron_probs.pbl' -> './config/species/chicken/chicken_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/chicken/chicken_metapars.cfg' -> './config/species/chicken/chicken_metapars.cfg' 1113s '/usr/share/augustus/config/species/chicken/chicken_metapars.utr.cfg' -> './config/species/chicken/chicken_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/chicken/chicken_parameters.cfg' -> './config/species/chicken/chicken_parameters.cfg' 1113s '/usr/share/augustus/config/species/chicken/chicken_weightmatrix.txt' -> './config/species/chicken/chicken_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/chiloscyllium' -> './config/species/chiloscyllium' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_exon_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_intron_probs.pbl' -> './config/species/chiloscyllium/chiloscyllium_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.cfg' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg' -> './config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg' -> './config/species/chiloscyllium/chiloscyllium_parameters.cfg' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1' -> './config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/chiloscyllium/chiloscyllium_weightmatrix.txt' -> './config/species/chiloscyllium/chiloscyllium_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/chlamy2011' -> './config/species/chlamy2011' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_exon_probs.pbl' -> './config/species/chlamy2011/chlamy2011_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_igenic_probs.pbl' -> './config/species/chlamy2011/chlamy2011_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_intron_probs.pbl' -> './config/species/chlamy2011/chlamy2011_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.cfg' -> './config/species/chlamy2011/chlamy2011_metapars.cfg' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.utr.cfg' -> './config/species/chlamy2011/chlamy2011_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_parameters.cfg' -> './config/species/chlamy2011/chlamy2011_parameters.cfg' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl' -> './config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl' -> './config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_utr_probs.pbl' -> './config/species/chlamy2011/chlamy2011_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamy2011/chlamy2011_weightmatrix.txt' -> './config/species/chlamy2011/chlamy2011_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/chlamydomonas' -> './config/species/chlamydomonas' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_exon_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_igenic_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_intron_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_metapars.cfg' -> './config/species/chlamydomonas/chlamydomonas_metapars.cfg' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_parameters.cfg' -> './config/species/chlamydomonas/chlamydomonas_parameters.cfg' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl' -> './config/species/chlamydomonas/chlamydomonas_trans_shadow_partial.pbl' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl' -> './config/species/chlamydomonas/chlamydomonas_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_utr_probs.pbl' -> './config/species/chlamydomonas/chlamydomonas_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/chlamydomonas/chlamydomonas_weightmatrix.txt' -> './config/species/chlamydomonas/chlamydomonas_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/chlorella' -> './config/species/chlorella' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_exon_probs.pbl' -> './config/species/chlorella/chlorella_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_igenic_probs.pbl' -> './config/species/chlorella/chlorella_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_intron_probs.pbl' -> './config/species/chlorella/chlorella_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_metapars.cfg' -> './config/species/chlorella/chlorella_metapars.cfg' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_metapars.utr.cfg' -> './config/species/chlorella/chlorella_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_parameters.cfg' -> './config/species/chlorella/chlorella_parameters.cfg' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_utr_probs.pbl' -> './config/species/chlorella/chlorella_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/chlorella/chlorella_weightmatrix.txt' -> './config/species/chlorella/chlorella_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/ciona' -> './config/species/ciona' 1113s '/usr/share/augustus/config/species/ciona/README.TXT' -> './config/species/ciona/README.TXT' 1113s '/usr/share/augustus/config/species/ciona/ciona_exon_probs.pbl' -> './config/species/ciona/ciona_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/ciona/ciona_igenic_probs.pbl' -> './config/species/ciona/ciona_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/ciona/ciona_intron_probs.pbl' -> './config/species/ciona/ciona_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/ciona/ciona_metapars.cfg' -> './config/species/ciona/ciona_metapars.cfg' 1113s '/usr/share/augustus/config/species/ciona/ciona_metapars.cgp.cfg' -> './config/species/ciona/ciona_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/ciona/ciona_metapars.utr.cfg' -> './config/species/ciona/ciona_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/ciona/ciona_parameters.cfg' -> './config/species/ciona/ciona_parameters.cfg' 1113s '/usr/share/augustus/config/species/ciona/ciona_parameters.cfg.orig1' -> './config/species/ciona/ciona_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/ciona/ciona_weightmatrix.txt' -> './config/species/ciona/ciona_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/coccidioides_immitis' -> './config/species/coccidioides_immitis' 1113s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_exon_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_igenic_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_intron_probs.pbl' -> './config/species/coccidioides_immitis/coccidioides_immitis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_metapars.cfg' -> './config/species/coccidioides_immitis/coccidioides_immitis_metapars.cfg' 1113s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg' -> './config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg' 1113s '/usr/share/augustus/config/species/coccidioides_immitis/coccidioides_immitis_weightmatrix.txt' -> './config/species/coccidioides_immitis/coccidioides_immitis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/coprinus' -> './config/species/coprinus' 1113s '/usr/share/augustus/config/species/coprinus/coprinus_exon_probs.pbl' -> './config/species/coprinus/coprinus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/coprinus/coprinus_igenic_probs.pbl' -> './config/species/coprinus/coprinus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/coprinus/coprinus_intron_probs.pbl' -> './config/species/coprinus/coprinus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/coprinus/coprinus_parameters.cfg' -> './config/species/coprinus/coprinus_parameters.cfg' 1113s '/usr/share/augustus/config/species/coprinus/coprinus_weightmatrix.txt' -> './config/species/coprinus/coprinus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/coprinus_cinereus' -> './config/species/coprinus_cinereus' 1113s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_exon_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_igenic_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_intron_probs.pbl' -> './config/species/coprinus_cinereus/coprinus_cinereus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_metapars.cfg' -> './config/species/coprinus_cinereus/coprinus_cinereus_metapars.cfg' 1113s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg' -> './config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg' 1113s '/usr/share/augustus/config/species/coprinus_cinereus/coprinus_cinereus_weightmatrix.txt' -> './config/species/coprinus_cinereus/coprinus_cinereus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/coyote_tobacco' -> './config/species/coyote_tobacco' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_metapars.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_metapars.cfg' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_parameters.cfg' -> './config/species/coyote_tobacco/coyote_tobacco_parameters.