Mercurial > repos > iuc > umi_tools_extract

diff test-data/out_single.log @ 1:79436b3019e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
author iuc
date Tue, 29 Aug 2017 17:37:07 -0400
parents 418b961e0576
children d1015c2516b7
line wrap: on
line diff
--- a/test-data/out_single.log	Thu Aug 10 06:37:09 2017 -0400
+++ b/test-data/out_single.log	Tue Aug 29 17:37:07 2017 -0400
@@ -1,92 +1,37 @@
-# output generated by extract --bc-pattern=XXXNNN --stdin=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat --stdout /home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat
-# job started at Wed Aug  9 09:51:05 2017 on packer-test -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b
-# pid: 7652, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64
+# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpREDhtd/files/003/dataset_3766.dat --stdout /tmp/tmpREDhtd/files/003/dataset_3767.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpREDhtd/files/003/dataset_3768.dat
+# job started at Tue Aug 29 14:20:26 2017 on gaius -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393
+# pid: 21338, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
+# blacklist                               : None
+# compresslevel                           : 6
+# error_correct_cell                      : False
+# extract_method                          : string
+# filter_cell_barcode                     : None
+# filter_cell_barcodes                    : False
 # log2stderr                              : False
 # loglevel                                : 1
 # pattern                                 : XXXNNN
 # pattern2                                : None
 # prime3                                  : True
 # quality_encoding                        : phred33
+# quality_filter_mask                     : None
 # quality_filter_threshold                : 10
 # random_seed                             : None
 # read2_in                                : None
-# read2_out                               : None
+# read2_out                               : False
+# read2_stdout                            : False
+# reads_subset                            : None
+# reconcile                               : False
 # short_help                              : None
-# split                                   : False
-# stats                                   : True
 # stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
-# stdin                                   : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat' mode='r' encoding='UTF-8'>
-# stdlog                                  : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat' mode='a' encoding='UTF-8'>
-# stdout                                  : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat' mode='w' encoding='UTF-8'>
+# stdin                                   : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3766.dat' mode='r' encoding='UTF-8'>
+# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3768.dat' mode='a' encoding='UTF-8'>
+# stdout                                  : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3767.dat' mode='w' encoding='UTF-8'>
 # timeit_file                             : None
 # timeit_header                           : None
 # timeit_name                             : all
-Barcode	UMI	Sample	Count
-AAGTTA	TTA	AAG	1
-GGATTT	TTT	GGA	1
-GGATAG	TAG	GGA	1
-TTTTTT	TTT	TTT	4
-GAGAGG	AGG	GAG	1
-TTAGTT	GTT	TTA	1
-TGTAGA	AGA	TGT	1
-AGAGAT	GAT	AGA	1
-GAATAA	TAA	GAA	1
-TTGAGT	AGT	TTG	1
-TTTATT	ATT	TTT	1
-GTAAGG	AGG	GTA	1
-GAAGAG	GAG	GAA	1
-TGTTTG	TTG	TGT	1
-ATAATG	ATG	ATA	1
-TTAGAT	GAT	TTA	1
-GTCTGA	TGA	GTC	1
-ATCATC	ATC	ATC	1
-GTCACC	ACC	GTC	1
-AACTCC	TCC	AAC	1
-TTATTA	TTA	TTA	1
-TGTTGT	TGT	TGT	2
-GTTTAT	TAT	GTT	1
-ATGAGT	AGT	ATG	1
-ATAATT	ATT	ATA	1
-TTGGTT	GTT	TTG	1
-GTTTTG	TTG	GTT	1
-CACGTC	GTC	CAC	1
-TTGTGT	TGT	TTG	1
-TGAATT	ATT	TGA	1
-GGATGT	TGT	GGA	1
-AGTCAC	CAC	AGT	1
-GTTTTT	TTT	GTT	1
-TATAGT	AGT	TAT	1
-TTTTAT	TAT	TTT	1
-TAAAAA	AAA	TAA	1
-ATAGGT	GGT	ATA	1
-ATTTTA	TTA	ATT	1
-TGTATA	ATA	TGT	1
-TGTTTT	TTT	TGT	2
-AGATTT	TTT	AGA	1
-TAGAAT	AAT	TAG	1
-GAAGGA	GGA	GAA	1
-GTTTGA	TGA	GTT	1
-TTTTGT	TGT	TTT	1
-ATTTTT	TTT	ATT	1
-TGTTAT	TAT	TGT	1
-CAGGAT	GAT	CAG	1
-GTATTT	TTT	GTA	1
-TGGGTA	GTA	TGG	1
-AAAGTT	GTT	AAA	1
-GGTGTG	GTG	GGT	1
-AAGATC	ATC	AAG	1
-TAGGTT	GTT	TAG	1
-GAGTTA	TTA	GAG	1
-TTATTT	TTT	TTA	1
-GTTGTT	GTT	GTT	1
-AGGTTT	TTT	AGG	1
-TAAAGT	AGT	TAA	1
-AGTTTT	TTT	AGT	1
-TTTGAT	GAT	TTT	1
-ATAAAT	AAT	ATA	1
-GTTATT	ATT	GTT	1
-TTTTTA	TTA	TTT	1
-AAGTGT	TGT	AAG	1
-ATATAG	TAG	ATA	1
-TATAGA	AGA	TAT	1
-# job finished in 0 seconds at Wed Aug  9 09:51:05 2017 --  0.36  0.02  0.00  0.00 -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b
+# whitelist                               : None
+2017-08-29 14:20:26,493 INFO Starting barcode extraction
+2017-08-29 14:20:26,495 INFO Input Reads: 100
+2017-08-29 14:20:26,495 INFO Reads output: 72
+2017-08-29 14:20:26,495 INFO filtered: umi quality: 28
+# job finished in 0 seconds at Tue Aug 29 14:20:26 2017 --  0.75  0.02  0.00  0.00 -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393