annotate test-data/summary_pbat.txt @ 21:120b7b35e442 draft default tip

"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
parents aa9bf0f29a9f
children
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aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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1 Create a temporary index with the offered files from the user. Utilizing the script: bismark_genome_preparation
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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2 Generating index with: 'bismark_genome_preparation --bowtie2 /tmp/tmpuqE7r1'
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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3 Writing bisulfite genomes out into a single MFA (multi FastA) file
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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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
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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8
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9
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10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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11 Total number of conversions performed:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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12 C->T: 146875
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13 G->A: 150504
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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14
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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15 Step II - Genome bisulfite conversions - completed
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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16
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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17
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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18 Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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19 Please be aware that this process can - depending on genome size - take several hours!
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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20 Settings:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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21 Output files: "BS_CT.*.bt2"
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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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)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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24 Offset rate: 4 (one in 16)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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25 FTable chars: 10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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26 Strings: unpacked
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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27 Max bucket size: default
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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28 Max bucket size, sqrt multiplier: default
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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29 Max bucket size, len divisor: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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30 Difference-cover sample period: 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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31 Endianness: little
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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32 Actual local endianness: little
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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33 Sanity checking: disabled
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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34 Assertions: disabled
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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35 Random seed: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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36 Sizeofs: void*:8, int:4, long:8, size_t:8
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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37 Input files DNA, FASTA:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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38 genome_mfa.CT_conversion.fa
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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39 Building a SMALL index
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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40 Reading reference sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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41 Time reading reference sizes: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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42 Calculating joined length
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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43 Writing header
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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44 Reserving space for joined string
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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45 Joining reference sequences
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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46 Time to join reference sequences: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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47 bmax according to bmaxDivN setting: 189039
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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48 Using parameters --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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49 Doing ahead-of-time memory usage test
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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50 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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51 Constructing suffix-array element generator
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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52 Building DifferenceCoverSample
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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53 Building sPrime
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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54 Building sPrimeOrder
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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55 V-Sorting samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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56 V-Sorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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57 Allocating rank array
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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58 Ranking v-sort output
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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59 Ranking v-sort output time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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60 Invoking Larsson-Sadakane on ranks
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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61 Invoking Larsson-Sadakane on ranks time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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62 Sanity-checking and returning
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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63 Building samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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64 Reserving space for 12 sample suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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65 Generating random suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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66 QSorting 12 sample offsets, eliminating duplicates
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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67 QSorting sample offsets, eliminating duplicates time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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68 Multikey QSorting 12 samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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69 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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70 Multikey QSorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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71 Calculating bucket sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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72 Splitting and merging