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl' -> './config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/coyote_tobacco/coyote_tobacco_weightmatrix.txt' -> './config/species/coyote_tobacco/coyote_tobacco_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/cryptococcus' -> './config/species/cryptococcus' 1113s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_exon_probs.pbl' -> './config/species/cryptococcus/cryptococcus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_igenic_probs.pbl' -> './config/species/cryptococcus/cryptococcus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_intron_probs.pbl' -> './config/species/cryptococcus/cryptococcus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_parameters.cfg' -> './config/species/cryptococcus/cryptococcus_parameters.cfg' 1113s '/usr/share/augustus/config/species/cryptococcus/cryptococcus_weightmatrix.txt' -> './config/species/cryptococcus/cryptococcus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii' -> './config/species/cryptococcus_neoformans_gattii' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_metapars.cfg' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_metapars.cfg' 1113s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg' 1113s '/usr/share/augustus/config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_weightmatrix.txt' -> './config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_B' -> './config/species/cryptococcus_neoformans_neoformans_B' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/cryptococcus_neoformans_neoformans_JEC21' -> './config/species/cryptococcus_neoformans_neoformans_JEC21' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/culex' -> './config/species/culex' 1113s '/usr/share/augustus/config/species/culex/culex_exon_probs.pbl' -> './config/species/culex/culex_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/culex/culex_exon_probs.pbl.wech' -> './config/species/culex/culex_exon_probs.pbl.wech' 1113s '/usr/share/augustus/config/species/culex/culex_igenic_probs.pbl' -> './config/species/culex/culex_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/culex/culex_igenic_probs.pbl.wech' -> './config/species/culex/culex_igenic_probs.pbl.wech' 1113s '/usr/share/augustus/config/species/culex/culex_intron_probs.pbl' -> './config/species/culex/culex_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/culex/culex_intron_probs.pbl.wech' -> './config/species/culex/culex_intron_probs.pbl.wech' 1113s '/usr/share/augustus/config/species/culex/culex_metapars.cfg' -> './config/species/culex/culex_metapars.cfg' 1113s '/usr/share/augustus/config/species/culex/culex_parameters.cfg' -> './config/species/culex/culex_parameters.cfg' 1113s '/usr/share/augustus/config/species/culex/culex_parameters.old.cfg' -> './config/species/culex/culex_parameters.old.cfg' 1113s '/usr/share/augustus/config/species/culex/culex_trans_shadow_partial_utr.pbl' -> './config/species/culex/culex_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/culex/culex_utr_probs.pbl' -> './config/species/culex/culex_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/culex/culex_weightmatrix.txt' -> './config/species/culex/culex_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii' -> './config/species/debaryomyces_hansenii' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_exon_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_igenic_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_intron_probs.pbl' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_metapars.cfg' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_metapars.cfg' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg' 1113s '/usr/share/augustus/config/species/debaryomyces_hansenii/debaryomyces_hansenii_weightmatrix.txt' -> './config/species/debaryomyces_hansenii/debaryomyces_hansenii_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/elephant_shark' -> './config/species/elephant_shark' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_exon_probs.pbl' -> './config/species/elephant_shark/elephant_shark_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_igenic_probs.pbl' -> './config/species/elephant_shark/elephant_shark_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_intron_probs.pbl' -> './config/species/elephant_shark/elephant_shark_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_metapars.cfg' -> './config/species/elephant_shark/elephant_shark_metapars.cfg' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_metapars.utr.cfg' -> './config/species/elephant_shark/elephant_shark_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_parameters.cfg' -> './config/species/elephant_shark/elephant_shark_parameters.cfg' 1113s '/usr/share/augustus/config/species/elephant_shark/elephant_shark_weightmatrix.txt' -> './config/species/elephant_shark/elephant_shark_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB' -> './config/species/encephalitozoon_cuniculi_GB' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_metapars.cfg' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_metapars.cfg' 1113s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg' 1113s '/usr/share/augustus/config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_weightmatrix.txt' -> './config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii' -> './config/species/eremothecium_gossypii' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_exon_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_igenic_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_intron_probs.pbl' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_metapars.cfg' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_metapars.cfg' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg' 1113s '/usr/share/augustus/config/species/eremothecium_gossypii/eremothecium_gossypii_weightmatrix.txt' -> './config/species/eremothecium_gossypii/eremothecium_gossypii_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/fly' -> './config/species/fly' 1113s '/usr/share/augustus/config/species/fly/fly_exon_probs.pbl' -> './config/species/fly/fly_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/fly/fly_igenic_probs.pbl' -> './config/species/fly/fly_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/fly/fly_intron_probs.pbl' -> './config/species/fly/fly_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/fly/fly_metapars.cfg' -> './config/species/fly/fly_metapars.cfg' 1113s '/usr/share/augustus/config/species/fly/fly_metapars.utr.cfg' -> './config/species/fly/fly_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/fly/fly_parameters.cfg' -> './config/species/fly/fly_parameters.cfg' 1113s '/usr/share/augustus/config/species/fly/fly_utr_probs.pbl' -> './config/species/fly/fly_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/fly/fly_weightmatrix.txt' -> './config/species/fly/fly_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/fly_exp' -> './config/species/fly_exp' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_exon_probs.pbl' -> './config/species/fly_exp/fly_exp_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_igenic_probs.pbl' -> './config/species/fly_exp/fly_exp_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_intron_probs.pbl' -> './config/species/fly_exp/fly_exp_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_metapars.cfg' -> './config/species/fly_exp/fly_exp_metapars.cfg' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_metapars.utr.cfg' -> './config/species/fly_exp/fly_exp_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_parameters.cfg' -> './config/species/fly_exp/fly_exp_parameters.cfg' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_utr_probs.pbl' -> './config/species/fly_exp/fly_exp_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/fly_exp/fly_exp_weightmatrix.txt' -> './config/species/fly_exp/fly_exp_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/fusarium' -> './config/species/fusarium' 1113s '/usr/share/augustus/config/species/fusarium/fusarium_exon_probs.pbl' -> './config/species/fusarium/fusarium_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/fusarium/fusarium_igenic_probs.pbl' -> './config/species/fusarium/fusarium_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/fusarium/fusarium_intron_probs.pbl' -> './config/species/fusarium/fusarium_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/fusarium/fusarium_parameters.cfg' -> './config/species/fusarium/fusarium_parameters.cfg' 1113s '/usr/share/augustus/config/species/fusarium/fusarium_weightmatrix.txt' -> './config/species/fusarium/fusarium_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/fusarium_graminearum' -> './config/species/fusarium_graminearum' 1113s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_exon_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_igenic_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_intron_probs.pbl' -> './config/species/fusarium_graminearum/fusarium_graminearum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_metapars.cfg' -> './config/species/fusarium_graminearum/fusarium_graminearum_metapars.cfg' 1113s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg' -> './config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg' 1113s '/usr/share/augustus/config/species/fusarium_graminearum/fusarium_graminearum_weightmatrix.txt' -> './config/species/fusarium_graminearum/fusarium_graminearum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/galdieria' -> './config/species/galdieria' 1113s '/usr/share/augustus/config/species/galdieria/extrinsic.PE.cfg' -> './config/species/galdieria/extrinsic.PE.cfg' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_exon_probs.pbl' -> './config/species/galdieria/galdieria_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_igenic_probs.pbl' -> './config/species/galdieria/galdieria_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_intron_probs.pbl' -> './config/species/galdieria/galdieria_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_metapars.cfg' -> './config/species/galdieria/galdieria_metapars.cfg' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_parameters.cfg' -> './config/species/galdieria/galdieria_parameters.cfg' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_splicefile' -> './config/species/galdieria/galdieria_splicefile' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl' -> './config/species/galdieria/galdieria_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_utr_probs.pbl' -> './config/species/galdieria/galdieria_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/galdieria/galdieria_weightmatrix.txt' -> './config/species/galdieria/galdieria_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/generic' -> './config/species/generic' 1113s '/usr/share/augustus/config/species/generic/generic_metapars.cfg' -> './config/species/generic/generic_metapars.cfg' 