# HG changeset patch # User nick # Date 1503554353 14400 # Node ID 134117de3cd0e4d7cbe2107a6c02b29768d2cf4e # Parent 004187820b7c6d59c57d22228fce48f5bf3487f3 planemo upload for repository https://github.com/galaxyproject/dunovo commit b'b133d7a65a2371efa097a11ccf123587007e1662\n'-dirty diff -r 004187820b7c -r 134117de3cd0 stderr.log --- a/stderr.log Thu Aug 24 01:56:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -DEBUG:galaxy.app:python path is: /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/scripts, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/lib, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/plat-x86_64-linux-gnu, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/lib-tk, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/lib-old, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/lib/python2.7/lib-dynload, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/local/lib/python2.7/site-packages -WARNING:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config -INFO:galaxy.config:Logging at '20' level to 'stdout' -/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. - 'storage.' % (dialect.name, dialect.driver)) -/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/default_comparator.py:153: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. - 'strategies for improved performance.' % expr) -127.0.0.1 - - [24/Aug/2017:00:44:41 -0500] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:43 -0500] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /api/genomes HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /welcome HTTP/1.1" 302 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:44 -0500] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:45 -0500] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:45 -0500] "GET /api/histories/2891970512fa2d5a/contents?limit=500&offset=0&details=8155e4b4bf1581ff&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:45 -0500] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:44:47 -0500] "GET /api/histories/2891970512fa2d5a/contents?keys=type_id%2Celement_count&details=8155e4b4bf1581ff&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:05 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:06 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A44%3A44.973Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:06 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:11 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A07.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:16 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A11.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:20 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A16.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:23 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A20.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:24 -0500] "GET /api/tools/make_families/build?tool_version=0.7.6 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:25 -0500] "GET /api/tools/make_families/citations HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:28 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A23.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:32 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A28.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:32 -0500] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:32 -0500] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:33 -0500] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:33 -0500] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:36 -0500] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:37 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:38 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:38 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A32.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:43 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A39.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=make_families&version=0.7.6&__identifer=kaecv2vv1vc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:45 -0500] "GET /api/tools/correct_barcodes/build?tool_version=0.7.6 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:45 -0500] "GET /api/tools/correct_barcodes/citations HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:47 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A43.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:45:51 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A47.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A45%3A51.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:01 -0500] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:03 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:04 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:04 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A01.