Mercurial > repos > iuc > umi_tools_extract

comparison test-data/out_wl_paired.log @ 15:27ac32a22ad2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
author iuc
date Mon, 13 Sep 2021 14:52:06 +0000
parents 475ee31c61d9
children
comparison
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14:9fa7803d1c51 15:27ac32a22ad2
1 # output generated by whitelist --bc-pattern=CCCNNNNNNNNXXXXX --subset-reads=0 --stdin=/tmp/tmpibtvD6/files/000/dataset_5.dat --read2-in=/tmp/tmpibtvD6/files/000/dataset_6.dat --expect-cells=5 --error-correct-threshold=3 --method=reads --plot-prefix=OUT --log=/tmp/tmpibtvD6/files/000/dataset_8.dat 1 # UMI-tools version: 1.1.2
2 # job started at Sun Feb 25 10:50:16 2018 on bag -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18 2 # output generated by whitelist --bc-pattern=CCCNNNNNNNNXXXXX --extract-method=string --subset-reads=0 --knee-method=density --stdin=input_read1.gz --read2-in=input_read2.gz --expect-cells=5 --error-correct-threshold=3 --method=reads --plot-prefix=OUT --log=/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat --log2stderr
3 # pid: 2385, system: Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64 3 # job started at Tue Jul 13 15:21:12 2021 on MOLSYB009 -- ba3841c0-b2d5-4188-88ca-4ee241163293
4 # pid: 1155608, system: Linux 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64
5 # allow_threshold_error : False
4 # blacklist_tsv : None 6 # blacklist_tsv : None
5 # cell_number : False 7 # cell_number : False
6 # compresslevel : 6 8 # compresslevel : 6
9 # ed_above_threshold : None
7 # error_correct_threshold : 3 10 # error_correct_threshold : 3
8 # expect_cells : 5 11 # expect_cells : 5
9 # extract_method : string 12 # extract_method : string
10 # filter_cell_barcodes : False 13 # filtered_out : None
11 # log2stderr : False 14 # filtered_out2 : None
15 # ignore_suffix : False
16 # knee_method : density
17 # log2stderr : True
12 # loglevel : 1 18 # loglevel : 1
13 # method : reads 19 # method : reads
14 # pattern : CCCNNNNNNNNXXXXX 20 # pattern : CCCNNNNNNNNXXXXX
15 # pattern2 : None 21 # pattern2 : None
16 # plot_prefix : OUT 22 # plot_prefix : OUT
17 # prime3 : None 23 # prime3 : None
18 # random_seed : None 24 # random_seed : None
19 # read2_in : /tmp/tmpibtvD6/files/000/dataset_6.dat 25 # read2_in : input_read2.gz
20 # short_help : None 26 # short_help : None
21 # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'> 27 # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>
22 # stdin : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_5.dat' mode='r' encoding='UTF-8'> 28 # stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>
23 # stdlog : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_8.dat' mode='a' encoding='UTF-8'> 29 # stdlog : <_io.TextIOWrapper name='/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat' mode='a' encoding='UTF-8'>
24 # stdout : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> 30 # stdout : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
25 # subset_reads : 0 31 # subset_reads : 0
26 # timeit_file : None 32 # timeit_file : None
27 # timeit_header : None 33 # timeit_header : None
28 # timeit_name : all 34 # timeit_name : all
35 # tmpdir : None
29 # whitelist_tsv : None 36 # whitelist_tsv : None
30 2018-02-25 10:50:16,016 INFO Starting barcode extraction 37 2021-07-13 15:21:12,587 INFO Starting barcode extraction
31 2018-02-25 10:50:16,017 INFO Parsed 0 reads 38 2021-07-13 15:21:12,588 INFO Parsed 0 reads
32 2018-02-25 10:50:16,019 INFO Starting - whitelist determination 39 2021-07-13 15:21:12,590 INFO Starting - whitelist determination
33 2018-02-25 10:50:17,208 INFO Finished - whitelist determination 40 2021-07-13 15:21:14,249 INFO Finished - whitelist determination
34 2018-02-25 10:50:17,208 INFO Starting - finding putative error cell barcodes 41 2021-07-13 15:21:14,249 INFO Starting - finding putative error cell barcodes
35 2018-02-25 10:50:17,208 INFO Finished - finding putative error cell barcodes 42 2021-07-13 15:21:14,249 INFO building bktree
36 2018-02-25 10:50:17,208 INFO Writing out whitelist 43 2021-07-13 15:21:14,249 INFO done building bktree
37 2018-02-25 10:50:17,208 INFO Parsed 100 reads 44 2021-07-13 15:21:14,249 INFO Finished - finding putative error cell barcodes
38 2018-02-25 10:50:17,208 INFO 100 reads matched the barcode pattern 45 2021-07-13 15:21:14,249 INFO Top 1 cell barcodes passed the selected threshold
39 2018-02-25 10:50:17,208 INFO Found 23 unique cell barcodes 46 2021-07-13 15:21:14,249 INFO Writing out whitelist
40 # job finished in 1 seconds at Sun Feb 25 10:50:17 2018 -- 2.35 0.08 0.00 0.00 -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18 47 2021-07-13 15:21:14,249 INFO Parsed 100 reads
48 2021-07-13 15:21:14,249 INFO 100 reads matched the barcode pattern
49 2021-07-13 15:21:14,249 INFO Found 23 unique cell barcodes
50 2021-07-13 15:21:14,249 INFO Found 15 total reads matching the selected cell barcodes
51 2021-07-13 15:21:14,249 INFO Found 85 total reads which can be error corrected to the selected cell barcodes
52 # job finished in 1 seconds at Tue Jul 13 15:21:14 2021 -- 7.19 0.62 0.08 0.02 -- ba3841c0-b2d5-4188-88ca-4ee241163293