Mercurial > repos > yating-l > jbrowsearchivecreator
diff test-data/only_genome/__main__.log @ 7:5d5fdcb798da draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
| author | yating-l |
|---|---|
| date | Fri, 20 Apr 2018 13:51:23 -0400 |
| parents | 237707a6b74d |
| children |
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--- a/test-data/only_genome/__main__.log Thu Feb 15 17:05:05 2018 -0500 +++ b/test-data/only_genome/__main__.log Fri Apr 20 13:51:23 2018 -0400 @@ -1,16 +1,57 @@ -DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### +2018-04-20 07:39:49,692 - root - INFO - #### JBrowseArchiveCreator: Start #### + +2018-04-20 07:39:49,693 - root - DEBUG - ---- Welcome in JBrowseArchiveCreator Debug Mode ---- + +2018-04-20 07:39:49,693 - root - DEBUG - JSON parameters: {"extra_files_path": "/home/galaxy/galaxy/database/jobs/000/514/dataset_596_files", "feature_tracks_type": "CanvasFeatures", "debug_mode": "false", "genome_name": "Dbia3", "fasta": {"false_path": "/home/galaxy/galaxy/database/datasets/000/dataset_595.dat", "name": "dbia3.fa"}, "tool_directory": "/home/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/yating-l/jbrowsearchivecreator/4a69515eed63/jbrowsearchivecreator", "user_email": "demo@apollo.com"} + + +2018-04-20 07:39:49,693 - root - INFO - #### JBrowseArchiveCreator: Creating the Track Hub folder #### + +2018-04-20 07:39:49,693 - root - DEBUG - Calling faToTwoBit: +2018-04-20 07:39:49,693 - root - DEBUG - ['faToTwoBit', u'/home/galaxy/galaxy/database/datasets/000/dbia3.fa.fasta', '/tmp/tmpzDAir8'] +2018-04-20 07:39:49,693 - root - DEBUG - --------- +2018-04-20 07:39:49,722 - root - DEBUG - +2018-04-20 07:39:49,723 - root - DEBUG - Calling twoBitInfo: +2018-04-20 07:39:49,723 - root - DEBUG - ['twoBitInfo', '/tmp/tmpzDAir8', '/tmp/tmpgN38vZ'] +2018-04-20 07:39:49,723 - root - DEBUG - --------- +2018-04-20 07:39:49,731 - root - DEBUG - +2018-04-20 07:39:49,731 - root - DEBUG - Calling sort: +2018-04-20 07:39:49,731 - root - DEBUG - ['sort', '-k2rn', '/tmp/tmpgN38vZ', '-o', '/tmp/tmpwk5mtf.chrom.sizes'] +2018-04-20 07:39:49,731 - root - DEBUG - --------- +2018-04-20 07:39:49,735 - root - DEBUG - +2018-04-20 07:39:49,755 - root - DEBUG - Calling prepare-refseqs.pl: +2018-04-20 07:39:49,756 - root - DEBUG - ['prepare-refseqs.pl', '--indexed_fasta', u'/home/galaxy/galaxy/database/datasets/000/dbia3.fa.fasta', '--out', u'/home/galaxy/galaxy/database/jobs/000/514/dataset_596_files/myHub'] +2018-04-20 07:39:49,756 - root - DEBUG - --------- +2018-04-20 07:39:49,881 - root - DEBUG - +2018-04-20 07:39:49,882 - root - INFO - #### JBrowseArchiveCreator: Preparing track data #### -DEBUG:root:Calling faToTwoBit: -DEBUG:root:--------- -DEBUG:root: -DEBUG:root:Calling twoBitInfo: -DEBUG:root:--------- -DEBUG:root: -DEBUG:root:Calling sort: -DEBUG:root:--------- -DEBUG:root: -DEBUG:root:----- End of all_datatype_dictionary processing ----- -DEBUG:root:all_datatype_ordered_dictionary keys are: [] -DEBUG:root:----- Beginning of Track adding processing ----- -DEBUG:root:----- End of Track adding processing ----- -DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### +2018-04-20 07:39:49,882 - root - DEBUG - ----- End of all_datatype_dictionary processing ----- +2018-04-20 07:39:49,882 - root - INFO - #### JBrowseArchiveCreator: Adding tracks to Track Hub #### + +2018-04-20 07:39:49,882 - root - DEBUG - ----- Beginning of Track adding processing ----- +2018-04-20 07:39:49,882 - root - DEBUG - ----- End of Track adding processing ----- +2018-04-20 07:39:49,882 - root - INFO - #### JBrowseArchiveCreator: Creating the HTML file #### + +2018-04-20 07:39:49,882 - root - DEBUG - Calling generate-names.pl: +2018-04-20 07:39:49,882 - root - DEBUG - ['generate-names.pl', '--hashBits', '4', '-v', '--out', u'/home/galaxy/galaxy/database/jobs/000/514/dataset_596_files/myHub'] +2018-04-20 07:39:49,882 - root - DEBUG - --------- +2018-04-20 07:39:49,992 - root - DEBUG - Tracks: + DNA +Sampled input stats: + total namerec bytes 1120 + namerecs converted to operations 70 + total input bytes 0 + avg record text bytes 16 + operations made 551 + name input records 70 + operation stream estimated count 0 + namerecs buffered 70 + record stream estimated count 0 +Removing existing contents of target dir /home/galaxy/galaxy/database/jobs/000/514/dataset_596_files/myHub/names +Hash store cache size: 2684 buckets +Using 1 chars for sort log names (16 sort logs) + +2018-04-20 07:39:49,998 - root - DEBUG - ---- End of JBrowseArchiveCreator Debug Mode: Bye! ---- + +2018-04-20 07:39:49,998 - root - INFO - #### JBrowseArchiveCreator: Congratulation! Assembly Hub is created! #### +