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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73 Splitting and merging time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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74 Avg bucket size: 756159 (target: 141779)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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75 Converting suffix-array elements to index image
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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76 Allocating ftab, absorbFtab
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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77 Entering Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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78 Getting block 1 of 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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79 No samples; assembling all-inclusive block
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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80 Sorting block of length 756159 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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81 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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82 Sorting block time: xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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83 Returning block of 756160 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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84 Exited Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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85 fchr[A]: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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86 fchr[C]: 235897
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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87 fchr[G]: 235897
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
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diff changeset
88 fchr[T]: 386401
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
89 fchr[$]: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
90 Exiting Ebwt::buildToDisk()
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
91 Returning from initFromVector
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
92 Wrote 4446745 bytes to primary EBWT file: BS_CT.1.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
93 Wrote 189044 bytes to secondary EBWT file: BS_CT.2.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
94 Re-opening _in1 and _in2 as input streams
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
95 Returning from Ebwt constructor
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
96 Headers:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
97 len: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
98 bwtLen: 756160
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
99 sz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
100 bwtSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
101 lineRate: 6
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
102 offRate: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
103 offMask: 0xfffffff0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
104 ftabChars: 10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
105 eftabLen: 20
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
106 eftabSz: 80
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
107 ftabLen: 1048577
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
108 ftabSz: 4194308
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
109 offsLen: 47260
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
110 offsSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
111 lineSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
112 sideSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
113 sideBwtSz: 48
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
114 sideBwtLen: 192
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
115 numSides: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
116 numLines: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
117 ebwtTotLen: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
118 ebwtTotSz: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
119 color: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
120 reverse: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
121 Total time for call to driver() for forward index: xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
122 Reading reference sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
123 Time reading reference sizes: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
124 Calculating joined length
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
125 Writing header
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
126 Reserving space for joined string
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
127 Joining reference sequences
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
128 Time to join reference sequences: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
129 Time to reverse reference sequence: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
130 bmax according to bmaxDivN setting: 189039
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
131 Using parameters --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
132 Doing ahead-of-time memory usage test
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
133 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
134 Constructing suffix-array element generator
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
135 Building DifferenceCoverSample
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
136 Building sPrime
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
137 Building sPrimeOrder
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
138 V-Sorting samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
139 V-Sorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
140 Allocating rank array
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
141 Ranking v-sort output
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
142 Ranking v-sort output time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
143 Invoking Larsson-Sadakane on ranks
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
144 Invoking Larsson-Sadakane on ranks time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
145 Sanity-checking and returning
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
146 Building samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
147 Reserving space for 12 sample suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
148 Generating random suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
149 QSorting 12 sample offsets, eliminating duplicates
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
150 QSorting sample offsets, eliminating duplicates time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
151 Multikey QSorting 12 samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
152 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
153 Multikey QSorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
154 Calculating bucket sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
155 Splitting and merging
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
156 Splitting and merging time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
157 Avg bucket size: 756159 (target: 141779)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
158 Converting suffix-array elements to index image
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
159 Allocating ftab, absorbFtab
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
160 Entering Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
161 Getting block 1 of 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
162 No samples; assembling all-inclusive block
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
163 Sorting block of length 756159 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
164 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
165 Sorting block time: xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
166 Returning block of 756160 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
167 Exited Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
168 fchr[A]: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
169 fchr[C]: 235897
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
170 fchr[G]: 235897
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
171 fchr[T]: 386401
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
172 fchr[$]: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
173 Exiting Ebwt::buildToDisk()
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
174 Returning from initFromVector
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
175 Wrote 4446745 bytes to primary EBWT file: BS_CT.rev.1.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
176 Wrote 189044 bytes to secondary EBWT file: BS_CT.rev.2.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
