Mercurial > repos > yating-l > jbrowsearchivecreator

comparison test-data/only_genome/__main__.log @ 7:5d5fdcb798da draft

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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
comparison
equal deleted inserted replaced
6:237707a6b74d 7:5d5fdcb798da
1 DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode #### 1 2018-04-20 07:39:49,692 - root - INFO - #### JBrowseArchiveCreator: Start ####
2 2
3 DEBUG:root:Calling faToTwoBit: 3 2018-04-20 07:39:49,693 - root - DEBUG - ---- Welcome in JBrowseArchiveCreator Debug Mode ----
4 DEBUG:root:--------- 4
5 DEBUG:root: 5 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"}
6 DEBUG:root:Calling twoBitInfo: 6
7 DEBUG:root:--------- 7
8 DEBUG:root: 8 2018-04-20 07:39:49,693 - root - INFO - #### JBrowseArchiveCreator: Creating the Track Hub folder ####
9 DEBUG:root:Calling sort: 9
10 DEBUG:root:--------- 10 2018-04-20 07:39:49,693 - root - DEBUG - Calling faToTwoBit:
11 DEBUG:root: 11 2018-04-20 07:39:49,693 - root - DEBUG - ['faToTwoBit', u'/home/galaxy/galaxy/database/datasets/000/dbia3.fa.fasta', '/tmp/tmpzDAir8']
12 DEBUG:root:----- End of all_datatype_dictionary processing ----- 12 2018-04-20 07:39:49,693 - root - DEBUG - ---------
13 DEBUG:root:all_datatype_ordered_dictionary keys are: [] 13 2018-04-20 07:39:49,722 - root - DEBUG -
14 DEBUG:root:----- Beginning of Track adding processing ----- 14 2018-04-20 07:39:49,723 - root - DEBUG - Calling twoBitInfo:
15 DEBUG:root:----- End of Track adding processing ----- 15 2018-04-20 07:39:49,723 - root - DEBUG - ['twoBitInfo', '/tmp/tmpzDAir8', '/tmp/tmpgN38vZ']
16 DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! #### 16 2018-04-20 07:39:49,723 - root - DEBUG - ---------
17 2018-04-20 07:39:49,731 - root - DEBUG -
18 2018-04-20 07:39:49,731 - root - DEBUG - Calling sort:
19 2018-04-20 07:39:49,731 - root - DEBUG - ['sort', '-k2rn', '/tmp/tmpgN38vZ', '-o', '/tmp/tmpwk5mtf.chrom.sizes']
20 2018-04-20 07:39:49,731 - root - DEBUG - ---------
21 2018-04-20 07:39:49,735 - root - DEBUG -
22 2018-04-20 07:39:49,755 - root - DEBUG - Calling prepare-refseqs.pl:
23 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']
24 2018-04-20 07:39:49,756 - root - DEBUG - ---------
25 2018-04-20 07:39:49,881 - root - DEBUG -
26 2018-04-20 07:39:49,882 - root - INFO - #### JBrowseArchiveCreator: Preparing track data ####
27
28 2018-04-20 07:39:49,882 - root - DEBUG - ----- End of all_datatype_dictionary processing -----
29 2018-04-20 07:39:49,882 - root - INFO - #### JBrowseArchiveCreator: Adding tracks to Track Hub ####
30
31 2018-04-20 07:39:49,882 - root - DEBUG - ----- Beginning of Track adding processing -----
32 2018-04-20 07:39:49,882 - root - DEBUG - ----- End of Track adding processing -----
33 2018-04-20 07:39:49,882 - root - INFO - #### JBrowseArchiveCreator: Creating the HTML file ####
34
35 2018-04-20 07:39:49,882 - root - DEBUG - Calling generate-names.pl:
36 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']
37 2018-04-20 07:39:49,882 - root - DEBUG - ---------
38 2018-04-20 07:39:49,992 - root - DEBUG - Tracks:
39 DNA
40 Sampled input stats:
41 total namerec bytes 1120
42 namerecs converted to operations 70
43 total input bytes 0
44 avg record text bytes 16
45 operations made 551
46 name input records 70
47 operation stream estimated count 0
48 namerecs buffered 70
49 record stream estimated count 0
50 Removing existing contents of target dir /home/galaxy/galaxy/database/jobs/000/514/dataset_596_files/myHub/names
51 Hash store cache size: 2684 buckets
52 Using 1 chars for sort log names (16 sort logs)
53
54 2018-04-20 07:39:49,998 - root - DEBUG - ---- End of JBrowseArchiveCreator Debug Mode: Bye! ----
55
56 2018-04-20 07:39:49,998 - root - INFO - #### JBrowseArchiveCreator: Congratulation! Assembly Hub is created! ####
57