1113s '/usr/share/augustus/config/species/generic/generic_metapars.cgp.cfg' -> './config/species/generic/generic_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/generic/generic_metapars.utr.cfg' -> './config/species/generic/generic_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/generic/generic_parameters.cfg' -> './config/species/generic/generic_parameters.cfg' 1113s '/usr/share/augustus/config/species/generic/generic_weightmatrix.txt' -> './config/species/generic/generic_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/gigaspora_margarita' -> './config/species/gigaspora_margarita' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/README.TXT' -> './config/species/gigaspora_margarita/README.TXT' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_exon_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_igenic_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_intron_probs.pbl' -> './config/species/gigaspora_margarita/gigaspora_margarita_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg' -> './config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gigaspora_margarita_weightmatrix.txt' -> './config/species/gigaspora_margarita/gigaspora_margarita_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/gigaspora_margarita/gth.cfg' -> './config/species/gigaspora_margarita/gth.cfg' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1' -> './config/species/heliconius_melpomene1' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_exon_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_igenic_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_intron_probs.pbl' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.cfg' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.utr.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg' 1113s '/usr/share/augustus/config/species/heliconius_melpomene1/heliconius_melpomene1_weightmatrix.txt' -> './config/species/heliconius_melpomene1/heliconius_melpomene1_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/histoplasma' -> './config/species/histoplasma' 1113s '/usr/share/augustus/config/species/histoplasma/histoplasma_exon_probs.pbl' -> './config/species/histoplasma/histoplasma_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/histoplasma/histoplasma_igenic_probs.pbl' -> './config/species/histoplasma/histoplasma_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/histoplasma/histoplasma_intron_probs.pbl' -> './config/species/histoplasma/histoplasma_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/histoplasma/histoplasma_parameters.cfg' -> './config/species/histoplasma/histoplasma_parameters.cfg' 1113s '/usr/share/augustus/config/species/histoplasma/histoplasma_weightmatrix.txt' -> './config/species/histoplasma/histoplasma_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum' -> './config/species/histoplasma_capsulatum' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_exon_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_igenic_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_intron_probs.pbl' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_metapars.cfg' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_metapars.cfg' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg' 1113s '/usr/share/augustus/config/species/histoplasma_capsulatum/histoplasma_capsulatum_weightmatrix.txt' -> './config/species/histoplasma_capsulatum/histoplasma_capsulatum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/honeybee1' -> './config/species/honeybee1' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_exon_probs.pbl' -> './config/species/honeybee1/honeybee1_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_igenic_probs.pbl' -> './config/species/honeybee1/honeybee1_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_intron_probs.pbl' -> './config/species/honeybee1/honeybee1_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF' -> './config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_metapars.cfg' -> './config/species/honeybee1/honeybee1_metapars.cfg' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_metapars.utr.cfg' -> './config/species/honeybee1/honeybee1_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_parameters.cfg' -> './config/species/honeybee1/honeybee1_parameters.cfg' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_parameters.cfg.orig1' -> './config/species/honeybee1/honeybee1_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_utr_probs.pbl' -> './config/species/honeybee1/honeybee1_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/honeybee1/honeybee1_weightmatrix.txt' -> './config/species/honeybee1/honeybee1_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/human' -> './config/species/human' 1113s '/usr/share/augustus/config/species/human/README.TXT' -> './config/species/human/README.TXT' 1113s '/usr/share/augustus/config/species/human/human_exon_probs.pbl' -> './config/species/human/human_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/human/human_igenic_probs.pbl' -> './config/species/human/human_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/human/human_intron_probs.pbl' -> './config/species/human/human_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/human/human_parameters.cfg' -> './config/species/human/human_parameters.cfg' 1113s '/usr/share/augustus/config/species/human/human_trans_shadow_partial_utr.pbl' -> './config/species/human/human_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/human/human_utr_probs.pbl' -> './config/species/human/human_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/human/human_weightmatrix.txt' -> './config/species/human/human_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma' -> './config/species/hymenolepis_microstoma' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_exon_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_igenic_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_intron_probs.pbl' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/hymenolepis_microstoma_weightmatrix.txt' -> './config/species/hymenolepis_microstoma/hymenolepis_microstoma_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/hymenolepis_microstoma/make.doc' -> './config/species/hymenolepis_microstoma/make.doc' 1113s '/usr/share/augustus/config/species/japaneselamprey' -> './config/species/japaneselamprey' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_exon_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_intron_probs.pbl' -> './config/species/japaneselamprey/japaneselamprey_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_metapars.cfg' -> './config/species/japaneselamprey/japaneselamprey_metapars.cfg' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_metapars.utr.cfg' -> './config/species/japaneselamprey/japaneselamprey_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_parameters.cfg' -> './config/species/japaneselamprey/japaneselamprey_parameters.cfg' 1113s '/usr/share/augustus/config/species/japaneselamprey/japaneselamprey_weightmatrix.txt' -> './config/species/japaneselamprey/japaneselamprey_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis' -> './config/species/kluyveromyces_lactis' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_exon_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_igenic_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_intron_probs.pbl' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_metapars.cfg' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_metapars.cfg' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg' 1113s '/usr/share/augustus/config/species/kluyveromyces_lactis/kluyveromyces_lactis_weightmatrix.txt' -> './config/species/kluyveromyces_lactis/kluyveromyces_lactis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/laccaria_bicolor' -> './config/species/laccaria_bicolor' 1113s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_exon_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_igenic_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_intron_probs.pbl' -> './config/species/laccaria_bicolor/laccaria_bicolor_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_metapars.cfg' -> './config/species/laccaria_bicolor/laccaria_bicolor_metapars.cfg' 1113s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg' -> './config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg' 1113s '/usr/share/augustus/config/species/laccaria_bicolor/laccaria_bicolor_weightmatrix.txt' -> './config/species/laccaria_bicolor/laccaria_bicolor_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae' -> './config/species/leishmania_tarentolae' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_exon_probs.pbl' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_igenic_probs.pbl' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.cfg' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.utr.