### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg18/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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bismark_bt2_index/default/_refgenie_build/ * Pipeline started at: (04-07 20:13:56) 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`: `['hg18/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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bismark_bt2_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_bismark_bt2_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bismark_bt2_index/default` (13150)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 13150; Command: ln; Return code: 0; Memory used: 0.001GB > `bismark_genome_preparation --bowtie2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bismark_bt2_index/default` (13151)
[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: 589382566 G->A: 589735358 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 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: 00:00:41 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time reading reference sizes: 00:00:43 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:36 bmax according to bmaxDivN setting: 720355424 Using parameters --bmax 540266568 --dcv 1024 Doing ahead-of-time memory usage test Time to join reference sequences: 00:00:36 bmax according to bmaxDivN setting: 720355424 Using parameters --bmax 540266568 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 540266568 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder Passed! Constructing with these parameters: --bmax 540266568 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime V-Sorting samples Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:04:20 Allocating rank array Ranking v-sort output V-Sorting samples time: 00:04:20 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:01:02 Invoking Larsson-Sadakane on ranks Ranking v-sort output time: 00:01:04 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:01:45 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: 2.88142e+09 (target: 540266567) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Invoking Larsson-Sadakane on ranks time: 00:01:48 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: 2.88142e+09 (target: 540266567) 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 2881421696 for bucket 1 (Using difference cover) Sorting block of length 2881421696 for bucket 1 (Using difference cover) Sorting block time: 01:49:33 Returning block of 2881421697 for bucket 1 Sorting block time: 02:14:00 Returning block of 2881421697 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1440304264 fchr[G]: 2029686830 fchr[T]: 2029686830 fchr[$]: 2881421696 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 964772485 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 720355432 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2881421696 bwtLen: 2881421697 sz: 720355424 bwtSz: 720355425 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 180088857 offsSz: 720355428 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 15007405 numLines: 15007405 ebwtTotLen: 960473920 ebwtTotSz: 960473920 color: 0 reverse: 0 Total time for call to driver() for forward index: 02:23:32 Reading reference sizes Time reading reference sizes: 00:00:34 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:35 Time to reverse reference sequence: 00:00:05 bmax according to bmaxDivN setting: 720355424 Using parameters --bmax 540266568 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 540266568 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:04:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:01:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:01:46 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: 2.88142e+09 (target: 540266567) 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 2881421696 for bucket 1 (Using difference cover) Exited Ebwt loop fchr[A]: 0 fchr[C]: 850568906 fchr[G]: 850568906 fchr[T]: 1440304264 fchr[$]: 2881421696 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 964772485 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 720355432 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2881421696 bwtLen: 2881421697 sz: 720355424 bwtSz: 720355425 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 180088857 offsSz: 720355428 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 15007405 numLines: 15007405 ebwtTotLen: 960473920 ebwtTotSz: 960473920 color: 0 reverse: 0 Total time for call to driver() for forward index: 02:48:14 Reading reference sizes Time reading reference sizes: 00:00:32 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:37 Time to reverse reference sequence: 00:00:05 bmax according to bmaxDivN setting: 720355424 Using parameters --bmax 540266568 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 540266568 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:05:23 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:01:19 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:02:19 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: 2.88142e+09 (target: 540266567) 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 2881421696 for bucket 1 (Using difference cover) Sorting block time: 02:19:06 Returning block of 2881421697 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1440304264 fchr[G]: 2029686830 fchr[T]: 2029686830 fchr[$]: 2881421696 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 964772485 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 720355432 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2881421696 bwtLen: 2881421697 sz: 720355424 bwtSz: 720355425 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 180088857 offsSz: 720355428 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 15007405 numLines: 15007405 ebwtTotLen: 960473920 ebwtTotSz: 960473920 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 02:55:43 Sorting block time: 02:37:25 Returning block of 2881421697 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 850568906 fchr[G]: 850568906 fchr[T]: 1440304264 fchr[$]: 2881421696 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 964772485 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 720355432 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2881421696 bwtLen: 2881421697 sz: 720355424 bwtSz: 720355425 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 180088857 offsSz: 720355428 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 15007405 numLines: 15007405 ebwtTotLen: 960473920 ebwtTotSz: 960473920 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 03:01:05Command completed. Elapsed time: 5:51:20. Running peak memory: 29.808GB. PID: 13151; Command: bismark_genome_preparation; Return code: 0; Memory used: 29.808GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bismark_bt2_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_bismark_bt2_index__default.flag` (14266)
Command completed. Elapsed time: 0:00:00. Running peak memory: 29.808GB. PID: 14266; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 68c9fc012afea08096464d3f5dafe0d4 Default tag for '9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bismark_bt2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 5:51:51 * Total elapsed time (all runs): 5:51:20 * Peak memory (this run): 29.8082 GB * Pipeline completed time: 2021-04-08 02:05:47 Finished building 'bismark_bt2_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg18/bismark_bt2_index/default