177 Re-opening _in1 and _in2 as input streams
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
178 Returning from Ebwt constructor
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
179 Headers:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
180 len: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
181 bwtLen: 756160
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
182 sz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
183 bwtSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
184 lineRate: 6
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
185 offRate: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
186 offMask: 0xfffffff0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
187 ftabChars: 10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
188 eftabLen: 20
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
189 eftabSz: 80
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
190 ftabLen: 1048577
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
191 ftabSz: 4194308
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
192 offsLen: 47260
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
193 offsSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
194 lineSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
195 sideSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
196 sideBwtSz: 48
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
197 sideBwtLen: 192
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
198 numSides: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
199 numLines: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
200 ebwtTotLen: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
201 ebwtTotSz: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
202 color: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
203 reverse: 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
204 Total time for backward call to driver() for mirror index: 00:00:01
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
205 Settings:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
206 Output files: "BS_GA.*.bt2"
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
207 Line rate: 6 (line is 64 bytes)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
208 Lines per side: 1 (side is 64 bytes)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
209 Offset rate: 4 (one in 16)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
210 FTable chars: 10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
211 Strings: unpacked
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
212 Max bucket size: default
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
213 Max bucket size, sqrt multiplier: default
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
214 Max bucket size, len divisor: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
215 Difference-cover sample period: 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
216 Endianness: little
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
217 Actual local endianness: little
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
218 Sanity checking: disabled
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
219 Assertions: disabled
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
220 Random seed: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
221 Sizeofs: void*:8, int:4, long:8, size_t:8
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
222 Input files DNA, FASTA:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
223 genome_mfa.GA_conversion.fa
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
224 Building a SMALL index
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
225 Reading reference sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
226 Time reading reference sizes: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
227 Calculating joined length
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
228 Writing header
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
229 Reserving space for joined string
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
230 Joining reference sequences
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
231 Time to join reference sequences: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
232 bmax according to bmaxDivN setting: 189039
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
233 Using parameters --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
234 Doing ahead-of-time memory usage test
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
235 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
236 Constructing suffix-array element generator
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
237 Building DifferenceCoverSample
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
238 Building sPrime
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
239 Building sPrimeOrder
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
240 V-Sorting samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
241 V-Sorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
242 Allocating rank array
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
243 Ranking v-sort output
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
244 Ranking v-sort output time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
245 Invoking Larsson-Sadakane on ranks
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
246 Invoking Larsson-Sadakane on ranks time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
247 Sanity-checking and returning
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
248 Building samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
249 Reserving space for 12 sample suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
250 Generating random suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
251 QSorting 12 sample offsets, eliminating duplicates
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
252 QSorting sample offsets, eliminating duplicates time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
253 Multikey QSorting 12 samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
254 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
255 Multikey QSorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
256 Calculating bucket sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
257 Splitting and merging
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
258 Splitting and merging time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
259 Avg bucket size: 756159 (target: 141779)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
260 Converting suffix-array elements to index image
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
261 Allocating ftab, absorbFtab
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
262 Entering Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
263 Getting block 1 of 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
264 No samples; assembling all-inclusive block
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
265 Sorting block of length 756159 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
266 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
267 Sorting block time: xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
268 Returning block of 756160 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
269 Exited Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
270 fchr[A]: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
271 fchr[C]: 386401
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
272 fchr[G]: 533276
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
273 fchr[T]: 533276
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
274 fchr[$]: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
275 Exiting Ebwt::buildToDisk()
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
276 Returning from initFromVector
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
277 Wrote 4446745 bytes to primary EBWT file: BS_GA.1.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
278 Wrote 189044 bytes to secondary EBWT file: BS_GA.2.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
279 Re-opening _in1 and _in2 as input streams
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
280 Returning from Ebwt constructor
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
281 Headers:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
282 len: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
283 bwtLen: 756160
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
284 sz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
285 bwtSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
286 lineRate: 6
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
287 offRate: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
288 offMask: 0xfffffff0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
289 ftabChars: 10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
290 eftabLen: 20
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
291 eftabSz: 80
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
292 ftabLen: 1048577
