Mercurial > repos > iuc > umi_tools_dedup

diff test-data/out_single.log @ 0:a6477bafd522 draft

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planemo upload commit eea727c3bdfe36d9d16036d5ab79fb8b27c4e82e
author iuc
date Wed, 10 Jan 2018 19:09:42 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_single.log	Wed Jan 10 19:09:42 2018 -0500
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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