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=correct_barcodes&version=0.7.6&__identifer=gguy4pae1ww" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:06 -0500] "GET /api/tools/align_families/build?tool_version=0.7.6 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:07 -0500] "GET /api/tools/align_families/citations HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:08 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A04.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:09 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:10 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:10 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A08.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=align_families&version=0.7.6&__identifer=v1t0xi3payc" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:12 -0500] "GET /api/tools/dunovo/build?tool_version=0.7.6 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:12 -0500] "GET /api/tools/dunovo/citations HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:14 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A10.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:16 -0500] "POST /api/tools HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:19 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A14.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:23 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A19.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:27 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A23.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:31 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/54f2a3a23292eb07 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:31 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff%2C54f2a3a23292eb07&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A27.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:32 -0500] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:32 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff%2C54f2a3a23292eb07&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A31.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:33 -0500] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:33 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/8155e4b4bf1581ff HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:33 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/8155e4b4bf1581ff HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:34 -0500] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:37 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A33.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:38 -0500] "GET /datasets/8155e4b4bf1581ff/show_params HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:41 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A37.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:42 -0500] "GET /datasets/8155e4b4bf1581ff/stderr HTTP/1.1" 200 - "http://localhost:9090/datasets/8155e4b4bf1581ff/show_params" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:46 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A41.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:50 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A46.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:54 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A50.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:46:58 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=8155e4b4bf1581ff&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A54.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:00 -0500] "GET /api/histories/2891970512fa2d5a/contents/datasets/7b55dbb89df8f4e5 HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:02 -0500] "GET /datasets/7b55dbb89df8f4e5/show_params HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:03 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=7b55dbb89df8f4e5&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A46%3A58.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:06 -0500] "GET /datasets/7b55dbb89df8f4e5/stderr HTTP/1.1" 200 - "http://localhost:9090/datasets/7b55dbb89df8f4e5/show_params" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:07 -0500] "GET /api/histories/2891970512fa2d5a/contents?details=7b55dbb89df8f4e5&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-08-24T05%3A47%3A03.