### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build mouse_chrM2x/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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/_refgenie_build/ * Pipeline started at: (04-07 16:29:59) 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`: `['mouse_chrM2x/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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_bowtie2_index__default.flag` > `bowtie2-build /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a` (1100)
WARNING: 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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.*.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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.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: 8149
Using parameters --bmax 6112 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 6112 --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: 32598 (target: 6111)
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 32598 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 32599 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 11258
fchr[G]: 19210
fchr[T]: 23236
fchr[$]: 32598
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4205352 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.1.bt2
Wrote 8156 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 32598
    bwtLen: 32599
    sz: 8150
    bwtSz: 8150
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 2038
    offsSz: 8152
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 170
    numLines: 170
    ebwtTotLen: 10880
    ebwtTotSz: 10880
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:01
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: 8149
Using parameters --bmax 6112 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 6112 --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: 32598 (target: 6111)
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 32598 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 32599 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 11258
fchr[G]: 19210
fchr[T]: 23236
fchr[$]: 32598
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4205352 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.rev.1.bt2
Wrote 8156 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 32598
    bwtLen: 32599
    sz: 8150
    bwtSz: 8150
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 2038
    offsSz: 8152
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 170
    numLines: 170
    ebwtTotLen: 10880
    ebwtTotSz: 10880
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.028GB. PID: 1100; Command: bowtie2-build; Return code: 0; Memory used: 0.028GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_bowtie2_index__default.flag` (1144)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.028GB.  
  PID: 1144;	Command: touch;	Return code: 0;	Memory used: 0.0GB

Asset digest: 738d82a0ff63864726c442b2276d06c0
Default tag for '43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/bowtie2_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:02
*  Total elapsed time (all runs):  0:00:01
*         Peak memory (this run):  0.0279 GB
*        Pipeline completed time: 2021-04-07 16:30:01
Finished building 'bowtie2_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/mouse_chrM2x/bowtie2_index/default