Mercurial > repos > bgruening > bismark

annotate test-data/summary_mate_two_samples.txt @ 21:120b7b35e442 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
author bgruening
date Thu, 22 Apr 2021 17:05:46 +0000
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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 Create a temporary index with the offered files from the user. Utilizing the script: bismark_genome_preparation
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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2 Generating index with: 'bismark_genome_preparation --bowtie2 /tmp/tmpfw7btd9x'
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3 Writing bisulfite genomes out into a single MFA (multi FastA) file
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4
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5 Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019)
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6
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7 Step I - Prepare genome folders - completed
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8
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9
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10
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11 Total number of conversions performed:
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12 C->T: 146875
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13 G->A: 150504
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14
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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15 Step II - Genome bisulfite conversions - completed
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16
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17
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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18 Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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19 Please be aware that this process can - depending on genome size - take several hours!
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20 Settings:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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21 Output files: "BS_CT.*.bt2"
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22 Line rate: 6 (line is 64 bytes)
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23 Lines per side: 1 (side is 64 bytes)
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24 Offset rate: 4 (one in 16)
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25 FTable chars: 10
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26 Strings: unpacked
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27 Max bucket size: default
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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28 Max bucket size, sqrt multiplier: default
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29 Max bucket size, len divisor: 4
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30 Difference-cover sample period: 1024
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31 Endianness: little
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32 Actual local endianness: little
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33 Sanity checking: disabled
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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34 Assertions: disabled
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35 Random seed: 0
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36 Sizeofs: void*:8, int:4, long:8, size_t:8
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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37 Input files DNA, FASTA:
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38 genome_mfa.CT_conversion.fa
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39 Building a SMALL index
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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40 Reading reference sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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41 Time reading reference sizes: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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42 Calculating joined length
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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43 Writing header
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44 Reserving space for joined string
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45 Joining reference sequences
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46 Time to join reference sequences: 00:00:00
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47 bmax according to bmaxDivN setting: 189039
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48 Using parameters --bmax 141780 --dcv 1024
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49 Doing ahead-of-time memory usage test
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50 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
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51 Constructing suffix-array element generator
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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52 Building DifferenceCoverSample
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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53 Building sPrime
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54 Building sPrimeOrder
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55 V-Sorting samples
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56 V-Sorting samples time: 00:00:00
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57 Allocating rank array
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58 Ranking v-sort output
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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59 Ranking v-sort output time: 00:00:00
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60 Invoking Larsson-Sadakane on ranks
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61 Invoking Larsson-Sadakane on ranks time: 00:00:00
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62 Sanity-checking and returning
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63 Building samples
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64 Reserving space for 12 sample suffixes
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65 Generating random suffixes
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66 QSorting 12 sample offsets, eliminating duplicates
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67 QSorting sample offsets, eliminating duplicates time: 00:00:00
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68 Multikey QSorting 12 samples
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69 (Using difference cover)
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70 Multikey QSorting samples time: 00:00:00
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71 Calculating bucket sizes
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72 Splitting and merging
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73 Splitting and merging time: 00:00:00
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74 Avg bucket size: 756159 (target: 141779)
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75 Converting suffix-array elements to index image
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76 Allocating ftab, absorbFtab
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77 Entering Ebwt loop
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78 Getting block 1 of 1
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79 No samples; assembling all-inclusive block
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80 Sorting block of length 756159 for bucket 1
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81 (Using difference cover)
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82 Sorting block time: 00:00:00
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83 Returning block of 756160 for bucket 1
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84 Exited Ebwt loop
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85 fchr[A]: 0
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86 fchr[C]: 235897
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87 fchr[G]: 235897
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88 fchr[T]: 386401
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89 fchr[$]: 756159
