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view test-data/out_wl_paired.log @ 8:e654095ab143 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 14:49:44 +0000
parents 8db56d2f8b72
children
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# UMI-tools version: 1.1.2
# 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
# job started at Tue Jul 13 15:21:12 2021 on MOLSYB009 -- ba3841c0-b2d5-4188-88ca-4ee241163293
# pid: 1155608, system: Linux 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64
# allow_threshold_error                   : False
# blacklist_tsv                           : None
# cell_number                             : False
# compresslevel                           : 6
# ed_above_threshold                      : None
# error_correct_threshold                 : 3
# expect_cells                            : 5
# extract_method                          : string
# filtered_out                            : None
# filtered_out2                           : None
# ignore_suffix                           : False
# knee_method                             : density
# log2stderr                              : True
# loglevel                                : 1
# method                                  : reads
# pattern                                 : CCCNNNNNNNNXXXXX
# pattern2                                : None
# plot_prefix                             : OUT
# prime3                                  : None
# random_seed                             : None
# read2_in                                : input_read2.gz
# short_help                              : None
# stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>
# stdin                                   : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>
# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat' mode='a' encoding='UTF-8'>
# stdout                                  : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
# subset_reads                            : 0
# timeit_file                             : None
# timeit_header                           : None
# timeit_name                             : all
# tmpdir                                  : None
# whitelist_tsv                           : None
2021-07-13 15:21:12,587 INFO Starting barcode extraction
2021-07-13 15:21:12,588 INFO Parsed 0 reads
2021-07-13 15:21:12,590 INFO Starting - whitelist determination
2021-07-13 15:21:14,249 INFO Finished - whitelist determination
2021-07-13 15:21:14,249 INFO Starting - finding putative error cell barcodes
2021-07-13 15:21:14,249 INFO building bktree
2021-07-13 15:21:14,249 INFO done building bktree
2021-07-13 15:21:14,249 INFO Finished - finding putative error cell barcodes
2021-07-13 15:21:14,249 INFO Top 1 cell barcodes passed the selected threshold
2021-07-13 15:21:14,249 INFO Writing out whitelist
2021-07-13 15:21:14,249 INFO Parsed 100 reads
2021-07-13 15:21:14,249 INFO 100 reads matched the barcode pattern
2021-07-13 15:21:14,249 INFO Found 23 unique cell barcodes
2021-07-13 15:21:14,249 INFO Found 15 total reads matching the selected cell barcodes
2021-07-13 15:21:14,249 INFO Found 85 total reads which can be error corrected to the selected cell barcodes
# 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