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
293 ftabSz: 4194308
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
294 offsLen: 47260
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
295 offsSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
296 lineSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
297 sideSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
298 sideBwtSz: 48
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
299 sideBwtLen: 192
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
300 numSides: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
301 numLines: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
302 ebwtTotLen: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
303 ebwtTotSz: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
304 color: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
305 reverse: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
306 Total time for call to driver() for forward index: xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
307 Reading reference sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
308 Time reading reference sizes: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
309 Calculating joined length
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
310 Writing header
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
311 Reserving space for joined string
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
312 Joining reference sequences
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
313 Time to join reference sequences: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
314 Time to reverse reference sequence: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
315 bmax according to bmaxDivN setting: 189039
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
316 Using parameters --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
317 Doing ahead-of-time memory usage test
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
318 Passed! Constructing with these parameters: --bmax 141780 --dcv 1024
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
319 Constructing suffix-array element generator
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
320 Building DifferenceCoverSample
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
321 Building sPrime
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
322 Building sPrimeOrder
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
323 V-Sorting samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
324 V-Sorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
325 Allocating rank array
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
326 Ranking v-sort output
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
327 Ranking v-sort output time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
328 Invoking Larsson-Sadakane on ranks
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
329 Invoking Larsson-Sadakane on ranks time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
330 Sanity-checking and returning
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
331 Building samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
332 Reserving space for 12 sample suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
333 Generating random suffixes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
334 QSorting 12 sample offsets, eliminating duplicates
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
335 QSorting sample offsets, eliminating duplicates time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
336 Multikey QSorting 12 samples
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
337 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
338 Multikey QSorting samples time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
339 Calculating bucket sizes
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
340 Splitting and merging
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
341 Splitting and merging time: 00:00:00
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
342 Avg bucket size: 756159 (target: 141779)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
343 Converting suffix-array elements to index image
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
344 Allocating ftab, absorbFtab
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
345 Entering Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
346 Getting block 1 of 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
347 No samples; assembling all-inclusive block
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
348 Sorting block of length 756159 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
349 (Using difference cover)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
350 Sorting block time: xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
351 Returning block of 756160 for bucket 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
352 Exited Ebwt loop
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
353 fchr[A]: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
354 fchr[C]: 386401
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
355 fchr[G]: 533276
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
356 fchr[T]: 533276
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
357 fchr[$]: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
358 Exiting Ebwt::buildToDisk()
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
359 Returning from initFromVector
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
360 Wrote 4446745 bytes to primary EBWT file: BS_GA.rev.1.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
361 Wrote 189044 bytes to secondary EBWT file: BS_GA.rev.2.bt2
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
362 Re-opening _in1 and _in2 as input streams
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
363 Returning from Ebwt constructor
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
364 Headers:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
365 len: 756159
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
366 bwtLen: 756160
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
367 sz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
368 bwtSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
369 lineRate: 6
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
370 offRate: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
371 offMask: 0xfffffff0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
372 ftabChars: 10
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
373 eftabLen: 20
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
374 eftabSz: 80
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
375 ftabLen: 1048577
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
376 ftabSz: 4194308
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
377 offsLen: 47260
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
378 offsSz: 189040
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
379 lineSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
380 sideSz: 64
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
381 sideBwtSz: 48
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
382 sideBwtLen: 192
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
383 numSides: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
384 numLines: 3939
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
385 ebwtTotLen: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
386 ebwtTotSz: 252096
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
387 color: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
388 reverse: 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
389 Total time for backward call to driver() for mirror index: 00:00:01
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
390 Running bismark with: 'bismark --bam --temp_dir /tmp/tmpi3V3GI -o /tmp/tmpi3V3GI/results --quiet --fastq -L 20 -D 15 -R 2 --pbat --un --ambiguous /tmp/tmpuqE7r1 input_1.fq'
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
391 Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.3.5])
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
392 Output format is BAM (default)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
393 Alignments will be written out in BAM format. Samtools found here: '/home/abretaud/miniconda3/envs/mulled-v1-9f2317dbfb405ed6926c55752e5c11678eee3256a6ea680d1c0f912251153030/bin/samtools'
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
394 Reference genome folder provided is /tmp/tmpuqE7r1/ (absolute path is '/tmp/tmpuqE7r1/)'
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
395 FastQ format specified
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
396
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
397 Input files to be analysed (in current folder '/tmp/tmpU_oiEI/job_working_directory/000/4/working'):
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
398 input_1.fq
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
399 Library was specified as PBAT-Seq (Post-Bisulfite Adapter Tagging), only performing alignments to the complementary strands (CTOT and CTOB)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
