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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
author yating-l
date Thu, 22 Dec 2016 17:53:00 -0500
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abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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1 DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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2
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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3 DEBUG:root:Calling faToTwoBit:
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4 DEBUG:root:---------
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5 DEBUG:root:
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6 DEBUG:root:Calling twoBitInfo:
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7 DEBUG:root:---------
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8 DEBUG:root:
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9 DEBUG:root:Calling sort:
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10 DEBUG:root:---------
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11 DEBUG:root:
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12 DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat
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13 DEBUG:root:data_value: {u'index': u'/home/svc_galaxy/new/galaxy/database/files/_metadata_files/000/metadata_77.dat', u'order_index': u'11', u'name': u'HISAT2_Accepted_Hits', u'track_color': u'#000000', u'group_name': u'Default group'}
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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14 DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat
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15 DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
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16 DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1188.dat
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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17 DEBUG:root:data_value: {u'order_index': u'21', u'name': u'Multi-Fasta_GlimmerHMM_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Other group'}
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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18 DEBUG:root:Calling gff3ToGenePred:
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19 DEBUG:root:---------
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20 DEBUG:root:
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21 DEBUG:root:Calling genePredToBigGenePred:
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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22 DEBUG:root:---------
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23 DEBUG:root:
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24 DEBUG:root:Calling sort:
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25 DEBUG:root:---------
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26 DEBUG:root:
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27 DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpC7M6B_.sorted.bigGenePred
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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28 DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmppQM471.chrom.sizes
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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29 DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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30 DEBUG:root:typeOption: bed12+8
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31 DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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32 DEBUG:root:tab option: True
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33 DEBUG:root:Calling bedToBigBed:
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34 DEBUG:root:---------
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35 DEBUG:root:
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36 DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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37 DEBUG:root:data_value: {u'order_index': u'20', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Other group'}
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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38 DEBUG:root:Calling gtfToGenePred:
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39 DEBUG:root:---------
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40 DEBUG:root:
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41 DEBUG:root:Calling genePredToBigGenePred:
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42 DEBUG:root:---------
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43 DEBUG:root:
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44 DEBUG:root:Calling sort:
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45 DEBUG:root:---------
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46 DEBUG:root:
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47 DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpirJDCW.sortedBed.bigGenePred
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48 DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmppQM471.chrom.sizes
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49 DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
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50 DEBUG:root:typeOption: bed12+8
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51 DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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52 DEBUG:root:tab option: True
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53 DEBUG:root:Calling bedToBigBed:
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54 DEBUG:root:---------
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55 DEBUG:root:
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56 DEBUG:root:----- End of all_datatype_dictionary processing -----
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57 DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x1b78b90>, <BigWig.BigWig object at 0x1b78e10>, <Gtf.Gtf object at 0x1b78e90>, <Gff3.Gff3 object at 0x1b78e50>]
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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58 DEBUG:root:----- Beginning of Track adding processing -----
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59 DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Default group
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60 DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group)
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61 DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Default group
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62 DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group)
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63 DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Other group
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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64 DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group other_group)
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65 DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Other group
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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66 DEBUG:root:We just added track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb (in group other_group)
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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67 DEBUG:root:----- End of Track adding processing -----
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68 DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####