### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build rn6/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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/_refgenie_build/
* Pipeline started at: (04-07 15:53:01) 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`: `['rn6/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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/_refgenie_build/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_bowtie2_index__default.flag`
> `bowtie2-build /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/fasta/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9` (23311)
[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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.*.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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/fasta/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.fa
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:28
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:18
bmax according to bmaxDivN setting: 682465522
Using parameters --bmax 511849142 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 511849142 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:01:42
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:26
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:46
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: 2.72986e+09 (target: 511849141)
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 2729862089 for bucket 1
(Using difference cover)
Sorting block time: 00:53:03
Returning block of 2729862090 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 792473342
fchr[G]: 1364770583
fchr[T]: 1937051585
fchr[$]: 2729862089
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 916016739 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.1.bt2
Wrote 682465528 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2729862089
bwtLen: 2729862090
sz: 682465523
bwtSz: 682465523
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 170616381
offsSz: 682465524
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 14218032
numLines: 14218032
ebwtTotLen: 909954048
ebwtTotSz: 909954048
color: 0
reverse: 0
Total time for call to driver() for forward index: 01:08:37
Reading reference sizes
Time reading reference sizes: 00:00:29
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:18
Time to reverse reference sequence: 00:00:02
bmax according to bmaxDivN setting: 682465522
Using parameters --bmax 511849142 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 511849142 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:01:57
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:29
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:48
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: 2.72986e+09 (target: 511849141)
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 2729862089 for bucket 1
(Using difference cover)
Sorting block time: 00:56:58
Returning block of 2729862090 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 792473342
fchr[G]: 1364770583
fchr[T]: 1937051585
fchr[$]: 2729862089
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 916016739 bytes to primary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.rev.1.bt2
Wrote 682465528 bytes to secondary EBWT file: /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2729862089
bwtLen: 2729862090
sz: 682465523
bwtSz: 682465523
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 170616381
offsSz: 682465524
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 14218032
numLines: 14218032
ebwtTotLen: 909954048
ebwtTotSz: 909954048
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 01:12:40
Command completed. Elapsed time: 2:21:18. Running peak memory: 14.135GB.
PID: 23311; Command: bowtie2-build; Return code: 0; Memory used: 14.135GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index/default/_refgenie_build/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_bowtie2_index__default.flag` (22130)
Command completed. Elapsed time: 0:00:00. Running peak memory: 14.135GB.
PID: 22130; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: cf7ecd73c42f5d93d737a44a1c21c9bf
Default tag for '79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bowtie2_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 2:21:27
* Total elapsed time (all runs): 2:21:18
* Peak memory (this run): 14.1349 GB
* Pipeline completed time: 2021-04-07 18:14:29
Finished building 'bowtie2_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rn6/bowtie2_index/default