Path to genome folder specified as: /gscratch/srlab/sam/data/C_virginica/genomes/ Aligner to be used: Bowtie 2 (default) Writing bisulfite genomes out into a single MFA (multi FastA) file Bismark Genome Preparation - Step I: Preparing folders Path to Bowtie 2 specified: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ Bisulfite Genome Indexer version v0.19.0 (last modified 07 November 2016) Created Bisulfite Genome folder /gscratch/srlab/sam/data/C_virginica/genomes/Bisulfite_Genome/ Created Bisulfite Genome folder /gscratch/srlab/sam/data/C_virginica/genomes/Bisulfite_Genome/CT_conversion/ Created Bisulfite Genome folder /gscratch/srlab/sam/data/C_virginica/genomes/Bisulfite_Genome/GA_conversion/ Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome conversions performed: chromosome C->T G->A NC_035780.1 11492316 11528162 NC_035781.1 10879823 10858285 NC_035782.1 13475475 13496235 NC_035783.1 10484268 10482193 NC_035784.1 17306783 17253434 NC_035785.1 8878985 8876470 NC_035786.1 9961761 9989843 NC_035787.1 13145205 13164212 NC_035788.1 17925605 17932896 NC_035789.1 5676071 5682065 NC_007175.2 2827 3882 Total number of conversions performed: C->T: 119229119 G->A: 119267677 Step II - Genome bisulfite conversions - completed Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer Please be aware that this process can - depending on genome size - take several hours! Preparing indexing of CT converted genome in /gscratch/srlab/sam/data/C_virginica/genomes/Bisulfite_Genome/CT_conversion/ Parent process: Starting to index C->T converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.CT_conversion.fa BS_CT Settings: Output files: "BS_CT.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.CT_conversion.fa Building a SMALL index Reading reference sizes Preparing indexing of GA converted genome in /gscratch/srlab/sam/data/C_virginica/genomes/Bisulfite_Genome/GA_conversion/ Child process: Starting to index G->A converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.GA_conversion.fa BS_GA Settings: Output files: "BS_GA.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.GA_conversion.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:02 bmax according to bmaxDivN setting: 171168832 Using parameters --bmax 128376624 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 128376624 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Time to join reference sequences: 00:00:02 bmax according to bmaxDivN setting: 171168832 Using parameters --bmax 128376624 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 128376624 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:14 Allocating rank array Ranking v-sort output V-Sorting samples time: 00:00:14 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.84675e+08 (target: 128376623) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 684675328 for bucket 1 (Using difference cover) Invoking Larsson-Sadakane on ranks time: 00:00:05 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.84675e+08 (target: 128376623) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 684675328 for bucket 1 (Using difference cover) Sorting block time: 00:04:04 Returning block of 684675329 for bucket 1 Sorting block time: 00:04:07 Returning block of 684675329 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 223134775 fchr[G]: 223134775 fchr[T]: 342402452 fchr[$]: 684675328 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 232427948 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 171168840 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 684675328 bwtLen: 684675329 sz: 171168832 bwtSz: 171168833 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 42792209 offsSz: 171168836 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3566018 numLines: 3566018 ebwtTotLen: 228225152 ebwtTotSz: 228225152 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:05:19 Reading reference sizes Exited Ebwt loop fchr[A]: 0 fchr[C]: 342402452 fchr[G]: 461631571 fchr[T]: 461631571 fchr[$]: 684675328 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 232427948 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 171168840 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 684675328 bwtLen: 684675329 sz: 171168832 bwtSz: 171168833 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 42792209 offsSz: 171168836 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3566018 numLines: 3566018 ebwtTotLen: 228225152 ebwtTotSz: 228225152 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:05:18 Reading reference sizes Time reading reference sizes: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:13 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 171168832 Using parameters --bmax 128376624 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 128376624 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Time to join reference sequences: 00:00:14 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 171168832 Using parameters --bmax 128376624 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 128376624 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:13 Allocating rank array Ranking v-sort output V-Sorting samples time: 00:00:12 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.84675e+08 (target: 128376623) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 684675328 for bucket 1 (Using difference cover) Invoking Larsson-Sadakane on ranks time: 00:00:05 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.84675e+08 (target: 128376623) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 684675328 for bucket 1 (Using difference cover) Sorting block time: 00:04:05 Returning block of 684675329 for bucket 1 Sorting block time: 00:04:09 Returning block of 684675329 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 342402452 fchr[G]: 461631571 fchr[T]: 461631571 fchr[$]: 684675328 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 232427948 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 171168840 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 684675328 bwtLen: 684675329 sz: 171168832 bwtSz: 171168833 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 42792209 offsSz: 171168836 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3566018 numLines: 3566018 ebwtTotLen: 228225152 ebwtTotSz: 228225152 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:05:29 Exited Ebwt loop fchr[A]: 0 fchr[C]: 223134775 fchr[G]: 223134775 fchr[T]: 342402452 fchr[$]: 684675328 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 232427948 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 171168840 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 684675328 bwtLen: 684675329 sz: 171168832 bwtSz: 171168833 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 42792209 offsSz: 171168836 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3566018 numLines: 3566018 ebwtTotLen: 228225152 ebwtTotSz: 228225152 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:05:30