### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38_chr22/bismark_bt2_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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bismark_bt2_index/default/_refgenie_build/ * Pipeline started at: (04-07 20:41:15) 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_chr22/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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bismark_bt2_index/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_bismark_bt2_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bismark_bt2_index/default` (1058)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.  
  PID: 1058;	Command: ln;	Return code: 0;	Memory used: 0.0GB


> `bismark_genome_preparation --bowtie2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bismark_bt2_index/default` (1060)
WARNING: 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:	9963208
G->A:	10083370

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
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
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 reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 10673160
Using parameters --bmax 8004870 --dcv 1024
  Doing ahead-of-time memory usage test
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 10673160
Using parameters --bmax 8004870 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 8004870 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  Passed!  Constructing with these parameters: --bmax 8004870 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:02
  Allocating rank array
  Ranking v-sort output
  V-Sorting samples time: 00:00:02
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  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: 4.26926e+07 (target: 8004869)
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 42692640 for bucket 1
  (Using difference cover)
  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: 4.26926e+07 (target: 8004869)
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 42692640 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 42692641 for bucket 1
  Sorting block time: 00:00:45
Returning block of 42692641 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 21429219
fchr[G]: 31392427
fchr[T]: 31392427
fchr[$]: 42692640
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 18428498 bytes to primary EBWT file: BS_GA.1.bt2
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 11345849
fchr[G]: 11345849
fchr[T]: 21429219
fchr[$]: 42692640
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 18428498 bytes to primary EBWT file: BS_CT.1.bt2
Wrote 10673168 bytes to secondary EBWT file: BS_GA.2.bt2
Wrote 10673168 bytes to secondary EBWT file: BS_CT.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 42692640
    bwtLen: 42692641
    sz: 10673160
    bwtSz: 10673161
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 2668291
    offsSz: 10673164
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 222358
    numLines: 222358
    ebwtTotLen: 14230912
    ebwtTotSz: 14230912
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:56
Reading reference sizes
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 42692640
    bwtLen: 42692641
    sz: 10673160
    bwtSz: 10673161
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 2668291
    offsSz: 10673164
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 222358
    numLines: 222358
    ebwtTotLen: 14230912
    ebwtTotSz: 14230912
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:56
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  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: 00:00:01
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 10673160
Using parameters --bmax 8004870 --dcv 1024
  Doing ahead-of-time memory usage test
  Time to join reference sequences: 00:00:01
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 10673160
Using parameters --bmax 8004870 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 8004870 --dcv 1024  Passed!  Constructing with these parameters: --bmax 8004870 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples

Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:02
  Allocating rank array
  Ranking v-sort output
  V-Sorting samples time: 00:00:02
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  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: 4.26926e+07 (target: 8004869)
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: 00:00:01
  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: 4.26926e+07 (target: 8004869)
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 42692640 for bucket 1
  (Using difference cover)
  Sorting block of length 42692640 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:45
Returning block of 42692641 for bucket 1
  Sorting block time: 00:00:45
Returning block of 42692641 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 21429219
fchr[G]: 31392427
fchr[T]: 31392427
fchr[$]: 42692640
Exited Ebwt loop
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 18428498 bytes to primary EBWT file: BS_GA.rev.1.bt2
fchr[A]: 0
fchr[C]: 11345849
fchr[G]: 11345849
fchr[T]: 21429219
fchr[$]: 42692640
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 18428498 bytes to primary EBWT file: BS_CT.rev.1.bt2
Wrote 10673168 bytes to secondary EBWT file: BS_GA.rev.2.bt2
Wrote 10673168 bytes to secondary EBWT file: BS_CT.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 42692640
    bwtLen: 42692641
    sz: 10673160
    bwtSz: 10673161
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 2668291
    offsSz: 10673164
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 222358
    numLines: 222358
    ebwtTotLen: 14230912
    ebwtTotSz: 14230912
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:55
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 42692640
    bwtLen: 42692641
    sz: 10673160
    bwtSz: 10673161
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 2668291
    offsSz: 10673164
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 222358
    numLines: 222358
    ebwtTotLen: 14230912
    ebwtTotSz: 14230912
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:55
Command completed. Elapsed time: 0:02:06. Running peak memory: 0.535GB. PID: 1060; Command: bismark_genome_preparation; Return code: 0; Memory used: 0.535GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bismark_bt2_index/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_bismark_bt2_index__default.flag` (1397)

Command completed. Elapsed time: 0:00:01. Running peak memory: 0.535GB.  
  PID: 1397;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: a79889b8cc0e7fbda6d3ca3cd9c6e651
Default tag for 'fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bismark_bt2_index' set to: default

### Pipeline completed. Epilogue