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg' 1113s '/usr/share/augustus/config/species/leishmania_tarentolae/leishmania_tarentolae_weightmatrix.txt' -> './config/species/leishmania_tarentolae/leishmania_tarentolae_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus' -> './config/species/lodderomyces_elongisporus' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg' 1113s '/usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt' -> './config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea' -> './config/species/magnaporthe_grisea' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg' 1113s '/usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt' -> './config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/maize' -> './config/species/maize' 1113s '/usr/share/augustus/config/species/maize/maize_exon_probs.pbl' -> './config/species/maize/maize_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/maize/maize_igenic_probs.pbl' -> './config/species/maize/maize_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/maize/maize_intron_probs.pbl' -> './config/species/maize/maize_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/maize/maize_metapars.cfg' -> './config/species/maize/maize_metapars.cfg' 1113s '/usr/share/augustus/config/species/maize/maize_parameters.cfg' -> './config/species/maize/maize_parameters.cfg' 1113s '/usr/share/augustus/config/species/maize/maize_splicefile.txt.gz' -> './config/species/maize/maize_splicefile.txt.gz' 1113s '/usr/share/augustus/config/species/maize/maize_weightmatrix.txt' -> './config/species/maize/maize_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/maize5' -> './config/species/maize5' 1113s '/usr/share/augustus/config/species/maize5/maize5_exon_probs.pbl' -> './config/species/maize5/maize5_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/maize5/maize5_igenic_probs.pbl' -> './config/species/maize5/maize5_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/maize5/maize5_intron_probs.pbl' -> './config/species/maize5/maize5_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/maize5/maize5_metapars.cfg' -> './config/species/maize5/maize5_metapars.cfg' 1113s '/usr/share/augustus/config/species/maize5/maize5_metapars.utr.cfg' -> './config/species/maize5/maize5_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/maize5/maize5_parameters.cfg' -> './config/species/maize5/maize5_parameters.cfg' 1113s '/usr/share/augustus/config/species/maize5/maize5_utr_probs.pbl' -> './config/species/maize5/maize5_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/maize5/maize5_weightmatrix.txt' -> './config/species/maize5/maize5_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi' -> './config/species/mnemiopsis_leidyi' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/README.TXT' -> './config/species/mnemiopsis_leidyi/README.TXT' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt' -> './config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/nasonia' -> './config/species/nasonia' 1113s '/usr/share/augustus/config/species/nasonia/nasonia_exon_probs.pbl' -> './config/species/nasonia/nasonia_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/nasonia/nasonia_igenic_probs.pbl' -> './config/species/nasonia/nasonia_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/nasonia/nasonia_intron_probs.pbl' -> './config/species/nasonia/nasonia_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/nasonia/nasonia_metapars.cfg' -> './config/species/nasonia/nasonia_metapars.cfg' 1113s '/usr/share/augustus/config/species/nasonia/nasonia_parameters.cfg' -> './config/species/nasonia/nasonia_parameters.cfg' 1113s '/usr/share/augustus/config/species/nasonia/nasonia_weightmatrix.txt' -> './config/species/nasonia/nasonia_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/nematostella_vectensis' -> './config/species/nematostella_vectensis' 1113s '/usr/share/augustus/config/species/nematostella_vectensis/README.TXT' -> './config/species/nematostella_vectensis/README.TXT' 1113s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl' -> './config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg' -> './config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg' 1113s '/usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt' -> './config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/neurospora' -> './config/species/neurospora' 1113s '/usr/share/augustus/config/species/neurospora/neurospora_exon_probs.pbl' -> './config/species/neurospora/neurospora_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/neurospora/neurospora_igenic_probs.pbl' -> './config/species/neurospora/neurospora_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/neurospora/neurospora_intron_probs.pbl' -> './config/species/neurospora/neurospora_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/neurospora/neurospora_parameters.cfg' -> './config/species/neurospora/neurospora_parameters.cfg' 1113s '/usr/share/augustus/config/species/neurospora/neurospora_weightmatrix.txt' -> './config/species/neurospora/neurospora_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/neurospora_crassa' -> './config/species/neurospora_crassa' 1113s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_exon_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_igenic_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_intron_probs.pbl' -> './config/species/neurospora_crassa/neurospora_crassa_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_metapars.cfg' -> './config/species/neurospora_crassa/neurospora_crassa_metapars.cfg' 1113s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_parameters.cfg' -> './config/species/neurospora_crassa/neurospora_crassa_parameters.cfg' 1113s '/usr/share/augustus/config/species/neurospora_crassa/neurospora_crassa_weightmatrix.txt' -> './config/species/neurospora_crassa/neurospora_crassa_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/parasteatoda' -> './config/species/parasteatoda' 1113s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_exon_probs.pbl' -> './config/species/parasteatoda/parasteatoda_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_igenic_probs.pbl' -> './config/species/parasteatoda/parasteatoda_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_intron_probs.pbl' -> './config/species/parasteatoda/parasteatoda_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_parameters.cfg' -> './config/species/parasteatoda/parasteatoda_parameters.cfg' 1113s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_utr_probs.pbl' -> './config/species/parasteatoda/parasteatoda_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/parasteatoda/parasteatoda_weightmatrix.txt' -> './config/species/parasteatoda/parasteatoda_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/pchrysosporium' -> './config/species/pchrysosporium' 1113s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_exon_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_igenic_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_intron_probs.pbl' -> './config/species/pchrysosporium/pchrysosporium_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_parameters.cfg' -> './config/species/pchrysosporium/pchrysosporium_parameters.cfg' 1113s '/usr/share/augustus/config/species/pchrysosporium/pchrysosporium_weightmatrix.txt' -> './config/species/pchrysosporium/pchrysosporium_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/pea_aphid' -> './config/species/pea_aphid' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_exon_probs.pbl' -> './config/species/pea_aphid/pea_aphid_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_igenic_probs.pbl' -> './config/species/pea_aphid/pea_aphid_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_intron_probs.pbl' -> './config/species/pea_aphid/pea_aphid_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_metapars.cfg' -> './config/species/pea_aphid/pea_aphid_metapars.cfg' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_parameters.cfg' -> './config/species/pea_aphid/pea_aphid_parameters.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_utr_probs.pbl' -> './config/species/pea_aphid/pea_aphid_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/pea_aphid/pea_aphid_weightmatrix.txt' -> './config/species/pea_aphid/pea_aphid_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/pfalciparum' -> './config/species/pfalciparum' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_exon_probs.pbl' -> './config/species/pfalciparum/pfalciparum_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_igenic_probs.pbl' -> './config/species/pfalciparum/pfalciparum_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_intron_probs.pbl' -> './config/species/pfalciparum/pfalciparum_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_metapars.cfg' -> './config/species/pfalciparum/pfalciparum_metapars.cfg' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_parameters.cfg' -> './config/species/pfalciparum/pfalciparum_parameters.cfg' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl' -> './config/species/pfalciparum/pfalciparum_trans_shadow_partial.pbl' 1113s '/usr/share/augustus/config/species/pfalciparum/pfalciparum_weightmatrix.txt' -> './config/species/pfalciparum/pfalciparum_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium' -> './config/species/phanerochaete_chrysosporium' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_exon_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_igenic_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_intron_probs.pbl' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_metapars.cfg' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_metapars.cfg' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg' 1113s '/usr/share/augustus/config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_weightmatrix.txt' -> './config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/pichia_stipitis' -> './config/species/pichia_stipitis' 1113s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_exon_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_igenic_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_intron_probs.pbl' -> './config/species/pichia_stipitis/pichia_stipitis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_metapars.cfg' -> './config/species/pichia_stipitis/pichia_stipitis_metapars.cfg' 