### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg18/bwa_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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index/default/_refgenie_build/
* Pipeline started at: (04-07 16:39:13) 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`: `['hg18/bwa_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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_bwa_index__default.flag`
> `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index/default` (3577)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 3577; Command: ln; Return code: 0; Memory used: 0.0GB
> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa` (3578)
[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
[bwa_index] Pack FASTA... 28.04 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6215354546, availableWord=449335076
[BWTIncConstructFromPacked] 10 iterations done. 99999986 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999986 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999986 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999986 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999986 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999986 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999986 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999986 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999986 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999986 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999986 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999986 characters processed.
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[BWTIncConstructFromPacked] 160 iterations done. 1599999986 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999986 characters processed.
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[BWTIncConstructFromPacked] 270 iterations done. 2699999986 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999986 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999986 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999986 characters processed.
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[BWTIncConstructFromPacked] 320 iterations done. 3199999986 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3299999986 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3399999986 characters processed.
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[BWTIncConstructFromPacked] 360 iterations done. 3599999986 characters processed.
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[BWTIncConstructFromPacked] 390 iterations done. 3899999986 characters processed.
[BWTIncConstructFromPacked] 400 iterations done. 3999999986 characters processed.
[BWTIncConstructFromPacked] 410 iterations done. 4099999986 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4199999986 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4299999986 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999986 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999986 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999986 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999986 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999986 characters processed.
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[BWTIncConstructFromPacked] 530 iterations done. 5299999986 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5399999986 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5499999986 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5597940706 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5685847378 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5763975058 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5833411138 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5895122082 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5949966914 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5998709138 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6042027314 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6080524594 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6114737074 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6145141154 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6172160338 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6196171026 characters processed.
[bwt_gen] Finished constructing BWT in 689 iterations.
[bwa_index] 3647.50 seconds elapse.
[bwa_index] Update BWT... 19.46 sec
[bwa_index] Pack forward-only FASTA... 18.01 sec
[bwa_index] Construct SA from BWT and Occ... 1374.44 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa
[main] Real time: 5144.708 sec; CPU: 5087.493 sec
Command completed. Elapsed time: 1:25:45. Running peak memory: 4.675GB.
PID: 3578; Command: bwa; Return code: 0; Memory used: 4.675GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_bwa_index__default.flag` (19981)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.675GB.
PID: 19981; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: d4c64ed81b3d52c17202659b915b804b
Default tag for '9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/bwa_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 1:25:58
* Total elapsed time (all runs): 1:25:45
* Peak memory (this run): 4.675 GB
* Pipeline completed time: 2021-04-07 18:05:11
Finished building 'bwa_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg18/bwa_index/default