Mercurial > repos > nick > dunovo
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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'b133d7a65a2371efa097a11ccf123587007e1662\n'-dirty
author | nick |
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date | Thu, 24 Aug 2017 01:56:34 -0400 |
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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 <handlers> 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 [31mplanemo couldn't find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.[0m [32m[1mStarting 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][0m