1113s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_parameters.cfg' -> './config/species/pichia_stipitis/pichia_stipitis_parameters.cfg' 1113s '/usr/share/augustus/config/species/pichia_stipitis/pichia_stipitis_weightmatrix.txt' -> './config/species/pichia_stipitis/pichia_stipitis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/pisaster' -> './config/species/pisaster' 1113s '/usr/share/augustus/config/species/pisaster/extrinsic.pisaster.cfg' -> './config/species/pisaster/extrinsic.pisaster.cfg' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_exon_probs.pbl' -> './config/species/pisaster/pisaster_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_igenic_probs.pbl' -> './config/species/pisaster/pisaster_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_intron_probs.pbl' -> './config/species/pisaster/pisaster_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.cfg' -> './config/species/pisaster/pisaster_metapars.cfg' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.cgp.cfg' -> './config/species/pisaster/pisaster_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_metapars.utr.cfg' -> './config/species/pisaster/pisaster_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_parameters.cfg' -> './config/species/pisaster/pisaster_parameters.cfg' 1113s '/usr/share/augustus/config/species/pisaster/pisaster_weightmatrix.txt' -> './config/species/pisaster/pisaster_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/pneumocystis' -> './config/species/pneumocystis' 1113s '/usr/share/augustus/config/species/pneumocystis/README.TXT' -> './config/species/pneumocystis/README.TXT' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_exon_probs.pbl' -> './config/species/pneumocystis/pneumocystis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_igenic_probs.pbl' -> './config/species/pneumocystis/pneumocystis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_intron_probs.pbl' -> './config/species/pneumocystis/pneumocystis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_metapars.cfg' -> './config/species/pneumocystis/pneumocystis_metapars.cfg' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_metaparsBAK.cfg' -> './config/species/pneumocystis/pneumocystis_metaparsBAK.cfg' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_parameters.cfg' -> './config/species/pneumocystis/pneumocystis_parameters.cfg' 1113s '/usr/share/augustus/config/species/pneumocystis/pneumocystis_weightmatrix.txt' -> './config/species/pneumocystis/pneumocystis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/rhincodon' -> './config/species/rhincodon' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_exon_probs.pbl' -> './config/species/rhincodon/rhincodon_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_igenic_probs.pbl' -> './config/species/rhincodon/rhincodon_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_intron_probs.pbl' -> './config/species/rhincodon/rhincodon_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.cfg' -> './config/species/rhincodon/rhincodon_metapars.cfg' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.cgp.cfg' -> './config/species/rhincodon/rhincodon_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_metapars.utr.cfg' -> './config/species/rhincodon/rhincodon_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_parameters.cfg' -> './config/species/rhincodon/rhincodon_parameters.cfg' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_parameters.cfg.orig1' -> './config/species/rhincodon/rhincodon_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/rhincodon/rhincodon_weightmatrix.txt' -> './config/species/rhincodon/rhincodon_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae' -> './config/species/rhizopus_oryzae' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_exon_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_igenic_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_intron_probs.pbl' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_metapars.cfg' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_metapars.cfg' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg' 1113s '/usr/share/augustus/config/species/rhizopus_oryzae/rhizopus_oryzae_weightmatrix.txt' -> './config/species/rhizopus_oryzae/rhizopus_oryzae_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/rhodnius' -> './config/species/rhodnius' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_exon_probs.pbl' -> './config/species/rhodnius/rhodnius_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_igenic_probs.pbl' -> './config/species/rhodnius/rhodnius_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_intron_probs.pbl' -> './config/species/rhodnius/rhodnius_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_metapars.cfg' -> './config/species/rhodnius/rhodnius_metapars.cfg' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_metapars.utr.cfg' -> './config/species/rhodnius/rhodnius_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_parameters.cfg' -> './config/species/rhodnius/rhodnius_parameters.cfg' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_utr_probs.pbl' -> './config/species/rhodnius/rhodnius_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/rhodnius/rhodnius_weightmatrix.txt' -> './config/species/rhodnius/rhodnius_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/rice' -> './config/species/rice' 1113s '/usr/share/augustus/config/species/rice/README.TXT' -> './config/species/rice/README.TXT' 1113s '/usr/share/augustus/config/species/rice/rice_exon_probs.pbl' -> './config/species/rice/rice_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/rice/rice_igenic_probs.pbl' -> './config/species/rice/rice_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/rice/rice_intron_probs.pbl' -> './config/species/rice/rice_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/rice/rice_metapars.cfg' -> './config/species/rice/rice_metapars.cfg' 1113s '/usr/share/augustus/config/species/rice/rice_metapars.utr.cfg' -> './config/species/rice/rice_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/rice/rice_parameters.cfg' -> './config/species/rice/rice_parameters.cfg' 1113s '/usr/share/augustus/config/species/rice/rice_utr_probs.pbl' -> './config/species/rice/rice_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/rice/rice_weightmatrix.txt' -> './config/species/rice/rice_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/s_aureus' -> './config/species/s_aureus' 1113s '/usr/share/augustus/config/species/s_aureus/README.TXT' -> './config/species/s_aureus/README.TXT' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_exon_probs.pbl' -> './config/species/s_aureus/s_aureus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_igenic_probs.pbl' -> './config/species/s_aureus/s_aureus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_metapars.cfg' -> './config/species/s_aureus/s_aureus_metapars.cfg' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_metapars.utr.cfg' -> './config/species/s_aureus/s_aureus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_ovlp_len.pbl' -> './config/species/s_aureus/s_aureus_ovlp_len.pbl' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_parameters.cfg' -> './config/species/s_aureus/s_aureus_parameters.cfg' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_parameters.cgp.cfg' -> './config/species/s_aureus/s_aureus_parameters.cgp.cfg' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl' -> './config/species/s_aureus/s_aureus_trans_shadow_bacterium.pbl' 1113s '/usr/share/augustus/config/species/s_aureus/s_aureus_weightmatrix.txt' -> './config/species/s_aureus/s_aureus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/s_pneumoniae' -> './config/species/s_pneumoniae' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_exon_probs.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_igenic_probs.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_metapars.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_metapars.cfg' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_metapars.utr.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_ovlp_len.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_ovlp_len.pbl' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig2' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig3' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4' -> './config/species/s_pneumoniae/s_pneumoniae_parameters.cfg.orig4' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl' -> './config/species/s_pneumoniae/s_pneumoniae_trans_shadow_bacterium.pbl' 1113s '/usr/share/augustus/config/species/s_pneumoniae/s_pneumoniae_weightmatrix.txt' -> './config/species/s_pneumoniae/s_pneumoniae_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/saccharomyces' -> './config/species/saccharomyces' 1113s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_exon_probs.pbl' -> './config/species/saccharomyces/saccharomyces_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_igenic_probs.pbl' -> './config/species/saccharomyces/saccharomyces_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_intron_probs.pbl' -> './config/species/saccharomyces/saccharomyces_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_parameters.cfg' -> './config/species/saccharomyces/saccharomyces_parameters.cfg' 1113s '/usr/share/augustus/config/species/saccharomyces/saccharomyces_weightmatrix.txt' -> './config/species/saccharomyces/saccharomyces_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C' -> './config/species/saccharomyces_cerevisiae_S288C' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_metapars.cfg' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_metapars.cfg' 1113s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg' 