Mercurial > repos > rmarenco > hubarchivecreator

annotate test-data/gtf_gff/__main__.log @ 29:7e8a8b732db3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Wed, 16 May 2018 18:04:20 -0400
parents
children
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7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
1 DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
2
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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3 DEBUG:root:Calling faToTwoBit:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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4 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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5 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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6 DEBUG:root:Calling twoBitInfo:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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7 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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8 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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9 DEBUG:root:Calling sort:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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10 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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11 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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12 DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1184.dat
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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13 DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'}
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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14 DEBUG:root:Calling gff3ToGenePred:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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15 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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16 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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17 DEBUG:root:Calling genePredToBigGenePred:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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18 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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19 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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20 DEBUG:root:Calling sort:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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21 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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22 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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23 DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp7sqcWp.sorted.bigGenePred
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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24 DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpp6ZdZ_.chrom.sizes
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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25 DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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26 DEBUG:root:typeOption: bed12+8
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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27 DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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28 DEBUG:root:tab option: True
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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29 DEBUG:root:Calling bedToBigBed:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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30 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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31 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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32 DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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33 DEBUG:root:data_value: {u'order_index': u'11', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'}
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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34 DEBUG:root:Calling gtfToGenePred:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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35 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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36 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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37 DEBUG:root:Calling genePredToBigGenePred:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
38 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
39 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
40 DEBUG:root:Calling sort:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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41 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
42 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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43 DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp66b4It.sortedBed.bigGenePred
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
44 DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpp6ZdZ_.chrom.sizes
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
45 DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
46 DEBUG:root:typeOption: bed12+8
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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47 DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
48 DEBUG:root:tab option: True
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
49 DEBUG:root:Calling bedToBigBed:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
50 DEBUG:root:---------
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
51 DEBUG:root:
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
52 DEBUG:root:----- End of all_datatype_dictionary processing -----
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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53 DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x1ecae10>, <Gff3.Gff3 object at 0x1ecad10>]
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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54 DEBUG:root:----- Beginning of Track adding processing -----
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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55 DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/groups.txt the group Default group
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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56 DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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57 DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/groups.txt the group Default group
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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58 DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff changeset
59 DEBUG:root:----- End of Track adding processing -----
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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60 DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####