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:08 -0500] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" -127.0.0.1 - - [24/Aug/2017:00:47:08 -0500] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/?tool_id=dunovo&version=0.7.6&__identifer=01cdg74ii97a" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:55.0) Gecko/20100101 Firefox/55.0" - -Aborted! diff -r 004187820b7c -r 134117de3cd0 stdout.log --- a/stdout.log Thu Aug 24 01:56:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,476 +0,0 @@ -Activating virtualenv at .venv -Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages -Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) -Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) -Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) -Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) -Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) -Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) -Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) -Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 15)) -Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) -Requirement already satisfied: docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) -Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) -Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) -Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) -Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) -Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) -Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) -Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) -Requirement already satisfied: Babel==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) -Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) -Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) -Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) -Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) -Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) -Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) -Requirement already satisfied: testfixtures==4.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) -Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) -Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) -Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) -Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) -Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) -Requirement already satisfied: requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) -Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 43)) -Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) -Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) -Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) -Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) -Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) -Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) -Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) -Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) -Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) -Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) -Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 62)) -Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) -Requirement already satisfied: Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) -Requirement already satisfied: paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) -Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 68)) -Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) -Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 52)) -Activating virtualenv at .venv -galaxy.queue_worker INFO 2017-08-24 00:35:46,653 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:// -galaxy.model.migrate.check INFO 2017-08-24 00:35:46,802 Migrating 127 -> 128... -galaxy.model.migrate.check INFO 2017-08-24 00:35:47,628 -galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 Migration script to add session update time (used for timeouts) -galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 -galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 -galaxy.model.migrate.check INFO 2017-08-24 00:35:47,629 Migrating 128 -> 129... -galaxy.model.migrate.check INFO 2017-08-24 00:35:48,566 -galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 Migration script to allow invalidation of job external output metadata temp files -galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 -galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 -galaxy.model.migrate.check INFO 2017-08-24 00:35:48,567 Migrating 129 -> 130... -galaxy.model.migrate.check INFO 2017-08-24 00:35:49,462 -galaxy.model.migrate.check INFO 2017-08-24 00:35:49,462 Migration script to change the 'value' column of 'user_preference' table from varchar to text. -galaxy.model.migrate.check INFO 2017-08-24 00:35:49,463 -galaxy.model.migrate.check INFO 2017-08-24 00:35:49,463 -galaxy.model.migrate.check INFO 2017-08-24 00:35:49,463 Migrating 130 -> 131... -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,375 -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 Migration script to support subworkflows and workflow request input parameters -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,376 Migrating 131 -> 132... -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,421 -galaxy.model.migrate.check INFO 2017-08-24 00:35:50,422 Migrating 132 -> 133... -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,403 -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 Add dependencies column to jobs table -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,404 Migrating 133 -> 134... -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,436 -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 Migration script to set the 'deleted' column of the -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 'history_dataset_association' table to True if 'purged' is True. -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 -galaxy.model.migrate.check INFO 2017-08-24 00:35:51,437 -galaxy.config INFO 2017-08-24 00:35:51,463 Install database targetting Galaxy's database configuration. -galaxy.visualization.genomes ERROR 2017-08-24 00:35:52,535 Error reading twobit.loc -Traceback (most recent call last): - File "/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes - for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ): -IOError: [Errno 2] No such file or directory: '/home/me/annex/Work/PSU/Nekrutenko/code/galaxy/tool-data/twobit.loc' -galaxy.util.handlers INFO 2017-08-24 00:35:52,551 Setting default to child with id 'main' -galaxy.tools.toolbox.watcher INFO 2017-08-24 00:35:52,552 Watchdog library unavailable, cannot monitor tools. -galaxy.tools.toolbox.base INFO 2017-08-24 00:35:52,678 Parsing the tool configuration /tmp/tmp07upmy58/tool_conf.xml -galaxy.tools.toolbox.base INFO 2017-08-24 00:35:52,708 Parsing the tool configuration /tmp/tmp07upmy58/shed_tools_conf.xml -galaxy.tools.toolbox.base INFO 2017-08-24 00:35:52,708 Parsing the tool configuration /tmp/tmp07upmy58/empty_tool_conf.xml -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,963 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,964 Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,976 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:52,986 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,006 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,015 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,017 Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,020 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.display_applications.application ERROR 2017-08-24 00:35:53,021 Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". -galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,254 VisualizationsRegistry, loaded plugin: charts -galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,256 Visualizations plugin disabled: Circster. Skipping... -galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,257 template syntax is deprecated: use entry_point instead -galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,257 VisualizationsRegistry, loaded plugin: csg -galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,258 template syntax is deprecated: use entry_point instead -galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,258 VisualizationsRegistry, loaded plugin: graphviz -galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,259 VisualizationsRegistry, loaded plugin: phyloviz -galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,260 VisualizationsRegistry, loaded plugin: scatterplot -galaxy.visualization.plugins.config_parser INFO 2017-08-24 00:35:53,261 Visualizations plugin disabled: Sweepster. Skipping... -galaxy.web.base.pluginframework INFO 2017-08-24 00:35:53,262 VisualizationsRegistry, loaded plugin: trackster -galaxy.tours INFO 2017-08-24 00:35:53,302 Loaded tour 'core.history' -galaxy.tours INFO 2017-08-24 00:35:53,352 Loaded tour 'core.galaxy_ui' -galaxy.tours INFO 2017-08-24 00:35:53,370 Loaded tour 'core.scratchbook' -galaxy.webhooks WARNING 2017-08-24 00:35:53,370 directory not found: /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config -galaxy.jobs INFO 2017-08-24 00:35:53,374 Handler 'main' will load all configured runner plugins -galaxy.jobs.handler INFO 2017-08-24 00:35:53,377 job handler stop queue started -galaxy.jobs.handler INFO 2017-08-24 00:35:53,397 job handler queue started -galaxy.app INFO 2017-08-24 00:35:53,417 Galaxy app startup finished (6932.671 ms) -galaxy.queue_worker INFO 2017-08-24 00:35:54,390 Binding and starting galaxy control worker for main -Starting server in PID 1730. -serving on http://127.0.0.1:9090 -galaxy.tools.actions.upload_common INFO 2017-08-24 00:45:06,455 tool upload1 created job id 1 -galaxy.jobs.handler INFO 2017-08-24 00:45:07,438 (1) Job dispatched -galaxy.tools.actions.upload_common INFO 2017-08-24 00:45:08,061 tool upload1 created job id 2 -galaxy.jobs.handler INFO 2017-08-24 00:45:08,599 (2) Job dispatched -Fetching package metadata ....Fetching package metadata ......................... -.Solving package specifications: . -......... - -Package plan for installation in environment /home/me/miniconda3/envs/__samtools@1.3.1: - -The following NEW packages will be INSTALLED: - - curl: 7.54.1-0 - krb5: 1.13.2-0 - libgcc: 5.2.0-0 - libssh2: 1.8.0-0 - openssl: 1.0.2l-0 - samtools: 1.3.1-5 bioconda - zlib: 1.2.11-0 - -Linking packages ... -[ ]| | 0% [krb5 ]| | 0% [libgcc ]|####### | 14% [openssl ]|############## | 28% [zlib ]|##################### | 42% [libssh2 ]|############################ | 57% [curl ]|################################### | 