### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38_chr22/fasta --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/hg38_chr22-fasta-fasta` * Compute host: udc-aw34-6c0 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:30:03) elapsed: 1.0 _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_chr22/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/hg38_chr22-fasta-fasta']]` * `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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_fasta__default.flag` > `cp /project/shefflab/www/refgenie_refgenomes.databio.org/hg38_chr22-fasta-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa.gz` (250771)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.0GB. PID: 250771; Command: cp; Return code: 0; Memory used: 0.0GB > `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa.gz` (250789)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.001GB. PID: 250789; Command: gzip; Return code: 0; Memory used: 0.001GB > `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa` (250818)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:02. Running peak memory: 0.009GB. PID: 250818; Command: samtools; Return code: 0; Memory used: 0.009GB > `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.chrom.sizes` (250965)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.009GB. PID: 250965; Command: cut; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_fasta__default.flag` (250980)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.009GB. PID: 250980; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: f197c1ac4b3e4c5dd013bd2021bb32e6 Default tag for 'fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:05 * Total elapsed time (all runs): 0:00:04 * Peak memory (this run): 0.0086 GB * Pipeline completed time: 2021-04-07 15:30:07 Finished building 'fasta' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_chr22/fasta/default