1113s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_weightmatrix.txt' -> './config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/saccharomyces_cerevisiae_rm11-1a_1' -> './config/species/saccharomyces_cerevisiae_rm11-1a_1' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/schistosoma' -> './config/species/schistosoma' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_exon_probs.pbl' -> './config/species/schistosoma/schistosoma_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_igenic_probs.pbl' -> './config/species/schistosoma/schistosoma_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_intron_probs.pbl' -> './config/species/schistosoma/schistosoma_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_metapars.cfg' -> './config/species/schistosoma/schistosoma_metapars.cfg' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_parameters.cfg' -> './config/species/schistosoma/schistosoma_parameters.cfg' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_parameters.cfg.opt' -> './config/species/schistosoma/schistosoma_parameters.cfg.opt' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_splicefile.txt' -> './config/species/schistosoma/schistosoma_splicefile.txt' 1113s '/usr/share/augustus/config/species/schistosoma/schistosoma_weightmatrix.txt' -> './config/species/schistosoma/schistosoma_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/schistosoma2' -> './config/species/schistosoma2' 1113s '/usr/share/augustus/config/species/schistosoma2/README.TXT' -> './config/species/schistosoma2/README.TXT' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_exon_probs.pbl' -> './config/species/schistosoma2/schistosoma2_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_igenic_probs.pbl' -> './config/species/schistosoma2/schistosoma2_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_intron_probs.pbl' -> './config/species/schistosoma2/schistosoma2_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.cfg' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.cgp.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_metapars.utr.cfg' -> './config/species/schistosoma2/schistosoma2_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_parameters.cfg' -> './config/species/schistosoma2/schistosoma2_parameters.cfg' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_utr_probs.pbl' -> './config/species/schistosoma2/schistosoma2_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/schistosoma2/schistosoma2_weightmatrix.txt' -> './config/species/schistosoma2/schistosoma2_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe' -> './config/species/schizosaccharomyces_pombe' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg' 1113s '/usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt' -> './config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/scyliorhinus' -> './config/species/scyliorhinus' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_exon_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_igenic_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_intron_probs.pbl' -> './config/species/scyliorhinus/scyliorhinus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.cfg' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.cgp.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_metapars.utr.cfg' -> './config/species/scyliorhinus/scyliorhinus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_parameters.cfg' -> './config/species/scyliorhinus/scyliorhinus_parameters.cfg' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1' -> './config/species/scyliorhinus/scyliorhinus_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/scyliorhinus/scyliorhinus_weightmatrix.txt' -> './config/species/scyliorhinus/scyliorhinus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/sealamprey' -> './config/species/sealamprey' 1113s '/usr/share/augustus/config/species/sealamprey/sealamprey_exon_probs.pbl' -> './config/species/sealamprey/sealamprey_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/sealamprey/sealamprey_igenic_probs.pbl' -> './config/species/sealamprey/sealamprey_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/sealamprey/sealamprey_intron_probs.pbl' -> './config/species/sealamprey/sealamprey_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/sealamprey/sealamprey_metapars.cfg' -> './config/species/sealamprey/sealamprey_metapars.cfg' 1113s '/usr/share/augustus/config/species/sealamprey/sealamprey_parameters.cfg' -> './config/species/sealamprey/sealamprey_parameters.cfg' 1113s '/usr/share/augustus/config/species/sealamprey/sealamprey_weightmatrix.txt' -> './config/species/sealamprey/sealamprey_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus' -> './config/species/strongylocentrotus_purpuratus' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/README.TXT' -> './config/species/strongylocentrotus_purpuratus/README.TXT' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt' -> './config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus' -> './config/species/sulfolobus_solfataricus' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_exon_probs.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_igenic_probs.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.cfg' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.utr.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_ovlp_len.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_ovlp_len.pbl' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_trans_shadow_bacterium.pbl' 1113s '/usr/share/augustus/config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_weightmatrix.txt' -> './config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/sunflower' -> './config/species/sunflower' 1113s '/usr/share/augustus/config/species/sunflower/README.TXT' -> './config/species/sunflower/README.TXT' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_exon_probs.pbl' -> './config/species/sunflower/sunflower_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_igenic_probs.pbl' -> './config/species/sunflower/sunflower_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_intron_probs.pbl' -> './config/species/sunflower/sunflower_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.cfg' -> './config/species/sunflower/sunflower_metapars.cfg' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.cgp.cfg' -> './config/species/sunflower/sunflower_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_metapars.utr.cfg' -> './config/species/sunflower/sunflower_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_parameters.cfg' -> './config/species/sunflower/sunflower_parameters.cfg' 1113s '/usr/share/augustus/config/species/sunflower/sunflower_weightmatrix.txt' -> './config/species/sunflower/sunflower_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/template_prokaryotic' -> './config/species/template_prokaryotic' 1113s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_metapars.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_metapars.cfg' 1113s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl' -> './config/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl' 1113s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_parameters.cfg' -> './config/species/template_prokaryotic/template_prokaryotic_parameters.cfg' 1113s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl' -> './config/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl' 1113s '/usr/share/augustus/config/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt' -> './config/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/tetrahymena' -> './config/species/tetrahymena' 1113s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_exon_probs.pbl' -> './config/species/tetrahymena/tetrahymena_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_igenic_probs.pbl' -> './config/species/tetrahymena/tetrahymena_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_intron_probs.pbl' -> './config/species/tetrahymena/tetrahymena_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_metapars.cfg' -> './config/species/tetrahymena/tetrahymena_metapars.cfg' 1113s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_parameters.cfg' -> './config/species/tetrahymena/tetrahymena_parameters.cfg' 1113s '/usr/share/augustus/config/species/tetrahymena/tetrahymena_weightmatrix.txt' -> './config/species/tetrahymena/tetrahymena_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis' -> './config/species/thermoanaerobacter_tengcongensis' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_exon_probs.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_igenic_probs.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.cfg' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.utr.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_ovlp_len.