### 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)
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/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: 01:13:17
Command 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