### 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 secCommand 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