### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg38_primary/bwa_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/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index/default/_refgenie_build/
* Pipeline started at: (04-07 17:39:59) 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_primary/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/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index/default/_refgenie_build/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae_bwa_index__default.flag`
> `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/fasta/default/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index/default` (28678)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 28678; Command: ln; Return code: 0; Memory used: 0.001GB
> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index/default/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae.fa` (28679)
[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... 26.33 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6176572802, availableWord=446606192
[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.
[BWTIncConstructFromPacked] 130 iterations done. 1299999986 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999986 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999986 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999986 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999986 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999986 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999986 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999986 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999986 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999986 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999986 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999986 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999986 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999986 characters processed.
[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.
[BWTIncConstructFromPacked] 310 iterations done. 3099999986 characters processed.
[BWTIncConstructFromPacked] 320 iterations done. 3199999986 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3299999986 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3399999986 characters processed.
[BWTIncConstructFromPacked] 350 iterations done. 3499999986 characters processed.
[BWTIncConstructFromPacked] 360 iterations done. 3599999986 characters processed.
[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.
[BWTIncConstructFromPacked] 460 iterations done. 4599999986 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999986 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999986 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999986 characters processed.
[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. 5594485778 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5678460994 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5753094370 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5819424706 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5878375266 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5930766642 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5977328210 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6018708242 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6055482898 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6088164258 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6117207522 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6143017202 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6165952882 characters processed.
[bwt_gen] Finished constructing BWT in 686 iterations.
[bwa_index] 2910.66 seconds elapse.
[bwa_index] Update BWT... 17.84 sec
[bwa_index] Pack forward-only FASTA... 16.73 sec
[bwa_index] Construct SA from BWT and Occ... 790.97 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index/default/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae.fa
[main] Real time: 3797.032 sec; CPU: 3762.573 sec
Command completed. Elapsed time: 1:03:17. Running peak memory: 4.651GB.
PID: 28679; Command: bwa; Return code: 0; Memory used: 4.651GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index/default/_refgenie_build/047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae_bwa_index__default.flag` (9145)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.651GB.
PID: 9145; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 41e1499d24e3c118811716186b08a1bc
Default tag for '047c6e1eda552b50c5add59ff0995a40bc4ce1732e3cc4ae/bwa_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 1:03:29
* Total elapsed time (all runs): 1:03:17
* Peak memory (this run): 4.651 GB
* Pipeline completed time: 2021-04-07 18:43:29
Finished building 'bwa_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_primary/bwa_index/default