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_ovlp_len.pbl' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_trans_shadow_bacterium.pbl' 1113s '/usr/share/augustus/config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_weightmatrix.txt' -> './config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/tomato' -> './config/species/tomato' 1113s '/usr/share/augustus/config/species/tomato/tomato_exon_probs.pbl' -> './config/species/tomato/tomato_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/tomato/tomato_igenic_probs.pbl' -> './config/species/tomato/tomato_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/tomato/tomato_intron_probs.pbl' -> './config/species/tomato/tomato_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/tomato/tomato_metapars.cfg' -> './config/species/tomato/tomato_metapars.cfg' 1113s '/usr/share/augustus/config/species/tomato/tomato_metapars.utr.cfg' -> './config/species/tomato/tomato_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/tomato/tomato_parameters.cfg' -> './config/species/tomato/tomato_parameters.cfg' 1113s '/usr/share/augustus/config/species/tomato/tomato_utr_probs.pbl' -> './config/species/tomato/tomato_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/tomato/tomato_weightmatrix.txt' -> './config/species/tomato/tomato_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/toxoplasma' -> './config/species/toxoplasma' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_exon_probs.pbl' -> './config/species/toxoplasma/toxoplasma_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_igenic_probs.pbl' -> './config/species/toxoplasma/toxoplasma_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_intron_probs.pbl' -> './config/species/toxoplasma/toxoplasma_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_metaparameters.cfg' -> './config/species/toxoplasma/toxoplasma_metaparameters.cfg' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_parameters.cfg' -> './config/species/toxoplasma/toxoplasma_parameters.cfg' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl' -> './config/species/toxoplasma/toxoplasma_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_utr_probs.pbl' -> './config/species/toxoplasma/toxoplasma_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/toxoplasma/toxoplasma_weightmatrix.txt' -> './config/species/toxoplasma/toxoplasma_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/tribolium2012' -> './config/species/tribolium2012' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl1' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl2' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl3' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_exon_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_exon_probs.pbl4' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl1' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl2' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl3' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_igenic_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_igenic_probs.pbl4' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl1' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl1' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl2' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl2' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl3' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl3' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_intron_probs.pbl4' -> './config/species/tribolium2012/tribolium2012_intron_probs.pbl4' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_metapars.cfg' -> './config/species/tribolium2012/tribolium2012_metapars.cfg' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_metapars.utr.cfg' -> './config/species/tribolium2012/tribolium2012_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg' -> './config/species/tribolium2012/tribolium2012_parameters.cfg' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig1' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig2' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig2' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig3' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig3' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig4' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig4' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig5' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig5' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig6' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig6' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_parameters.cfg.orig7' -> './config/species/tribolium2012/tribolium2012_parameters.cfg.orig7' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl' -> './config/species/tribolium2012/tribolium2012_trans_shadow_partial_utr.pbl' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_utr_probs.pbl' -> './config/species/tribolium2012/tribolium2012_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM' -> './config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/tribolium2012/tribolium2012_weightmatrix.txt' -> './config/species/tribolium2012/tribolium2012_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/trichinella' -> './config/species/trichinella' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_exon_probs.pbl' -> './config/species/trichinella/trichinella_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_igenic_probs.pbl' -> './config/species/trichinella/trichinella_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_intron_probs.pbl' -> './config/species/trichinella/trichinella_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_metapars.cfg' -> './config/species/trichinella/trichinella_metapars.cfg' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_metapars.utr.cfg' -> './config/species/trichinella/trichinella_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_parameters.cfg' -> './config/species/trichinella/trichinella_parameters.cfg' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_utr_probs.pbl' -> './config/species/trichinella/trichinella_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/trichinella/trichinella_weightmatrix.txt' -> './config/species/trichinella/trichinella_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/ustilago' -> './config/species/ustilago' 1113s '/usr/share/augustus/config/species/ustilago/ustilago_exon_probs.pbl' -> './config/species/ustilago/ustilago_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/ustilago/ustilago_igenic_probs.pbl' -> './config/species/ustilago/ustilago_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/ustilago/ustilago_intron_probs.pbl' -> './config/species/ustilago/ustilago_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/ustilago/ustilago_parameters.cfg' -> './config/species/ustilago/ustilago_parameters.cfg' 1113s '/usr/share/augustus/config/species/ustilago/ustilago_weightmatrix.txt' -> './config/species/ustilago/ustilago_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/ustilago_maydis' -> './config/species/ustilago_maydis' 1113s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_exon_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_igenic_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_intron_probs.pbl' -> './config/species/ustilago_maydis/ustilago_maydis_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_metapars.cfg' -> './config/species/ustilago_maydis/ustilago_maydis_metapars.cfg' 1113s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_parameters.cfg' -> './config/species/ustilago_maydis/ustilago_maydis_parameters.cfg' 1113s '/usr/share/augustus/config/species/ustilago_maydis/ustilago_maydis_weightmatrix.txt' -> './config/species/ustilago_maydis/ustilago_maydis_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/verticillium_albo_atrum1' -> './config/species/verticillium_albo_atrum1' 1113s '/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' 1113s '/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' 1113s '/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' 1113s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_metapars.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg' 1113s '/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' 1113s '/usr/share/augustus/config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_weightmatrix.txt' -> './config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1' -> './config/species/verticillium_longisporum1' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_exon_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_igenic_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_intron_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.cfg' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.utr.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_utr_probs.pbl' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/verticillium_longisporum1/verticillium_longisporum1_weightmatrix.txt' -> './config/species/verticillium_longisporum1/verticillium_longisporum1_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/volvox' -> './config/species/volvox' 1113s '/usr/share/augustus/config/species/volvox/volvox_exon_probs.pbl' -> './config/species/volvox/volvox_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/volvox/volvox_igenic_probs.pbl' -> './config/species/volvox/volvox_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/volvox/volvox_intron_probs.pbl' -> './config/species/volvox/volvox_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/volvox/volvox_metapars.cfg' -> './config/species/volvox/volvox_metapars.cfg' 1113s '/usr/share/augustus/config/species/volvox/volvox_metapars.cgp.cfg' -> './config/species/volvox/volvox_metapars.cgp.cfg' 1113s '/usr/share/augustus/config/species/volvox/volvox_metapars.utr.cfg' -> './config/species/volvox/volvox_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/volvox/volvox_parameters.cfg' -> './config/species/volvox/volvox_parameters.cfg' 1113s '/usr/share/augustus/config/species/volvox/volvox_utr_probs.pbl' -> './config/species/volvox/volvox_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/volvox/volvox_weightmatrix.txt' -> './config/species/volvox/volvox_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/wheat' -> './config/species/wheat' 1113s '/usr/share/augustus/config/species/wheat/README.txt' -> './config/species/wheat/README.txt' 1113s '/usr/share/augustus/config/species/wheat/wheat_exon_probs.pbl' -> './config/species/wheat/wheat_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/wheat/wheat_igenic_probs.pbl' -> './config/species/wheat/wheat_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/wheat/wheat_intron_probs.pbl' -> './config/species/wheat/wheat_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/wheat/wheat_parameters.cfg' -> './config/species/wheat/wheat_parameters.cfg' 1113s '/usr/share/augustus/config/species/wheat/wheat_utr_probs.pbl' -> './config/species/wheat/wheat_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/wheat/wheat_weightmatrix.txt' -> './config/species/wheat/wheat_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica' -> './config/species/yarrowia_lipolytica' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_exon_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_igenic_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_intron_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.cfg' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.utr.