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90 Exiting Ebwt::buildToDisk()
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91 Returning from initFromVector
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92 Wrote 4446745 bytes to primary EBWT file: BS_CT.1.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
93 Wrote 189044 bytes to secondary EBWT file: BS_CT.2.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
94 Re-opening _in1 and _in2 as input streams
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
95 Returning from Ebwt constructor
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
96 Headers:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
97 len: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
98 bwtLen: 756160
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
99 sz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
100 bwtSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
101 lineRate: 6
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
102 offRate: 4
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
103 offMask: 0xfffffff0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
104 ftabChars: 10
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
105 eftabLen: 20
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
106 eftabSz: 80
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
107 ftabLen: 1048577
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
108 ftabSz: 4194308
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
109 offsLen: 47260
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
110 offsSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
111 lineSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
112 sideSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
113 sideBwtSz: 48
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
114 sideBwtLen: 192
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
115 numSides: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
116 numLines: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
117 ebwtTotLen: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
118 ebwtTotSz: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
119 color: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
120 reverse: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
121 Total time for call to driver() for forward index: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
122 Reading reference sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
123 Time reading reference sizes: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
124 Calculating joined length
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
125 Writing header
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
126 Reserving space for joined string
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
127 Joining reference sequences
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
128 Time to join reference sequences: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
129 Time to reverse reference sequence: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
130 bmax according to bmaxDivN setting: 189039
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
131 Using parameters --bmax 141780 --dcv 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
132 Doing ahead-of-time memory usage test
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
133 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
134 Constructing suffix-array element generator
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
135 Building DifferenceCoverSample
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
136 Building sPrime
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
137 Building sPrimeOrder
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
138 V-Sorting samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
139 V-Sorting samples time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
140 Allocating rank array
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
141 Ranking v-sort output
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
142 Ranking v-sort output time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
143 Invoking Larsson-Sadakane on ranks
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
144 Invoking Larsson-Sadakane on ranks time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
145 Sanity-checking and returning
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
146 Building samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
147 Reserving space for 12 sample suffixes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
148 Generating random suffixes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
149 QSorting 12 sample offsets, eliminating duplicates
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
150 QSorting sample offsets, eliminating duplicates time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
151 Multikey QSorting 12 samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
152 (Using difference cover)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
153 Multikey QSorting samples time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
154 Calculating bucket sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
155 Splitting and merging
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
156 Splitting and merging time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
157 Avg bucket size: 756159 (target: 141779)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
158 Converting suffix-array elements to index image
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
159 Allocating ftab, absorbFtab
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
160 Entering Ebwt loop
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
161 Getting block 1 of 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
162 No samples; assembling all-inclusive block
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
163 Sorting block of length 756159 for bucket 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
164 (Using difference cover)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
165 Sorting block time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
166 Returning block of 756160 for bucket 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
167 Exited Ebwt loop
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
168 fchr[A]: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
169 fchr[C]: 235897
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
170 fchr[G]: 235897
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
171 fchr[T]: 386401
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
172 fchr[$]: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
173 Exiting Ebwt::buildToDisk()
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
174 Returning from initFromVector
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
175 Wrote 4446745 bytes to primary EBWT file: BS_CT.rev.1.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
176 Wrote 189044 bytes to secondary EBWT file: BS_CT.rev.2.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
177 Re-opening _in1 and _in2 as input streams
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
178 Returning from Ebwt constructor
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
179 Headers:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
180 len: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
181 bwtLen: 756160
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
182 sz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
183 bwtSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
184 lineRate: 6
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
185 offRate: 4
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
186 offMask: 0xfffffff0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
187 ftabChars: 10
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
188 eftabLen: 20
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
189 eftabSz: 80
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
190 ftabLen: 1048577
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
191 ftabSz: 4194308
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
192 offsLen: 47260
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
193 offsSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
194 lineSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
195 sideSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
196 sideBwtSz: 48
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
197 sideBwtLen: 192
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
