### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38_noalt_decoy/bowtie2_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/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/_refgenie_build/ * Pipeline started at: (04-07 16:15:55) 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`: `['hg38_noalt_decoy/bowtie2_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/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_bowtie2_index__default.flag` > `bowtie2-build /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/fasta/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79` (29432)
[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 Settings: Output files: "/project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.*.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: /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/fasta/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:23 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:19 bmax according to bmaxDivN setting: 735167243 Using parameters --bmax 551375433 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 551375433 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:01:52 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:31 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:54 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: 2.94067e+09 (target: 551375432) 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 2940668973 for bucket 1 (Using difference cover) Sorting block time: 00:55:09 Returning block of 2940668974 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 868075685 fchr[G]: 1468033461 fchr[T]: 2070123530 fchr[$]: 2940668973 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 984794015 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.1.bt2 Wrote 735167248 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2940668973 bwtLen: 2940668974 sz: 735167244 bwtSz: 735167244 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 183791811 offsSz: 735167244 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 15315985 numLines: 15315985 ebwtTotLen: 980223040 ebwtTotSz: 980223040 color: 0 reverse: 0 Total time for call to driver() for forward index: 01:12:30 Reading reference sizes Time reading reference sizes: 00:00:17 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:19 Time to reverse reference sequence: 00:00:02 bmax according to bmaxDivN setting: 735167243 Using parameters --bmax 551375433 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 551375433 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:01:59 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:31 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:51 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: 2.94067e+09 (target: 551375432) 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 2940668973 for bucket 1 (Using difference cover) Sorting block time: 00:56:39 Returning block of 2940668974 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 868075685 fchr[G]: 1468033461 fchr[T]: 2070123530 fchr[$]: 2940668973 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 984794015 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.rev.1.bt2 Wrote 735167248 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 2940668973 bwtLen: 2940668974 sz: 735167244 bwtSz: 735167244 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 183791811 offsSz: 735167244 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 15315985 numLines: 15315985 ebwtTotLen: 980223040 ebwtTotSz: 980223040 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 01:13:17Command completed. Elapsed time: 2:25:48. Running peak memory: 15.215GB. PID: 29432; Command: bowtie2-build; Return code: 0; Memory used: 15.215GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_bowtie2_index__default.flag` (27543)
Command completed. Elapsed time: 0:00:00. Running peak memory: 15.215GB. PID: 27543; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: de11c3669656e8a117143f76afff2a25 Default tag for 'a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bowtie2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 2:25:58 * Total elapsed time (all runs): 2:25:48 * Peak memory (this run): 15.2147 GB * Pipeline completed time: 2021-04-07 18:41:53 Finished building 'bowtie2_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_noalt_decoy/bowtie2_index/default