### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build dm6/bowtie2_index` * Compute host: udc-ba25-17 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/_refgenie_build/ * Pipeline started at: (04-07 16:37:23) 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`: `['dm6/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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/_refgenie_build/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_bowtie2_index__default.flag` > `bowtie2-build /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/fasta/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158` (16261)
[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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.*.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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/fasta/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 35643256 Using parameters --bmax 26732442 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 26732442 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:04 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: 00:00:01 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: 1.42573e+08 (target: 26732441) 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 142573024 for bucket 1 (Using difference cover) Sorting block time: 00:01:00 Returning block of 142573025 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41351058 fchr[G]: 71311730 fchr[T]: 101240543 fchr[$]: 142573024 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 51887963 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.1.bt2 Wrote 35643264 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 142573024 bwtLen: 142573025 sz: 35643256 bwtSz: 35643257 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 8910815 offsSz: 35643260 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 742568 numLines: 742568 ebwtTotLen: 47524352 ebwtTotSz: 47524352 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:18 Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 35643256 Using parameters --bmax 26732442 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 26732442 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:01 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: 1.42573e+08 (target: 26732441) 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 142573024 for bucket 1 (Using difference cover) Sorting block time: 00:01:01 Returning block of 142573025 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41351058 fchr[G]: 71311730 fchr[T]: 101240543 fchr[$]: 142573024 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 51887963 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.rev.1.bt2 Wrote 35643264 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 142573024 bwtLen: 142573025 sz: 35643256 bwtSz: 35643257 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 8910815 offsSz: 35643260 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 742568 numLines: 742568 ebwtTotLen: 47524352 ebwtTotSz: 47524352 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:17Command completed. Elapsed time: 0:02:35. Running peak memory: 0.825GB. PID: 16261; Command: bowtie2-build; Return code: 0; Memory used: 0.825GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index/default/_refgenie_build/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_bowtie2_index__default.flag` (16671)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.825GB. PID: 16671; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 3e3c651f1aca155b3498cade39a3694a Default tag for '8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/bowtie2_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:02:37 * Total elapsed time (all runs): 0:02:35 * Peak memory (this run): 0.8254 GB * Pipeline completed time: 2021-04-07 16:40:00 Finished building 'bowtie2_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/dm6/bowtie2_index/default