Mercurial > repos > bgruening > bismark

annotate test-data/mapping_report_mate_two_samples.txt @ 22:8c191acde702 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author bgruening
date Tue, 01 Aug 2023 11:42:10 +0000
parents 120b7b35e442
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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1 Bismark report for: input1.fq_1.fq and input1.fq_2.fq (version: v0.22.1)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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2 Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmp8oj0_k8v/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 0 --maxins 500 --quiet
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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3 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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4
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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5 Final Alignment report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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6 ======================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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7 Sequence pairs analysed in total: 1000
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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8 Number of paired-end alignments with a unique best hit: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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9 Mapping efficiency: 0.0%
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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10 Sequence pairs with no alignments under any condition: 1000
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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11 Sequence pairs did not map uniquely: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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12 Sequence pairs which were discarded because genomic sequence could not be extracted: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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14 Number of sequence pairs with unique best (first) alignment came from the bowtie output:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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15 CT/GA/CT: 0 ((converted) top strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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16 GA/CT/CT: 0 (complementary to (converted) top strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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17 GA/CT/GA: 0 (complementary to (converted) bottom strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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18 CT/GA/GA: 0 ((converted) bottom strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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20 Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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22 Final Cytosine Methylation Report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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23 =================================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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24 Total number of C's analysed: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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26 Total methylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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27 Total methylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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28 Total methylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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29 Total methylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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31 Total unmethylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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32 Total unmethylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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33 Total unmethylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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34 Total unmethylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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36 Can't determine percentage of methylated Cs in CpG context if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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37 Can't determine percentage of methylated Cs in CHG context if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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38 Can't determine percentage of methylated Cs in CHH context if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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39 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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42 Bismark completed in 0d 0h 0m 7s
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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43 Bismark report for: input2.fq_1.fq and input2.fq_2.fq (version: v0.22.1)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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44 Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmp8oj0_k8v/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 0 --maxins 500 --quiet
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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45 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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46
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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47 Final Alignment report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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48 ======================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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49 Sequence pairs analysed in total: 1000
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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50 Number of paired-end alignments with a unique best hit: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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51 Mapping efficiency: 0.0%
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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52 Sequence pairs with no alignments under any condition: 1000
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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53 Sequence pairs did not map uniquely: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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54 Sequence pairs which were discarded because genomic sequence could not be extracted: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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56 Number of sequence pairs with unique best (first) alignment came from the bowtie output:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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57 CT/GA/CT: 0 ((converted) top strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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58 GA/CT/CT: 0 (complementary to (converted) top strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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59 GA/CT/GA: 0 (complementary to (converted) bottom strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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60 CT/GA/GA: 0 ((converted) bottom strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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61
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62 Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
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64 Final Cytosine Methylation Report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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65 =================================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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66 Total number of C's analysed: 0
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68 Total methylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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69 Total methylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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70 Total methylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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71 Total methylated C's in Unknown context: 0
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73 Total unmethylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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74 Total unmethylated C's in CHG context: 0
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75 Total unmethylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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76 Total unmethylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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78 Can't determine percentage of methylated Cs in CpG context if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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79 Can't determine percentage of methylated Cs in CHG context if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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80 Can't determine percentage of methylated Cs in CHH context if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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81 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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84 Bismark completed in 0d 0h 0m 9s