Mercurial > repos > iuc > umi_tools_extract

comparison test-data/out_single.log @ 1:c4db6345a30b draft

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planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
author iuc
date Tue, 29 Aug 2017 17:36:22 -0400
parents 34740e5db333
children 3b1fa3eb961f
comparison
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0:34740e5db333 1:c4db6345a30b
1 # 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 1 # 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
2 # job started at Wed Aug 9 09:51:05 2017 on packer-test -- e5896848-87b1-4bf4-a96c-b7a4a83a0b8b 2 # job started at Tue Aug 29 14:20:26 2017 on gaius -- 1cfd46e7-5d74-4c25-8cdd-89cf8f41a393
3 # pid: 7652, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 3 # pid: 21338, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
4 # blacklist : None
5 # compresslevel : 6
6 # error_correct_cell : False
7 # extract_method : string
8 # filter_cell_barcode : None
9 # filter_cell_barcodes : False
4 # log2stderr : False 10 # log2stderr : False
5 # loglevel : 1 11 # loglevel : 1
6 # pattern : XXXNNN 12 # pattern : XXXNNN
7 # pattern2 : None 13 # pattern2 : None
8 # prime3 : True 14 # prime3 : True
9 # quality_encoding : phred33 15 # quality_encoding : phred33
16 # quality_filter_mask : None
10 # quality_filter_threshold : 10 17 # quality_filter_threshold : 10
11 # random_seed : None 18 # random_seed : None
12 # read2_in : None 19 # read2_in : None
13 # read2_out : None 20 # read2_out : False
21 # read2_stdout : False
22 # reads_subset : None
23 # reconcile : False
14 # short_help : None 24 # short_help : None
15 # split : False
16 # stats : True
17 # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> 25 # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
18 # stdin : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_867.dat' mode='r' encoding='UTF-8'> 26 # stdin : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3766.dat' mode='r' encoding='UTF-8'>
19 # stdlog : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_887.dat' mode='a' encoding='UTF-8'> 27 # stdlog : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3768.dat' mode='a' encoding='UTF-8'>
20 # stdout : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_886.dat' mode='w' encoding='UTF-8'> 28 # stdout : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3767.dat' mode='w' encoding='UTF-8'>
21 # timeit_file : None 29 # timeit_file : None
22 # timeit_header : None 30 # timeit_header : None
23 # timeit_name : all 31 # timeit_name : all
24 Barcode UMI Sample Count 32 # whitelist : None
25 AAGTTA TTA AAG 1 33 2017-08-29 14:20:26,493 INFO Starting barcode extraction
26 GGATTT TTT GGA 1 34 2017-08-29 14:20:26,495 INFO Input Reads: 100
27 GGATAG TAG GGA 1 35 2017-08-29 14:20:26,495 INFO Reads output: 72
28 TTTTTT TTT TTT 4 36 2017-08-29 14:20:26,495 INFO filtered: umi quality: 28
29 GAGAGG AGG GAG 1 37 # 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
30 TTAGTT GTT TTA 1
31 TGTAGA AGA TGT 1
32 AGAGAT GAT AGA 1
33 GAATAA TAA GAA 1
34 TTGAGT AGT TTG 1
35 TTTATT ATT TTT 1
36 GTAAGG AGG GTA 1
37 GAAGAG GAG GAA 1
38 TGTTTG TTG TGT 1
39 ATAATG ATG ATA 1
40 TTAGAT GAT TTA 1
41 GTCTGA TGA GTC 1
42 ATCATC ATC ATC 1
43 GTCACC ACC GTC 1
44 AACTCC TCC AAC 1
45 TTATTA TTA TTA 1
46 TGTTGT TGT TGT 2
47 GTTTAT TAT GTT 1
48 ATGAGT AGT ATG 1
49 ATAATT ATT ATA 1
50 TTGGTT GTT TTG 1
51 GTTTTG TTG GTT 1
52 CACGTC GTC CAC 1
53 TTGTGT TGT TTG 1
54 TGAATT ATT TGA 1
55 GGATGT TGT GGA 1
56 AGTCAC CAC AGT 1
57 GTTTTT TTT GTT 1
58 TATAGT AGT TAT 1
59 TTTTAT TAT TTT 1
60 TAAAAA AAA TAA 1
61 ATAGGT GGT ATA 1
62 ATTTTA TTA ATT 1
63 TGTATA ATA TGT 1
64 TGTTTT TTT TGT 2
65 AGATTT TTT AGA 1
66 TAGAAT AAT TAG 1
67 GAAGGA GGA GAA 1
68 GTTTGA TGA GTT 1
69 TTTTGT TGT TTT 1
70 ATTTTT TTT ATT 1
71 TGTTAT TAT TGT 1
72 CAGGAT GAT CAG 1
73 GTATTT TTT GTA 1
74 TGGGTA GTA TGG 1
75 AAAGTT GTT AAA 1
76 GGTGTG GTG GGT 1
77 AAGATC ATC AAG 1
78 TAGGTT GTT TAG 1
79 GAGTTA TTA GAG 1
80 TTATTT TTT TTA 1
81 GTTGTT GTT GTT 1
82 AGGTTT TTT AGG 1
83 TAAAGT AGT TAA 1
84 AGTTTT TTT AGT 1
85 TTTGAT GAT TTT 1
86 ATAAAT AAT ATA 1
87 GTTATT ATT GTT 1
88 TTTTTA TTA TTT 1
89 AAGTGT TGT AAG 1
90 ATATAG TAG ATA 1
91 TATAGA AGA TAT 1
92 # 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