400 Created output directory /tmp/tmpi3V3GI/results/!
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
401
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
402 Output will be written into the directory: /tmp/tmpi3V3GI/results/
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
403
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
404 Using temp directory: /tmp/tmpi3V3GI
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
405 Temporary files will be written into the directory: /tmp/tmpi3V3GI/
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
406 Setting parallelization to single-threaded (default)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
407
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
408 Summary of all aligner options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
409 Current working directory is: /tmp/tmpU_oiEI/job_working_directory/000/4/working
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
410
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
411 Now reading in and storing sequence information of the genome specified in: /tmp/tmpuqE7r1/
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
412
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
413 chr chrY_JH584300_random (182347 bp)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
414 chr chrY_JH584301_random (259875 bp)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
415 chr chrY_JH584302_random (155838 bp)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
416 chr chrY_JH584303_random (158099 bp)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
417
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
418 Single-core mode: setting pid to 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
419
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
420 Single-end alignments will be performed
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
421 =======================================
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
422
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
423 Input file is in FastQ format
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
424 Writing a G -> A converted version of the input file input_1.fq to /tmp/tmpi3V3GI/input_1.fq_G_to_A.fastq
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
425
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
426 Created G -> A converted version of the FastQ file input_1.fq (44115 sequences in total)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
427
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
428 Input file is input_1.fq_G_to_A.fastq (FastQ)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
429
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
430 Now running 2 instances of Bowtie 2 against the bisulfite genome of /tmp/tmpuqE7r1/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
431
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
432 Now starting the Bowtie 2 aligner for GAreadCTgenome (reading in sequences from /tmp/tmpi3V3GI/input_1.fq_G_to_A.fastq with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --nofw)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
433 Using Bowtie 2 index: /tmp/tmpuqE7r1/Bisulfite_Genome/CT_conversion/BS_CT
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
434
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
435 Found first alignment: 1_1 4 * 0 0 * * 0 0 TTATATATATTAAATAAATTAATTTTTTTTATTTATATATTAAATTTTTTAATTAATTTATTAATATTTTATAAATTTTTAAATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UU
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
436 Now starting the Bowtie 2 aligner for GAreadGAgenome (reading in sequences from /tmp/tmpi3V3GI/input_1.fq_G_to_A.fastq with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --norc)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
437 Using Bowtie 2 index: /tmp/tmpuqE7r1/Bisulfite_Genome/GA_conversion/BS_GA
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
438
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
439 Found first alignment: 1_1 4 * 0 0 * * 0 0 TTATATATATTAAATAAATTAATTTTTTTTATTTATATATTAAATTTTTTAATTAATTTATTAATATTTTATAAATTTTTAAATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UU
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
440
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
441 >>> Writing bisulfite mapping results to /tmp/tmpi3V3GI/results/input_1_bismark_bt2.bam <<<
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
442
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
443 Unmapped sequences will be written to /tmp/tmpi3V3GI/results/input_1.fq_unmapped_reads.fq.gz
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
444 Ambiguously mapping sequences will be written to /tmp/tmpi3V3GI/results/input_1.fq_ambiguous_reads.fq.gz
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
445
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
446 Reading in the sequence file input_1.fq
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
447 Processed 44115 sequences in total
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
448
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
449
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
450 Successfully deleted the temporary file /tmp/tmpi3V3GI/input_1.fq_G_to_A.fastq
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
451
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
452 Final Alignment report
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
453 ======================
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
454 Sequences analysed in total: 44115
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
455 Number of alignments with a unique best hit from the different alignments: 13
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
456 Mapping efficiency: 0.0%
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
457
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
458 Sequences with no alignments under any condition: 44059
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
459 Sequences did not map uniquely: 43
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
460 Sequences which were discarded because genomic sequence could not be extracted: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
461
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
462 Number of sequences with unique best (first) alignment came from the bowtie output:
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
463 CT/CT: 0 ((converted) top strand)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
464 CT/GA: 0 ((converted) bottom strand)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
465 GA/CT: 11 (complementary to (converted) top strand)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
466 GA/GA: 2 (complementary to (converted) bottom strand)
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
467
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
468 Final Cytosine Methylation Report
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
469 =================================
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
470 Total number of C's analysed: 307
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
471
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
472 Total methylated C's in CpG context: 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
473 Total methylated C's in CHG context: 3
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
474 Total methylated C's in CHH context: 227
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
475 Total methylated C's in Unknown context: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
476
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
477 Total unmethylated C's in CpG context: 1
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
478 Total unmethylated C's in CHG context: 4
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
479 Total unmethylated C's in CHH context: 71
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
480 Total unmethylated C's in Unknown context: 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
481
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
482 C methylated in CpG context: 50.0%
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
483 C methylated in CHG context: 42.9%
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
484 C methylated in CHH context: 76.2%
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
485 Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
486
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
487
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
488 Bismark completed in xxxx
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
489
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
490 ====================
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
491 Bismark run complete
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
492 ====================
aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
bgruening
parents:
diff changeset
493