### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38/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/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/bismark_bt2_index/default/_refgenie_build/ * Pipeline started at: (04-07 20:45:46) 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/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/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/bismark_bt2_index/default/_refgenie_build/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4_bismark_bt2_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta/default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/bismark_bt2_index/default` (2599)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.  
  PID: 2599;	Command: ln;	Return code: 0;	Memory used: 0.0GB


> `bismark_genome_preparation --bowtie2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/bismark_bt2_index/default` (2600)
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:	598683433
G->A:	600854940

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
Building a SMALL index
Reading reference sizes
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
  Time reading reference sizes: 00:00:40
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time reading reference sizes: 00:00:40
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:32
bmax according to bmaxDivN setting: 733719112
Using parameters --bmax 550289334 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 550289334 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Time to join reference sequences: 00:00:33
bmax according to bmaxDivN setting: 733719112
Using parameters --bmax 550289334 --dcv 1024
  Doing ahead-of-time memory usage test
  Building sPrimeOrder
  V-Sorting samples
  Passed!  Constructing with these parameters: --bmax 550289334 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:02:24
  Allocating rank array
  Ranking v-sort output
  V-Sorting samples time: 00:02:23
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:35
  Invoking Larsson-Sadakane on ranks
  Ranking v-sort output time: 00:00:35
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:01:09
  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: 2.93488e+09 (target: 550289333)
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: 00:01:09
  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: 2.93488e+09 (target: 550289333)
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 2934876451 for bucket 1
  (Using difference cover)
  Sorting block of length 2934876451 for bucket 1
  (Using difference cover)
  Sorting block time: 00:44:27
Returning block of 2934876452 for bucket 1
  Sorting block time: 00:45:50
Returning block of 2934876452 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 1467274941
fchr[G]: 2065958374
fchr[T]: 2065958374
fchr[$]: 2934876451
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 982507425 bytes to primary EBWT file: BS_GA.1.bt2
Wrote 733719120 bytes to secondary EBWT file: BS_GA.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2934876451
    bwtLen: 2934876452
    sz: 733719113
    bwtSz: 733719113
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 183429779
    offsSz: 733719116
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 15285815
    numLines: 15285815
    ebwtTotLen: 978292160
    ebwtTotSz: 978292160
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:57:54
Reading reference sizes
  Time reading reference sizes: 00:00:30
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:33
  Time to reverse reference sequence: 00:00:05
bmax according to bmaxDivN setting: 733719112
Using parameters --bmax 550289334 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 550289334 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 866420001
fchr[G]: 866420001
fchr[T]: 1467274941
fchr[$]: 2934876451
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 982507425 bytes to primary EBWT file: BS_CT.1.bt2
Wrote 733719120 bytes to secondary EBWT file: BS_CT.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2934876451
    bwtLen: 2934876452
    sz: 733719113
    bwtSz: 733719113
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 183429779
    offsSz: 733719116
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 15285815
    numLines: 15285815
    ebwtTotLen: 978292160
    ebwtTotSz: 978292160
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:59:39
Reading reference sizes
  Time reading reference sizes: 00:00:31
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:33
  Time to reverse reference sequence: 00:00:05
bmax according to bmaxDivN setting: 733719112
Using parameters --bmax 550289334 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 550289334 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:02:24
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:34
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:01:10
  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: 2.93488e+09 (target: 550289333)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
  No samples; assembling all-inclusive block
  V-Sorting samples time: 00:02:24
  Allocating rank array
  Ranking v-sort output
  Sorting block of length 2934876451 for bucket 1
  (Using difference cover)
  Ranking v-sort output time: 00:00:35
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:01:09
  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: 2.93488e+09 (target: 550289333)
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 2934876451 for bucket 1
  (Using difference cover)
  Sorting block time: 00:44:24
Returning block of 2934876452 for bucket 1
  Sorting block time: 00:45:50
Returning block of 2934876452 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 1467274941
fchr[G]: 2065958374
fchr[T]: 2065958374
fchr[$]: 2934876451
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 982507425 bytes to primary EBWT file: BS_GA.rev.1.bt2
Wrote 733719120 bytes to secondary EBWT file: BS_GA.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2934876451
    bwtLen: 2934876452
    sz: 733719113
    bwtSz: 733719113
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 183429779
    offsSz: 733719116
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 15285815
    numLines: 15285815
    ebwtTotLen: 978292160
    ebwtTotSz: 978292160
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:57:53
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 866420001
fchr[G]: 866420001
fchr[T]: 1467274941
fchr[$]: 2934876451
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 982507425 bytes to primary EBWT file: BS_CT.rev.1.bt2
Wrote 733719120 bytes to secondary EBWT file: BS_CT.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2934876451
    bwtLen: 2934876452
    sz: 733719113
    bwtSz: 733719113
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 183429779
    offsSz: 733719116
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 15285815
    numLines: 15285815
    ebwtTotLen: 978292160
    ebwtTotSz: 978292160
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:57:50
Command completed. Elapsed time: 1:59:14. Running peak memory: 30.371GB. PID: 2600; Command: bismark_genome_preparation; Return code: 0; Memory used: 30.371GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/bismark_bt2_index/default/_refgenie_build/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4_bismark_bt2_index__default.flag` (4711)

Command completed. Elapsed time: 0:00:00. Running peak memory: 30.371GB.  
  PID: 4711;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: 3ad42e5278d5efa9ad62827faa0eb828
Default tag for '2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/bismark_bt2_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  1:59:47
*  Total elapsed time (all runs):  1:59:14
*         Peak memory (this run):  30.3712 GB
*        Pipeline completed time: 2021-04-07 22:45:33
Finished building 'bismark_bt2_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38/bismark_bt2_index/default