### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg38_noalt_decoy/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/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index/default/_refgenie_build/
* Pipeline started at: (04-07 16:44:18) 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_noalt_decoy/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/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_bwa_index__default.flag`
> `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/fasta/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index/default` (5079)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 5079; Command: ln; Return code: 0; Memory used: 0.0GB
> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa` (5080)
[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... 27.26 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6211430126, availableWord=449059136
[BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999998 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999998 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999998 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999998 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999998 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999998 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999998 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999998 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999998 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999998 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999998 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1299999998 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999998 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999998 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999998 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999998 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999998 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999998 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999998 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999998 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999998 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999998 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999998 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999998 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999998 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2699999998 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999998 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999998 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999998 characters processed.
[BWTIncConstructFromPacked] 310 iterations done. 3099999998 characters processed.
[BWTIncConstructFromPacked] 320 iterations done. 3199999998 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3299999998 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3399999998 characters processed.
[BWTIncConstructFromPacked] 350 iterations done. 3499999998 characters processed.
[BWTIncConstructFromPacked] 360 iterations done. 3599999998 characters processed.
[BWTIncConstructFromPacked] 370 iterations done. 3699999998 characters processed.
[BWTIncConstructFromPacked] 380 iterations done. 3799999998 characters processed.
[BWTIncConstructFromPacked] 390 iterations done. 3899999998 characters processed.
[BWTIncConstructFromPacked] 400 iterations done. 3999999998 characters processed.
[BWTIncConstructFromPacked] 410 iterations done. 4099999998 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4199999998 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4299999998 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999998 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999998 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999998 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999998 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999998 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999998 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4999999998 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999998 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5199999998 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5299999998 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5399999998 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5499999998 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5597672750 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5685172830 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5762939134 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5832054014 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5893479486 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5948070590 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5996587278 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6039704990 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6078024110 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6112078222 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6142341550 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6169235662 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6193135198 characters processed.
[bwt_gen] Finished constructing BWT in 689 iterations.
[bwa_index] 3589.81 seconds elapse.
[bwa_index] Update BWT... 20.60 sec
[bwa_index] Pack forward-only FASTA... 17.27 sec
[bwa_index] Construct SA from BWT and Occ... 1527.45 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa
[main] Real time: 5245.734 sec; CPU: 5182.442 sec
Command completed. Elapsed time: 1:27:26. Running peak memory: 4.672GB.
PID: 5080; Command: bwa; Return code: 0; Memory used: 4.672GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_bwa_index__default.flag` (21706)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.672GB.
PID: 21706; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 65ce02a1ae39e2dc45d954b864ba29fd
Default tag for 'a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/bwa_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 1:27:39
* Total elapsed time (all runs): 1:27:26
* Peak memory (this run): 4.672 GB
* Pipeline completed time: 2021-04-07 18:11:58
Finished building 'bwa_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_noalt_decoy/bwa_index/default