198 numSides: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
199 numLines: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
200 ebwtTotLen: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
201 ebwtTotSz: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
202 color: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
203 reverse: 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
204 Total time for backward call to driver() for mirror index: 00:00:01
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
205 Settings:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
206 Output files: "BS_GA.*.bt2"
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
207 Line rate: 6 (line is 64 bytes)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
208 Lines per side: 1 (side is 64 bytes)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
209 Offset rate: 4 (one in 16)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
210 FTable chars: 10
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
211 Strings: unpacked
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
212 Max bucket size: default
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
213 Max bucket size, sqrt multiplier: default
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
214 Max bucket size, len divisor: 4
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
215 Difference-cover sample period: 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
216 Endianness: little
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
217 Actual local endianness: little
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
218 Sanity checking: disabled
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
219 Assertions: disabled
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
220 Random seed: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
221 Sizeofs: void*:8, int:4, long:8, size_t:8
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
222 Input files DNA, FASTA:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
223 genome_mfa.GA_conversion.fa
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
224 Building a SMALL index
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
225 Reading reference sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
226 Time reading reference sizes: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
227 Calculating joined length
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
228 Writing header
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
229 Reserving space for joined string
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
230 Joining reference sequences
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
231 Time to join reference sequences: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
232 bmax according to bmaxDivN setting: 189039
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
233 Using parameters --bmax 141780 --dcv 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
234 Doing ahead-of-time memory usage test
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
235 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
236 Constructing suffix-array element generator
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
237 Building DifferenceCoverSample
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
238 Building sPrime
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
239 Building sPrimeOrder
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
240 V-Sorting samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
241 V-Sorting samples time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
242 Allocating rank array
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
243 Ranking v-sort output
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
244 Ranking v-sort output time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
245 Invoking Larsson-Sadakane on ranks
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
246 Invoking Larsson-Sadakane on ranks time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
247 Sanity-checking and returning
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
248 Building samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
249 Reserving space for 12 sample suffixes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
250 Generating random suffixes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
251 QSorting 12 sample offsets, eliminating duplicates
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
252 QSorting sample offsets, eliminating duplicates time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
253 Multikey QSorting 12 samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
254 (Using difference cover)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
255 Multikey QSorting samples time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
256 Calculating bucket sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
257 Splitting and merging
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
258 Splitting and merging time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
259 Avg bucket size: 756159 (target: 141779)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
260 Converting suffix-array elements to index image
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
261 Allocating ftab, absorbFtab
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
262 Entering Ebwt loop
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
263 Getting block 1 of 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
264 No samples; assembling all-inclusive block
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
265 Sorting block of length 756159 for bucket 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
266 (Using difference cover)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
267 Sorting block time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
268 Returning block of 756160 for bucket 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
269 Exited Ebwt loop
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
270 fchr[A]: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
271 fchr[C]: 386401
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
272 fchr[G]: 533276
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
273 fchr[T]: 533276
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
274 fchr[$]: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
275 Exiting Ebwt::buildToDisk()
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
276 Returning from initFromVector
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
277 Wrote 4446745 bytes to primary EBWT file: BS_GA.1.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
278 Wrote 189044 bytes to secondary EBWT file: BS_GA.2.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
279 Re-opening _in1 and _in2 as input streams
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
280 Returning from Ebwt constructor
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
281 Headers:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
282 len: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
283 bwtLen: 756160
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
284 sz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
285 bwtSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
286 lineRate: 6
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
287 offRate: 4
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
288 offMask: 0xfffffff0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
289 ftabChars: 10
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
290 eftabLen: 20
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
291 eftabSz: 80
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
292 ftabLen: 1048577
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
293 ftabSz: 4194308
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
294 offsLen: 47260
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
295 offsSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
296 lineSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
297 sideSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
298 sideBwtSz: 48
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
299 sideBwtLen: 192
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
300 numSides: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
301 numLines: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
302 ebwtTotLen: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
303 ebwtTotSz: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
304 color: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
