### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg19/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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default/_refgenie_build/ * Pipeline started at: (04-07 16:39:20) 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`: `['hg19/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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_bwa_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default` (3749)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.  
  PID: 3749;	Command: ln;	Return code: 0;	Memory used: 0.0GB


> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa` (3751)
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... 28.07 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6274322528, availableWord=453484340
[BWTIncConstructFromPacked] 10 iterations done. 100000000 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 200000000 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 300000000 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 400000000 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 500000000 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 600000000 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 700000000 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 800000000 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 900000000 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 1000000000 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1100000000 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1200000000 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1300000000 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1400000000 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1500000000 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1600000000 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1700000000 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1800000000 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1900000000 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 2000000000 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2100000000 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2200000000 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2300000000 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2400000000 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2500000000 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2600000000 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2700000000 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2800000000 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2900000000 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 3000000000 characters processed.
[BWTIncConstructFromPacked] 310 iterations done. 3100000000 characters processed.
[BWTIncConstructFromPacked] 320 iterations done. 3200000000 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3300000000 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3400000000 characters processed.
[BWTIncConstructFromPacked] 350 iterations done. 3500000000 characters processed.
[BWTIncConstructFromPacked] 360 iterations done. 3600000000 characters processed.
[BWTIncConstructFromPacked] 370 iterations done. 3700000000 characters processed.
[BWTIncConstructFromPacked] 380 iterations done. 3800000000 characters processed.
[BWTIncConstructFromPacked] 390 iterations done. 3900000000 characters processed.
[BWTIncConstructFromPacked] 400 iterations done. 4000000000 characters processed.
[BWTIncConstructFromPacked] 410 iterations done. 4100000000 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4200000000 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4300000000 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4400000000 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4500000000 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4600000000 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4700000000 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4800000000 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4900000000 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 5000000000 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5100000000 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5200000000 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5300000000 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5400000000 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5500000000 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5600000000 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5694239600 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5777996048 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5852434944 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5918592432 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5977389360 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 6029644208 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6076084432 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6117356576 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6154035344 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6186631520 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6215599040 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6241341392 characters processed.
[BWTIncConstructFromPacked] 690 iterations done. 6264217232 characters processed.
[bwt_gen] Finished constructing BWT in 695 iterations.
[bwa_index] 3843.23 seconds elapse.
[bwa_index] Update BWT... 19.99 sec
[bwa_index] Pack forward-only FASTA... 18.14 sec
[bwa_index] Construct SA from BWT and Occ... 1384.89 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa
[main] Real time: 5378.493 sec; CPU: 5294.368 sec
Command completed. Elapsed time: 1:29:39. Running peak memory: 4.719GB. PID: 3751; Command: bwa; Return code: 0; Memory used: 4.719GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_bwa_index__default.flag` (20820)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.719GB.  
  PID: 20820;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: f1024e230dc0176db46ccb69b7e187e0
Default tag for 'baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  1:29:52
*  Total elapsed time (all runs):  1:29:39
*         Peak memory (this run):  4.7191 GB
*        Pipeline completed time: 2021-04-07 18:09:12
Finished building 'bwa_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19/bwa_index/default