### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build rCRSd/bismark_bt2_index` * Compute host: udc-ba25-18 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bismark_bt2_index/default/_refgenie_build/ * Pipeline started at: (04-07 20:45:45) elapsed: 0.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/mjs5kd/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/qumulo/qhome/mjs5kd/.local/bin` * Pipeline version: None ### Arguments passed to pipeline: * `asset_registry_paths`: `['rCRSd/bismark_bt2_index']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `None` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `None` * `logdev`: `False` * `new_start`: `False` * `outfolder`: `/project/shefflab/deploy/rg.databio.org_full/genomes/data` * `params`: `None` * `recipe`: `None` * `recover`: `False` * `requirements`: `False` * `silent`: `False` * `skip_read_lock`: `False` * `tag_description`: `None` * `verbosity`: `None` * `volumes`: `None` ---------------------------------------- Target to produce: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bismark_bt2_index/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_bismark_bt2_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bismark_bt2_index/default` (19544)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB. PID: 19544; Command: ln; Return code: 0; Memory used: 0.0GB > `bismark_genome_preparation --bowtie2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bismark_bt2_index/default` (19545)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Writing bisulfite genomes out into a single MFA (multi FastA) file Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019) Step I - Prepare genome folders - completed Total number of conversions performed: C->T: 10362 G->A: 4338 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! 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 Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 8284 Using parameters --bmax 6213 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 6213 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 33136 (target: 6212) 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 33136 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 33137 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 10248 fchr[G]: 10248 fchr[T]: 14586 fchr[$]: 33136 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4205580 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 8292 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 33136 bwtLen: 33137 sz: 8284 bwtSz: 8285 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2072 offsSz: 8288 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 173 numLines: 173 ebwtTotLen: 11072 ebwtTotSz: 11072 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 8284 Using parameters --bmax 6213 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 6213 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 33136 (target: 6212) 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 33136 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 33137 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 10248 fchr[G]: 10248 fchr[T]: 14586 fchr[$]: 33136 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4205580 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 8292 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 33136 bwtLen: 33137 sz: 8284 bwtSz: 8285 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2072 offsSz: 8288 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 173 numLines: 173 ebwtTotLen: 11072 ebwtTotSz: 11072 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:00 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: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 8284 Using parameters --bmax 6213 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 6213 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 33136 (target: 6212) 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 33136 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 33137 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 14586 fchr[G]: 24948 fchr[T]: 24948 fchr[$]: 33136 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4205580 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 8292 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 33136 bwtLen: 33137 sz: 8284 bwtSz: 8285 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2072 offsSz: 8288 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 173 numLines: 173 ebwtTotLen: 11072 ebwtTotSz: 11072 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 8284 Using parameters --bmax 6213 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 6213 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 33136 (target: 6212) 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 33136 for bucket 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 33137 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 14586 fchr[G]: 24948 fchr[T]: 24948 fchr[$]: 33136 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4205580 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 8292 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 33136 bwtLen: 33137 sz: 8284 bwtSz: 8285 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 2072 offsSz: 8288 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 173 numLines: 173 ebwtTotLen: 11072 ebwtTotSz: 11072 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:00Command completed. Elapsed time: 0:00:07. Running peak memory: 0.017GB. PID: 19545; Command: bismark_genome_preparation; Return code: 0; Memory used: 0.017GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bismark_bt2_index/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_bismark_bt2_index__default.flag` (19604)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.017GB. PID: 19604; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 0caeadefe17f77826e99cb4036a994ed Default tag for '94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bismark_bt2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:08 * Total elapsed time (all runs): 0:00:07 * Peak memory (this run): 0.0171 GB * Pipeline completed time: 2021-04-07 20:45:53 Finished building 'bismark_bt2_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rCRSd/bismark_bt2_index/default