305 reverse: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
306 Total time for call to driver() for forward index: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
307 Reading reference sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
308 Time reading reference sizes: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
309 Calculating joined length
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
310 Writing header
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
311 Reserving space for joined string
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
312 Joining reference sequences
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
313 Time to join reference sequences: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
314 Time to reverse reference sequence: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
315 bmax according to bmaxDivN setting: 189039
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
316 Using parameters --bmax 141780 --dcv 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
317 Doing ahead-of-time memory usage test
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
318 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
319 Constructing suffix-array element generator
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
320 Building DifferenceCoverSample
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
321 Building sPrime
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
322 Building sPrimeOrder
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
323 V-Sorting samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
324 V-Sorting samples time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
325 Allocating rank array
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
326 Ranking v-sort output
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
327 Ranking v-sort output time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
328 Invoking Larsson-Sadakane on ranks
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
329 Invoking Larsson-Sadakane on ranks time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
330 Sanity-checking and returning
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
331 Building samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
332 Reserving space for 12 sample suffixes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
333 Generating random suffixes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
334 QSorting 12 sample offsets, eliminating duplicates
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
335 QSorting sample offsets, eliminating duplicates time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
336 Multikey QSorting 12 samples
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
337 (Using difference cover)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
338 Multikey QSorting samples time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
339 Calculating bucket sizes
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
340 Splitting and merging
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
341 Splitting and merging time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
342 Avg bucket size: 756159 (target: 141779)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
343 Converting suffix-array elements to index image
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
344 Allocating ftab, absorbFtab
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
345 Entering Ebwt loop
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
346 Getting block 1 of 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
347 No samples; assembling all-inclusive block
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
348 Sorting block of length 756159 for bucket 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
349 (Using difference cover)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
350 Sorting block time: 00:00:00
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
351 Returning block of 756160 for bucket 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
352 Exited Ebwt loop
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
353 fchr[A]: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
354 fchr[C]: 386401
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
355 fchr[G]: 533276
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
356 fchr[T]: 533276
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
357 fchr[$]: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
358 Exiting Ebwt::buildToDisk()
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
359 Returning from initFromVector
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
360 Wrote 4446745 bytes to primary EBWT file: BS_GA.rev.1.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
361 Wrote 189044 bytes to secondary EBWT file: BS_GA.rev.2.bt2
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
362 Re-opening _in1 and _in2 as input streams
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
363 Returning from Ebwt constructor
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
364 Headers:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
365 len: 756159
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
366 bwtLen: 756160
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
367 sz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
368 bwtSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
369 lineRate: 6
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
370 offRate: 4
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
371 offMask: 0xfffffff0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
372 ftabChars: 10
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
373 eftabLen: 20
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
374 eftabSz: 80
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
375 ftabLen: 1048577
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
376 ftabSz: 4194308
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
377 offsLen: 47260
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
378 offsSz: 189040
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
379 lineSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
380 sideSz: 64
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
381 sideBwtSz: 48
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
382 sideBwtLen: 192
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
383 numSides: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
384 numLines: 3939
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
385 ebwtTotLen: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
386 ebwtTotSz: 252096
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
387 color: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
388 reverse: 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
389 Total time for backward call to driver() for mirror index: 00:00:01
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
390 Running bismark with: 'bismark --bam --temp_dir /tmp/tmp0n2gudqm -o /tmp/tmp0n2gudqm/results --quiet --gzip --fastq -L 20 -D 15 -R 2 --un --ambiguous /tmp/tmpfw7btd9x -1 input1.fq_1.fq,input2.fq_1.fq -2 input1.fq_2.fq,input2.fq_2.fq -I 0 -X 500'
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
391 Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.3.5])
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
392 Output format is BAM (default)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
393 Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools'
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
394 Reference genome folder provided is /tmp/tmpfw7btd9x/ (absolute path is '/tmp/tmpfw7btd9x/)'
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
395 FastQ format specified
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
396
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
397 Input files to be analysed (in current folder '/tmp/tmpfl_1r4y7/job_working_directory/000/17/working'):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
398 input1.fq_1.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
399 input1.fq_2.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
400 input2.fq_1.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
401 input2.fq_2.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
402 Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
403 Created output directory /tmp/tmp0n2gudqm/results/!
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
404
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
405 Output will be written into the directory: /tmp/tmp0n2gudqm/results/
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
