### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build rn6/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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index/default/_refgenie_build/
* Pipeline started at: (04-07 16:40:28) 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/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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index/default/_refgenie_build/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_bwa_index__default.flag`
> `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/fasta/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index/default` (17117)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 17117; Command: ln; Return code: 0; Memory used: 0.001GB
> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.fa` (17120)
[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... 24.12 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5740368386, availableWord=415913560
[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. 5099303554 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5189822354 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5270271714 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5341771298 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5405316274 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5461791186 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5511982210 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5556588130 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5596229970 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5631459698 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5662767954 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5690590754 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 5715315730 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 5737287298 characters processed.
[bwt_gen] Finished constructing BWT in 642 iterations.
[bwa_index] 2698.27 seconds elapse.
[bwa_index] Update BWT... 16.48 sec
[bwa_index] Pack forward-only FASTA... 15.10 sec
[bwa_index] Construct SA from BWT and Occ... 733.30 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.fa
[main] Real time: 3520.823 sec; CPU: 3487.317 sec
Command completed. Elapsed time: 0:58:41. Running peak memory: 4.322GB.
PID: 17120; Command: bwa; Return code: 0; Memory used: 4.322GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index/default/_refgenie_build/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_bwa_index__default.flag` (28375)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.322GB.
PID: 28375; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: c85365f5de6a443585455917ce489908
Default tag for '79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/bwa_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:58:52
* Total elapsed time (all runs): 0:58:41
* Peak memory (this run): 4.3222 GB
* Pipeline completed time: 2021-04-07 17:39:20
Finished building 'bwa_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rn6/bwa_index/default