Mercurial > repos > iuc > umi_tools_extract

view test-data/out_single.log @ 8:3cfd8e1073d7 draft

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planemo upload commit f6178c9e071a2158a35b82a3607f6dc8a767675c
author iuc
date Mon, 16 Jul 2018 17:35:16 -0400
parents d1015c2516b7
children
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# output generated by extract --bc-pattern=XXXNNN --stdin=/tmp/tmpAvWtMd/files/000/dataset_13.dat --stdout /tmp/tmpAvWtMd/files/000/dataset_14.dat --3prime --quality-filter-threshold 10 --quality-encoding phred33 --log=/tmp/tmpAvWtMd/files/000/dataset_15.dat
# job started at Wed Jan  3 17:06:20 2018 on tzk-ThinkPad-T450s -- 8897b3b4-c6e2-4ee3-b6c0-71044a63b7e1
# pid: 22794, system: Linux 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 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                               : False
# read2_stdout                            : False
# reads_subset                            : None
# reconcile                               : False
# retain_umi                              : None
# short_help                              : None
# stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
# stdin                                   : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_13.dat' mode='r' encoding='UTF-8'>
# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_15.dat' mode='a' encoding='UTF-8'>
# stdout                                  : <_io.TextIOWrapper name='/tmp/tmpAvWtMd/files/000/dataset_14.dat' mode='w' encoding='UTF-8'>
# timeit_file                             : None
# timeit_header                           : None
# timeit_name                             : all
# whitelist                               : None
2018-01-03 17:06:20,360 INFO Starting barcode extraction
2018-01-03 17:06:20,362 INFO Input Reads: 100
2018-01-03 17:06:20,362 INFO Reads output: 72
2018-01-03 17:06:20,362 INFO filtered: umi quality: 28
# job finished in 0 seconds at Wed Jan  3 17:06:20 2018 --  0.58  0.06  0.00  0.00 -- 8897b3b4-c6e2-4ee3-b6c0-71044a63b7e1