406
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
407 Using temp directory: /tmp/tmp0n2gudqm
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
408 Temporary files will be written into the directory: /tmp/tmp0n2gudqm/
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
409 Setting parallelization to single-threaded (default)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
410
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
411 Summary of all aligner 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"
bgruening
parents:
diff changeset
412 Current working directory is: /tmp/tmpfl_1r4y7/job_working_directory/000/17/working
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
413
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
414 Now reading in and storing sequence information of the genome specified in: /tmp/tmpfw7btd9x/
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
415
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
416 chr chrY_JH584300_random (182347 bp)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
417 chr chrY_JH584301_random (259875 bp)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
418 chr chrY_JH584302_random (155838 bp)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
419 chr chrY_JH584303_random (158099 bp)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
420
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
421 Single-core mode: setting pid to 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
422
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
423 Paired-end alignments will be performed
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
424 =======================================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
425
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
426 The provided filenames for paired-end alignments are input1.fq_1.fq and input1.fq_2.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
427 Input files are in FastQ format
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
428 Writing a C -> T converted version of the input file input1.fq_1.fq to /tmp/tmp0n2gudqm/input1.fq_1.fq_C_to_T.fastq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
429
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
430 Created C -> T converted version of the FastQ file input1.fq_1.fq (1000 sequences in total)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
431
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
432 Writing a G -> A converted version of the input file input1.fq_2.fq to /tmp/tmp0n2gudqm/input1.fq_2.fq_G_to_A.fastq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
433
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
434 Created G -> A converted version of the FastQ file input1.fq_2.fq (1000 sequences in total)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
435
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
436 Input files are input1.fq_1.fq_C_to_T.fastq.gz and input1.fq_2.fq_G_to_A.fastq.gz (FastQ)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
437 Now running 2 instances of Bowtie 2 against the bisulfite genome of /tmp/tmpfw7btd9x/ 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"
bgruening
parents:
diff changeset
438
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
439 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/tmp0n2gudqm/input1.fq_1.fq_C_to_T.fastq.gz and /tmp/tmp0n2gudqm/input1.fq_2.fq_G_to_A.fastq.gz, with the 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 --norc))
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
440 Found first alignment:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
441 1_1/1 77 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
442 1_1/2 141 * 0 0 * * 0 0 TTATATATATTAAATAAATTAATTTTTTTTATTTATATATTAAATTTTTTAATTAATTTATTAATATTTTATAAATTTTTAAATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
443 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/tmp0n2gudqm/input1.fq_1.fq_C_to_T.fastq.gz and /tmp/tmp0n2gudqm/input1.fq_2.fq_G_to_A.fastq.gz, with the 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 --nofw))
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
444 Found first alignment:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
445 1_1/1 77 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
446 1_1/2 141 * 0 0 * * 0 0 TTATATATATTAAATAAATTAATTTTTTTTATTTATATATTAAATTTTTTAATTAATTTATTAATATTTTATAAATTTTTAAATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
447
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
448 >>> Writing bisulfite mapping results to input1.fq_1_bismark_bt2_pe.bam <<<
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
449
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
450 Unmapped sequences will be written to input1.fq_1.fq_unmapped_reads_1.fq.gz and input1.fq_2.fq_unmapped_reads_2.fq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
451 Ambiguously mapping sequences will be written to input1.fq_1.fq_ambiguous_reads_1.fq.gz and input1.fq_2.fq_ambiguous_reads_2.fq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
452
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
453 Reading in the sequence files input1.fq_1.fq and input1.fq_2.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
454 Processed 1000 sequences in total
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
455
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
456
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
457 Successfully deleted the temporary files /tmp/tmp0n2gudqm/input1.fq_1.fq_C_to_T.fastq.gz and /tmp/tmp0n2gudqm/input1.fq_2.fq_G_to_A.fastq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
458
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
459 Final Alignment report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
460 ======================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
461 Sequence pairs analysed in total: 1000
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
462 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"
bgruening
parents:
diff changeset
463 Mapping efficiency: 0.0%
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
464
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
465 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"
bgruening
parents:
diff changeset
466 Sequence pairs did not map uniquely: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
467 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"
bgruening
parents:
diff changeset
468
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
469 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"
bgruening
parents:
diff changeset
470 CT/GA/CT: 0 ((converted) top strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
471 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"
bgruening
parents:
diff changeset
472 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"
bgruening
parents:
diff changeset
473 CT/GA/GA: 0 ((converted) bottom strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
474
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
475 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"
bgruening
parents:
diff changeset
476
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
477 Final Cytosine Methylation Report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
478 =================================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
479 Total number of C's analysed: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
480
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
481 Total methylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
482 Total methylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
483 Total methylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
484 Total methylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
485
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
486 Total unmethylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
487 Total unmethylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
488 Total unmethylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
489 Total unmethylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
490
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
491 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"
bgruening
parents:
diff changeset
492 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"
bgruening
parents:
diff changeset
493 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"
bgruening
parents:
diff changeset
494 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"
bgruening
parents:
diff changeset
495
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
496
