Mercurial > repos > iuc > umi_tools_extract

diff 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
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line diff
--- a/test-data/out_wl_paired.log	Wed Jun 02 18:27:33 2021 +0000
+++ b/test-data/out_wl_paired.log	Mon Sep 13 14:52:06 2021 +0000
@@ -1,14 +1,20 @@
-# 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
-# job started at Sun Feb 25 10:50:16 2018 on bag -- e78e4e5b-e99e-426a-8a92-c8b3beeadf18
-# pid: 2385, system: Linux 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64
+# 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
-# filter_cell_barcodes                    : False
-# log2stderr                              : False
+# filtered_out                            : None
+# filtered_out2                           : None
+# ignore_suffix                           : False
+# knee_method                             : density
+# log2stderr                              : True
 # loglevel                                : 1
 # method                                  : reads
 # pattern                                 : CCCNNNNNNNNXXXXX
@@ -16,25 +22,31 @@
 # plot_prefix                             : OUT
 # prime3                                  : None
 # random_seed                             : None
-# read2_in                                : /tmp/tmpibtvD6/files/000/dataset_6.dat
+# read2_in                                : input_read2.gz
 # short_help                              : None
-# stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
-# stdin                                   : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_5.dat' mode='r' encoding='UTF-8'>
-# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpibtvD6/files/000/dataset_8.dat' mode='a' encoding='UTF-8'>
-# stdout                                  : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>
+# 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
-2018-02-25 10:50:16,016 INFO Starting barcode extraction
-2018-02-25 10:50:16,017 INFO Parsed 0 reads
-2018-02-25 10:50:16,019 INFO Starting - whitelist determination
-2018-02-25 10:50:17,208 INFO Finished - whitelist determination
-2018-02-25 10:50:17,208 INFO Starting - finding putative error cell barcodes
-2018-02-25 10:50:17,208 INFO Finished - finding putative error cell barcodes
-2018-02-25 10:50:17,208 INFO Writing out whitelist
-2018-02-25 10:50:17,208 INFO Parsed 100 reads
-2018-02-25 10:50:17,208 INFO 100 reads matched the barcode pattern
-2018-02-25 10:50:17,208 INFO Found 23 unique cell barcodes
-# 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
+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