### 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)
WARNING: 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.
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[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] 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] 330 iterations done. 3299999986 characters processed.
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[BWTIncConstructFromPacked] 370 iterations done. 3699999986 characters processed.
[BWTIncConstructFromPacked] 380 iterations done. 3799999986 characters processed.
[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.
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[BWTIncConstructFromPacked] 470 iterations done. 4699999986 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999986 characters processed.
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[BWTIncConstructFromPacked] 500 iterations done. 4999999986 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999986 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5199999986 characters processed.
[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