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
497 Bismark completed in 0d 0h 0m 6s
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
498
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
499 ====================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
500 Bismark run complete
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
501 ====================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
502
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
503 Single-core mode: setting pid to 1
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
504
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
505 Paired-end alignments will be performed
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
506 =======================================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
507
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
508 The provided filenames for paired-end alignments are input2.fq_1.fq and input2.fq_2.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
509 Input files are in FastQ format
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
510 Writing a C -> T converted version of the input file input2.fq_1.fq to /tmp/tmp0n2gudqm/input2.fq_1.fq_C_to_T.fastq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
511
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
512 Created C -> T converted version of the FastQ file input2.fq_1.fq (1000 sequences in total)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
513
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
514 Writing a G -> A converted version of the input file input2.fq_2.fq to /tmp/tmp0n2gudqm/input2.fq_2.fq_G_to_A.fastq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
515
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
516 Created G -> A converted version of the FastQ file input2.fq_2.fq (1000 sequences in total)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
517
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
518 Input files are input2.fq_1.fq_C_to_T.fastq.gz and input2.fq_2.fq_G_to_A.fastq.gz (FastQ)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
519 Now running 2 instances of Bowtie 2 against the bisulfite genome of /tmp/tmpfw7btd9x/ 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"
bgruening
parents:
diff changeset
520
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
521 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from /tmp/tmp0n2gudqm/input2.fq_1.fq_C_to_T.fastq.gz and /tmp/tmp0n2gudqm/input2.fq_2.fq_G_to_A.fastq.gz, with the 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 --norc))
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
522 Found first alignment:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
523 1_1/1 77 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
524 1_1/2 141 * 0 0 * * 0 0 TTATATATATTAAATAAATTAATTTTTTTTATTTATATATTAAATTTTTTAATTAATTTATTAATATTTTATAAATTTTTAAATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
525 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from /tmp/tmp0n2gudqm/input2.fq_1.fq_C_to_T.fastq.gz and /tmp/tmp0n2gudqm/input2.fq_2.fq_G_to_A.fastq.gz, with the 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 --nofw))
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
526 Found first alignment:
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
527 1_1/1 77 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
528 1_1/2 141 * 0 0 * * 0 0 TTATATATATTAAATAAATTAATTTTTTTTATTTATATATTAAATTTTTTAATTAATTTATTAATATTTTATAAATTTTTAAATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UP
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
529
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
530 >>> Writing bisulfite mapping results to input2.fq_1_bismark_bt2_pe.bam <<<
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
531
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
532 Unmapped sequences will be written to input2.fq_1.fq_unmapped_reads_1.fq.gz and input2.fq_2.fq_unmapped_reads_2.fq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
533 Ambiguously mapping sequences will be written to input2.fq_1.fq_ambiguous_reads_1.fq.gz and input2.fq_2.fq_ambiguous_reads_2.fq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
534
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
535 Reading in the sequence files input2.fq_1.fq and input2.fq_2.fq
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
536 Processed 1000 sequences in total
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
537
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
538
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
539 Successfully deleted the temporary files /tmp/tmp0n2gudqm/input2.fq_1.fq_C_to_T.fastq.gz and /tmp/tmp0n2gudqm/input2.fq_2.fq_G_to_A.fastq.gz
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
540
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
541 Final Alignment report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
542 ======================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
543 Sequence pairs analysed in total: 1000
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
544 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"
bgruening
parents:
diff changeset
545 Mapping efficiency: 0.0%
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
546
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
547 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"
bgruening
parents:
diff changeset
548 Sequence pairs did not map uniquely: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
549 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"
bgruening
parents:
diff changeset
550
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
551 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"
bgruening
parents:
diff changeset
552 CT/GA/CT: 0 ((converted) top strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
553 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"
bgruening
parents:
diff changeset
554 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"
bgruening
parents:
diff changeset
555 CT/GA/GA: 0 ((converted) bottom strand)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
556
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
557 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"
bgruening
parents:
diff changeset
558
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
559 Final Cytosine Methylation Report
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
560 =================================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
561 Total number of C's analysed: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
562
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
563 Total methylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
564 Total methylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
565 Total methylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
566 Total methylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
567
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
568 Total unmethylated C's in CpG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
569 Total unmethylated C's in CHG context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
570 Total unmethylated C's in CHH context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
571 Total unmethylated C's in Unknown context: 0
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
572
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
573 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"
bgruening
parents:
diff changeset
574 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"
bgruening
parents:
diff changeset
575 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"
bgruening
parents:
diff changeset
576 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"
bgruening
parents:
diff changeset
577
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
578
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
579 Bismark completed in 0d 0h 0m 8s
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
580
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
581 ====================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
582 Bismark run complete
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
583 ====================
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
584
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents:
diff changeset
585 Merging bams with: '['samtools', 'merge', '-@', '1', '-f', '/tmp/tmp0n2gudqm/results/tmpnqe_dadr', '/tmp/tmp0n2gudqm/results/input1.fq_1_bismark_bt2_pe.bam', '/tmp/tmp0n2gudqm/results/input2.fq_1_bismark_bt2_pe.bam']'