71% [samtools ]|########################################## | 85% [ COMPLETE ]|##################################################| 100% -# -# To activate this environment, use: -# > source activate __samtools@1.3.1 -# -# To deactivate this environment, use: -# > source deactivate __samtools@1.3.1 -# - -Solving package specifications: .....galaxy.jobs.command_factory INFO 2017-08-24 00:45:23,721 Built script [/tmp/tmp07upmy58/job_working_directory/000/1/tool_script.sh] for tool command [export PATH=$PATH:'/home/me/miniconda3/envs/__samtools@1.3.1/bin' ; python /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/tools/data_source/upload.py /home/me/annex/Work/PSU/Nekrutenko/code/galaxy /tmp/tmp07upmy58/tmp/tmpH5Wi0b /tmp/tmp07upmy58/tmp/tmpzTbkTw 1:/tmp/tmp07upmy58/job_working_directory/000/1/dataset_1_files:/tmp/tmp07upmy58/files/000/dataset_1.dat] -..... - -Package plan for installation in environment /home/me/miniconda3/envs/__samtools@1.3.1: - -The following NEW packages will be INSTALLED: - - curl: 7.54.1-0 - krb5: 1.13.2-0 - libgcc: 5.2.0-0 - libssh2: 1.8.0-0 - openssl: 1.0.2l-0 - samtools: 1.3.1-5 bioconda - zlib: 1.2.11-0 - -Linking packages ... -[ ]| | 0% [krb5 ]| | 0% [libgcc ]|####### | 14% [openssl ]|############## | 28% [zlib ]|##################### | 42% [libssh2 ]|############################ | 57% [curl ]|################################### | 71% [samtools ]|########################################## | 85% [ COMPLETE ]|##################################################| 100% -# -# To activate this environment, use: -# > source activate __samtools@1.3.1 -# -# To deactivate this environment, use: -# > source deactivate __samtools@1.3.1 -# - -galaxy.jobs.command_factory INFO 2017-08-24 00:45:25,065 Built script [/tmp/tmp07upmy58/job_working_directory/000/2/tool_script.sh] for tool command [export PATH=$PATH:'/home/me/miniconda3/envs/__samtools@1.3.1/bin' ; python /home/me/annex/Work/PSU/Nekrutenko/code/galaxy/tools/data_source/upload.py /home/me/annex/Work/PSU/Nekrutenko/code/galaxy /tmp/tmp07upmy58/tmp/tmpH5Wi0b /tmp/tmp07upmy58/tmp/tmpPyOeqY 2:/tmp/tmp07upmy58/job_working_directory/000/2/dataset_2_files:/tmp/tmp07upmy58/files/000/dataset_2.dat] -galaxy.tools.actions INFO 2017-08-24 00:45:38,032 Handled output named output for tool make_families (66.517 ms) -galaxy.tools.actions INFO 2017-08-24 00:45:38,085 Added output datasets to history (53.548 ms) -galaxy.tools.actions INFO 2017-08-24 00:45:38,226 Verified access to datasets for Job[unflushed,tool_id=make_families] (44.432 ms) -galaxy.tools.actions INFO 2017-08-24 00:45:38,227 Setup for job Job[unflushed,tool_id=make_families] complete, ready to flush (141.180 ms) -galaxy.tools.actions INFO 2017-08-24 00:45:38,272 Flushed transaction for job Job[id=3,tool_id=make_families] (44.434 ms) -galaxy.jobs.handler INFO 2017-08-24 00:45:38,638 (3) Job dispatched -Fetching package metadata ............... -Solving package specifications: .......... - -Package plan for installation in environment /home/me/miniconda3/envs/__dunovo@0.7.6: - -The following packages will be downloaded: - - package | build - ---------------------------|----------------- - dunovo-0.7.6 | py27_1 93 KB bioconda - -The following NEW packages will be INSTALLED: - - bowtie2: 2.2.5-py27_2 bioconda - decorator: 4.1.2-py27_0 - dunovo: 0.7.6-py27_1 bioconda - gawk: 4.1.3-1 bioconda - gmp: 6.1.0-0 - libgcc: 5.2.0-0 - mafft: 7.221-0 bioconda - mpfr: 3.1.5-0 - networkx: 1.11-py27_0 - openssl: 1.0.2l-0 - paste: 1.7.5.1-py27_0 - perl: 5.22.0.1-0 conda-forge - perl-threaded: 5.22.0-pl5.22.0_12 bioconda - pip: 9.0.1-py27_1 - python: 2.7.13-0 - readline: 6.2-2 - samtools: 0.1.18-0 bioconda - setuptools: 27.2.0-py27_0 - sqlite: 3.13.0-0 - tk: 8.5.18-0 - wheel: 0.29.0-py27_0 - zlib: 1.2.11-0 - -Fetching packages ... -dunovo-0.7.6-p 0% | | ETA: --:--:-- 0.00 B/s dunovo-0.7.6-p 17% |##### | ETA: 0:00:00 195.57 kB/s dunovo-0.7.6-p 34% |########## | ETA: 0:00:00 196.41 kB/s dunovo-0.7.6-p 51% |################ | ETA: 0:00:00 193.80 kB/s dunovo-0.7.6-p 69% |##################### | ETA: 0:00:00 245.93 kB/s dunovo-0.7.6-p 86% |########################## | ETA: 0:00:00 231.86 kB/s dunovo-0.7.6-p 100% |###############################| ETA: 0:00:00 267.10 kB/s dunovo-0.7.6-p 100% |###############################| Time: 0:00:00 266.82 kB/s -Extracting packages ... -[ ]| | 0% [dunovo ]| | 0% [ COMPLETE ]|##################################################| 100% -Linking packages ... -[ COMPLETE ]| | 0% [gmp ]| | 0% [gmp ]| | 0% [libgcc ]|## | 4% [mafft ]|#### | 9% [openssl ]|###### | 13% [perl ]|######### | 18% [readline ]|########### | 22% [samtools ]|############# | 27% [sqlite ]|############### | 31% [tk ]|################## | 36% [zlib ]|#################### | 40% [mpfr ]|###################### | 45% [perl-threaded ]|######################### | 50% [python ]|########################### | 54% [bowtie2 ]|############################# | 59% [decorator ]|############################### | 