Mercurial > repos > iuc > umi_tools_dedup

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
author iuc
date Sat, 05 Oct 2024 13:08:04 +0000
parents 4098ab380097
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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1 # UMI-tools version: 1.1.2
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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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
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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3 # job started at Tue Jul 13 15:21:12 2021 on MOLSYB009 -- ba3841c0-b2d5-4188-88ca-4ee241163293
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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4 # pid: 1155608, system: Linux 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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5 # allow_threshold_error : False
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c0691d1977dd planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
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6 # blacklist_tsv : None
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7 # cell_number : False
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8 # compresslevel : 6
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4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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9 # ed_above_threshold : None
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10 # error_correct_threshold : 3
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11 # expect_cells : 5
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12 # extract_method : string
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4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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13 # filtered_out : None
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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14 # filtered_out2 : None
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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15 # ignore_suffix : False
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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16 # knee_method : density
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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17 # log2stderr : True
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18 # loglevel : 1
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19 # method : reads
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20 # pattern : CCCNNNNNNNNXXXXX
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21 # pattern2 : None
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22 # plot_prefix : OUT
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23 # prime3 : None
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24 # random_seed : None
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25 # read2_in : input_read2.gz
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26 # short_help : None
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27 # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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28 # stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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29 # stdlog : <_io.TextIOWrapper name='/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat' mode='a' encoding='UTF-8'>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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30 # stdout : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
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31 # subset_reads : 0
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32 # timeit_file : None
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33 # timeit_header : None
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34 # timeit_name : all
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4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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35 # tmpdir : None
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36 # whitelist_tsv : None
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37 2021-07-13 15:21:12,587 INFO Starting barcode extraction
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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38 2021-07-13 15:21:12,588 INFO Parsed 0 reads
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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39 2021-07-13 15:21:12,590 INFO Starting - whitelist determination
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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40 2021-07-13 15:21:14,249 INFO Finished - whitelist determination
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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41 2021-07-13 15:21:14,249 INFO Starting - finding putative error cell barcodes
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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42 2021-07-13 15:21:14,249 INFO building bktree
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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43 2021-07-13 15:21:14,249 INFO done building bktree
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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44 2021-07-13 15:21:14,249 INFO Finished - finding putative error cell barcodes
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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45 2021-07-13 15:21:14,249 INFO Top 1 cell barcodes passed the selected threshold
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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46 2021-07-13 15:21:14,249 INFO Writing out whitelist
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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47 2021-07-13 15:21:14,249 INFO Parsed 100 reads
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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48 2021-07-13 15:21:14,249 INFO 100 reads matched the barcode pattern
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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49 2021-07-13 15:21:14,249 INFO Found 23 unique cell barcodes
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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50 2021-07-13 15:21:14,249 INFO Found 15 total reads matching the selected cell barcodes
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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51 2021-07-13 15:21:14,249 INFO Found 85 total reads which can be error corrected to the selected cell barcodes
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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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