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_parameters.cfg' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_utr_probs.pbl' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_utr_probs.pbl' 1113s '/usr/share/augustus/config/species/yarrowia_lipolytica/yarrowia_lipolytica_weightmatrix.txt' -> './config/species/yarrowia_lipolytica/yarrowia_lipolytica_weightmatrix.txt' 1113s '/usr/share/augustus/config/species/zebrafish' -> './config/species/zebrafish' 1113s '/usr/share/augustus/config/species/zebrafish/README.TXT' -> './config/species/zebrafish/README.TXT' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_exon_probs.pbl' -> './config/species/zebrafish/zebrafish_exon_probs.pbl' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_exon_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_exon_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_igenic_probs.pbl' -> './config/species/zebrafish/zebrafish_igenic_probs.pbl' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_intron_probs.pbl' -> './config/species/zebrafish/zebrafish_intron_probs.pbl' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_intron_probs.pbl.HMM' -> './config/species/zebrafish/zebrafish_intron_probs.pbl.HMM' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_metapars.cfg' -> './config/species/zebrafish/zebrafish_metapars.cfg' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_metapars.utr.cfg' -> './config/species/zebrafish/zebrafish_metapars.utr.cfg' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_parameters.cfg' -> './config/species/zebrafish/zebrafish_parameters.cfg' 1113s '/usr/share/augustus/config/species/zebrafish/zebrafish_weightmatrix.txt' -> './config/species/zebrafish/zebrafish_weightmatrix.txt' 1113s Will create parameters for a EUKARYOTIC species! 1113s creating directory /tmp/tmp.jZDIZLXLNs/config/species/test/ ... 1113s creating /tmp/tmp.jZDIZLXLNs/config/species/test/test_parameters.cfg ... 1113s creating /tmp/tmp.jZDIZLXLNs/config/species/test/test_weightmatrix.txt ... 1113s creating /tmp/tmp.jZDIZLXLNs/config/species/test/test_metapars.cfg ... 1113s The necessary files for training test have been created. 1113s Now, either run etraining or optimize_parameters.pl with --species=test. 1113s etraining quickly estimates the parameters from a file with training genes. 1113s optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters. 1113s 1113s # Read in 1 genbank sequences. 1113s Quantiles of the GC contents in the training set: 1113s 0% 0.402 1113s 5% 0.402 10% 0.402 1113s 15% 0.402 20% 0.402 1113s 25% 0.402 30% 0.402 1113s 35% 0.402 40% 0.402 1113s 45% 0.402 50% 0.402 1113s 55% 0.402 60% 0.402 1113s 65% 0.402 70% 0.402 1113s 75% 0.402 80% 0.402 1113s 85% 0.402 90% 0.402 1113s 95% 0.402 100% 0.402 1113s HMM-training the parameters... 1113s i= 0 bc= (0.237, 0.263, 0.263, 0.237) 1113s ** building model for exons *EXON* 1113s start codon frequencies: ATG(1) 1113s # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) 1113s number of bases in the reading frames: 570 571 570 1113s --- frame = 0 --- minPatSum = 233 1113s --- frame = 1 --- minPatSum = 233 1113s --- frame = 2 --- minPatSum = 233 1113s --- initial frame = 0 --- minPatSum = 233 1113s --- initial frame = 1 --- minPatSum = 233 1113s --- initial frame = 2 --- minPatSum = 233 1113s --- internal exon terminal frame = 0 --- minPatSum = 233 1113s --- internal exon terminal frame = 1 --- minPatSum = 233 1113s --- internal exon terminal frame = 2 --- minPatSum = 233 1113s single, initial, internal, terminal mean exon lengths : 1113s n.a. 627 191 7 1113s single exon : 0 1113s initial exon 0 : 1 1113s initial exon 1 : 0 1113s initial exon 2 : 0 1113s internal exon 0 : 3 1113s internal exon 1 : 0 1113s internal exon 2 : 3 1113s terminal exon : 1 1113s Frequency of stop codons: 1113s tag: 0 (0) 1113s taa: 1 (1) 1113s tga: 0 (0) 1113s end *EXON* 1113s Storing parameters to file... 1113s Writing exon model parameters [1] to file /tmp/tmp.jZDIZLXLNs/config/species/test/test_exon_probs.pbl. 1113s # This output was generated with AUGUSTUS (version 3.5.0). 1113s # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 1113s # O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. 1113s # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 1113s # Using native and syntenically mapped cDNA alignments to improve de novo gene finding 1113s # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 1113s # No extrinsic information on sequences given. 1113s # Sources of extrinsic information: M RM 1113s # Initializing the parameters using config directory /tmp/tmp.jZDIZLXLNs/config/ ... 1113s # test version. Using default transition matrix. 1113s # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) 1113s # Looks like /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/example.fa is in fasta format. 1113s # We have hints for 0 sequences and for 0 of the sequences in the input set. 1113s # 1113s # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- 1113s # 1113s # Predicted genes for sequence number 1 on both strands 1113s # start gene g1 1113s HS04636 AUGUSTUS gene 1 1163 0.06 + . g1 1113s HS04636 AUGUSTUS transcript 1 1163 0.06 + . g1.t1 1113s HS04636 AUGUSTUS intron 1 350 0.36 + . transcript_id "g1.t1"; gene_id "g1"; 1113s HS04636 AUGUSTUS intron 673 856 0.17 + . transcript_id "g1.t1"; gene_id "g1"; 1113s HS04636 AUGUSTUS CDS 351 672 0.11 + 2 transcript_id "g1.t1"; gene_id "g1"; 1113s HS04636 AUGUSTUS CDS 857 1163 0.32 + 1 transcript_id "g1.t1"; gene_id "g1"; 1113s HS04636 AUGUSTUS stop_codon 1161 1163 . + 0 transcript_id "g1.t1"; gene_id "g1"; 1113s # protein sequence = [VQTRHGGGGGRGDSLRPRTSGPLRFLERKPSVLLPSPGIPSKAISPELALGSARAKTAKKKRHLAETCAPGAVELGEE 1113s # REGSDRRVGTTPSAPKLGQLPGFPIFSFPVRSTSRNSSAAPPSAPQPDALRQQSLPPRRALPAARMLARALLLCAVLALSHTGEYLAPRTGDSGSTHP 1113s # GRVSALTSWVYPSTPTSLRIEKLRDLGKSLDR] 1113s # Evidence for and against this transcript: 1113s # % of transcript supported by hints (any source): 0 1113s # CDS exons: 0/2 1113s # CDS introns: 0/2 1113s # 5'UTR exons and introns: 0/0 1113s # 3'UTR exons and introns: 0/0 1113s # hint groups fully obeyed: 0 1113s # incompatible hint groups: 0 1113s # end gene g1 1113s ### 1113s # 1113s # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- 1113s # 1113s # Predicted genes for sequence number 2 on both strands 1113s # start gene g2 1113s HS08198 AUGUSTUS gene 1 2271 0.02 - . g2 1113s HS08198 AUGUSTUS transcript 1 2271 0.02 - . g2.t1 1113s HS08198 AUGUSTUS intron 1 112 0.38 - . transcript_id "g2.t1"; gene_id "g2"; 1113s HS08198 AUGUSTUS intron 950 1314 0.05 - . transcript_id "g2.t1"; gene_id "g2"; 1113s HS08198 AUGUSTUS intron 2041 2116 0.39 - . transcript_id "g2.t1"; gene_id "g2"; 1113s HS08198 AUGUSTUS CDS 113 949 0.16 - 1 transcript_id "g2.t1"; gene_id "g2"; 1113s HS08198 AUGUSTUS CDS 1315 2040 0.26 - 1 transcript_id "g2.t1"; gene_id "g2"; 1113s HS08198 AUGUSTUS CDS 2117 2271 0.39 - 0 transcript_id "g2.t1"; gene_id "g2"; 1113s HS08198 AUGUSTUS start_codon 2269 2271 . - 0 transcript_id "g2.t1"; gene_id "g2"; 1113s # protein sequence = [MAYAREDLPSQIPRAEIGPVTLRGLQPTGSAGLLKRRGGGREGLGGTGAGPDRQKIPCPGWQGPDLRLVSRRTGSGHP 1113s # TGGVVSRGTDFSALELCAGLTSSLLQQRRDSAGASGPPHHAAMLAPAVHSPSRTWNWSAASQKPGAPRQGSGWTSAREWGWLSWGPAGDTHRTWGSRR 1113s # SGPQSGGPPGPAAQTHSGPSRSQGASGLQGRQGSWGPGTRRRGGLWERGLCVPCPSGPSSLLPHQACLSLLPGPLLSRRIRMGERKCVPMAHPAPRGG 1113s # PVSVQSLSACLVTEAGPHIPPGAERRVGVRVQGCSGTHSFRKVLTAMAVPWGATCSVVASARWPCSCRKRQAEPTATRSQVPANWGQTMGELEGTVGG 1113s # PLTCFPLHPPQLHLLPSPPQQLLPVSLYPSHNFYLPPSTPPNFYLLRIKIGLGLDGADGGCGPAWPLRLLAQRASCQEQSQEGRSPRGQHGGGSRVAG 1113s # LWEAKGSTTKSQDRVYSAVTEPSPGSPCPSVASPPPTSSLLVSLASICTSWQGLAPCPMYKVRVDLWLFIHFSCTPDFHRQSLALYTLSSLNHHPVVL 1113s # SPWP] 1113s # Evidence for and against this transcript: 1113s # % of transcript supported by hints (any source): 0 1113s # CDS exons: 0/3 1113s # CDS introns: 0/3 1113s # 5'UTR exons and introns: 0/0 1113s # 3'UTR exons and introns: 0/0 1113s # hint groups fully obeyed: 0 1113s # incompatible hint groups: 0 1113s # end gene g2 1113s ### 1113s # command line: 1113s # augustus --species=test /tmp/autopkgtest.vkTNZz/build.LDj/src/examples/example.fa 1113s autopkgtest [11:58:10]: test test-example-with-training: -----------------------] 1114s test-example-with-training PASS 1114s autopkgtest [11:58:11]: test test-example-with-training: - - - - - - - - - - results - - - - - - - - - - 1115s autopkgtest [11:58:12]: @@@@@@@@@@@@@@@@@@@@ summary 1115s test-example PASS 1115s test-example-with-training PASS 1141s Creating nova instance adt-noble-s390x-augustus-20240313-113937-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240312.img (UUID b0773a3c-d6d5-492e-ad15-d4b10dff01a1)...