63% [gawk ]|################################## | 68% [paste ]|#################################### | 72% [setuptools ]|###################################### | 77% [wheel ]|######################################## | 81% [networkx ]|########################################### | 86% [pip ]|############################################# | 90% [dunovo ]|############################################### | 95% [ COMPLETE ]|##################################################| 100% -# -# To activate this environment, use: -# > source activate __dunovo@0.7.6 -# -# To deactivate this environment, use: -# > source deactivate __dunovo@0.7.6 -# - -galaxy.jobs.command_factory INFO 2017-08-24 00:45:51,239 Built script [/tmp/tmp07upmy58/job_working_directory/000/3/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/__dunovo@0.7.6" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/__dunovo@0.7.6' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; make-families.sh -t 12 -i 5 '/tmp/tmp07upmy58/files/000/dataset_1.dat' '/tmp/tmp07upmy58/files/000/dataset_2.dat' > '/tmp/tmp07upmy58/files/000/dataset_3.dat'] -galaxy.tools.actions INFO 2017-08-24 00:46:03,656 Handled output named output for tool correct_barcodes (40.340 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:03,694 Added output datasets to history (37.250 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:03,742 Verified access to datasets for Job[unflushed,tool_id=correct_barcodes] (17.873 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:03,743 Setup for job Job[unflushed,tool_id=correct_barcodes] complete, ready to flush (49.015 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:03,784 Flushed transaction for job Job[id=4,tool_id=correct_barcodes] (40.814 ms) -galaxy.jobs.handler INFO 2017-08-24 00:46:04,804 (4) Job dispatched -Fetching package metadata ............galaxy.tools.actions INFO 2017-08-24 00:46:10,065 Handled output named output for tool align_families (56.555 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:10,105 Added output datasets to history (39.822 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:10,192 Verified access to datasets for Job[unflushed,tool_id=align_families] (37.500 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:10,195 Setup for job Job[unflushed,tool_id=align_families] complete, ready to flush (88.615 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:10,237 Flushed transaction for job Job[id=5,tool_id=align_families] (41.788 ms) -... -Solving package specifications: .......... - -Package plan for installation in environment /home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963: - -The following NEW packages will be INSTALLED: - - bowtie2: 2.2.5-py27_2 bioconda - decorator: 4.1.2-py27_0 - dunovo: 0.7.6-py27_1 bioconda - gawk: 4.1.3-1 bioconda - gmp: 6.1.0-0 - libgcc: 5.2.0-0 - mafft: 7.221-0 bioconda - mpfr: 3.1.5-0 - networkx: 1.9.1-py27_0 - openssl: 1.0.2l-0 - paste: 1.7.5.1-py27_0 - perl: 5.22.0.1-0 conda-forge - perl-threaded: 5.22.0-pl5.22.0_12 bioconda - pip: 9.0.1-py27_1 - python: 2.7.13-0 - readline: 6.2-2 - samtools: 0.1.18-0 bioconda - setuptools: 27.2.0-py27_0 - sqlite: 3.13.0-0 - tk: 8.5.18-0 - wheel: 0.29.0-py27_0 - zlib: 1.2.11-0 - -Linking packages ... -[ ]| | 0% [gmp ]| | 0% [libgcc ]|## | 4% [mafft ]|#### | 9% [openssl ]|###### | 13% [perl ]|######### | 18% [readline ]|########### | 22% [samtools ]|############# | 27% [sqlite ]|############### | 31% [tk ]|################## | 36% [zlib ]|#################### | 40% [mpfr ]|###################### | 45% [perl-threaded ]|######################### | 50% [python ]|########################### | 54% [bowtie2 ]|############################# | 59% [decorator ]|############################### | 63% [gawk ]|################################## | 68% [paste ]|#################################### | 72% [setuptools ]|###################################### | 77% [wheel ]|######################################## | 81% [networkx ]|########################################### | 86% [pip ]|############################################# | 90% [dunovo ]|############################################### | 95% [ COMPLETE ]|##################################################| 100% -# -# To activate this environment, use: -# > source activate mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963 -# -# To deactivate this environment, use: -# > source deactivate mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963 -# - -galaxy.jobs.command_factory INFO 2017-08-24 00:46:16,539 Built script [/tmp/tmp07upmy58/job_working_directory/000/4/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-837716c913f249edfdaa53d2ee161a55357665e36901de6e5b9d84e69d2a1963' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; baralign.sh '/tmp/tmp07upmy58/files/000/dataset_3.dat' refdir barcodes.bam && samtools view -f 256 barcodes.bam | correct.py --test --galaxy --phone-home -d 1 -m 20 -p 2 '/tmp/tmp07upmy58/files/000/dataset_3.dat' refdir/barcodes.fa | sort > '/tmp/tmp07upmy58/files/000/dataset_4.dat'] -galaxy.tools.actions INFO 2017-08-24 00:46:17,240 Handled output named dcs1 for tool dunovo (147.411 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,371 Handled output named dcs2 for tool dunovo (130.913 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,434 Handled output named sscs1 for tool dunovo (61.859 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,503 Handled output named sscs2 for tool dunovo (68.277 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,535 Added output datasets to history (32.005 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,593 Verified access to datasets for Job[unflushed,tool_id=dunovo] (20.434 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,595 Setup for job Job[unflushed,tool_id=dunovo] complete, ready to flush (59.546 ms) -galaxy.tools.actions INFO 2017-08-24 00:46:17,647 Flushed transaction for job Job[id=6,tool_id=dunovo] (51.808 ms) -galaxy.jobs.handler INFO 2017-08-24 00:46:33,411 (5) Job dispatched -Fetching package metadata ............... -Solving package specifications: .......... - -Package plan for installation in environment /home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6: - -The following NEW packages will be INSTALLED: - - bowtie2: 2.2.5-py27_2 bioconda - decorator: 4.1.2-py27_0 - dunovo: 0.7.6-py27_1 bioconda - gawk: 4.1.3-1 bioconda - gmp: 6.1.0-0 - libgcc: 5.2.0-0 - mafft: 7.221-0 bioconda - mpfr: 3.1.5-0 - networkx: 1.11-py27_0 - openssl: 1.0.2l-0 - paste: 1.7.5.1-py27_0 - perl: 5.22.0.1-0 conda-forge - perl-threaded: 5.22.0-pl5.22.0_12 bioconda - pip: 9.0.1-py27_1 - python: 2.7.13-0 - readline: 6.2-2 - samtools: 0.1.18-0 bioconda - setuptools: 27.2.0-py27_0 - sqlite: 3.13.0-0 - tk: 8.5.18-0 - wheel: 0.29.0-py27_0 - zlib: 1.2.11-0 - -Linking packages ... -[ ]| | 0% [gmp ]| | 0% [libgcc ]|## | 4% [mafft ]|#### | 9% [openssl ]|###### | 13% [perl ]|######### | 18% [readline ]|########### | 22% [samtools ]|############# | 27% [sqlite ]|############### | 31% [tk ]|################## | 36% [zlib ]|#################### | 40% [mpfr ]|###################### | 45% [perl-threaded ]|######################### | 50% [python ]|########################### | 54% [bowtie2 ]|############################# | 59% [decorator ]|############################### | 63% [gawk ]|################################## | 68% [paste ]|#################################### | 72% [setuptools ]|###################################### | 77% [wheel ]|######################################## | 81% [networkx ]|########################################### | 86% [pip ]|############################################# | 90% [dunovo ]|############################################### | 95% [ COMPLETE ]|##################################################| 100% -# -# To activate this environment, use: -# > source activate mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6 -# -# To deactivate this environment, use: -# > source deactivate mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6 -# - -galaxy.jobs.command_factory INFO 2017-08-24 00:46:45,677 Built script [/tmp/tmp07upmy58/job_working_directory/000/5/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; [ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/mulled-v1-f130555a7ab5a2897b0d3a6b9195fe3b5879290766ec6b1a17ad1e97c4b1cdf6' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; align_families.py --test --galaxy --phone-home -p ${GALAXY_SLOTS:-1} '/tmp/tmp07upmy58/files/000/dataset_4.dat' > '/tmp/tmp07upmy58/files/000/dataset_5.dat'] -galaxy.jobs.handler INFO 2017-08-24 00:46:56,416 (6) Job dispatched -galaxy.jobs.command_factory INFO 2017-08-24 00:46:56,858 Built script [/tmp/tmp07upmy58/job_working_directory/000/6/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/me/miniconda3/envs/__dunovo@0.7.6" ] || -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . /home/me/miniconda3/bin/activate '/home/me/miniconda3/envs/__dunovo@0.7.6' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done ; dunovo.py --test --galaxy --phone-home -r 3 -q 25 -F sanger '/tmp/tmp07upmy58/files/000/dataset_5.dat' --sscs-file sscs.fa > duplex.fa && outconv.py duplex.fa -1 '/tmp/tmp07upmy58/files/000/dataset_6.dat' -2 '/tmp/tmp07upmy58/files/000/dataset_7.dat' && outconv.py sscs.fa -1 '/tmp/tmp07upmy58/files/000/dataset_8.dat' -2 '/tmp/tmp07upmy58/files/000/dataset_9.dat'] -Starting subprocess with file monitor -^C caught in monitor process -planemo couldn't find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data. -Starting galaxy with command [cd /home/me/bx/code/galaxy; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/me/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/me/annex/Work/PSU/Nekrutenko/code/duplex/.venv/bin/virtualenv -p /usr/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; /home/me/bx/code/galaxy/run.sh $COMMON_STARTUP_ARGS --server-name 'planemo99092' --reload]