### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_repeats/fasta --genome-description test description human repeats --files fasta=/project/shefflab/www/refgenie_rg.databio.org/human_repeats-fasta-fasta` * Compute host: udc-ba27-28c0 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:21:14) 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`: `['human_repeats/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_rg.databio.org/human_repeats-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `test description human repeats` * `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/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/7319f9237651755047bc40d7f7a9770d42a537e840f4e105_fasta__default.flag` > `cp /project/shefflab/www/refgenie_rg.databio.org/human_repeats-fasta-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.fa.gz` (122043)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 122043; Command: cp; Return code: 0; Memory used: 0.001GB > `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.fa.gz` (122044)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 122044; Command: gzip; Return code: 0; Memory used: 0.001GB > `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.fa` (122045)
[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: 0:00:00. Running peak memory: 0.001GB. PID: 122045; Command: samtools; Return code: 0; Memory used: 0.001GB > `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.chrom.sizes` (122085)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 122085; Command: cut; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/7319f9237651755047bc40d7f7a9770d42a537e840f4e105_fasta__default.flag` (122087)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 122087; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 4a749d4e74b057d0efa0c8398ebcb871 Default tag for '7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:01 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0.0015 GB * Pipeline completed time: 2021-04-07 15:21:15 Finished building 'fasta' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/human_repeats/fasta/default ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_repeats/fasta --genome-description test description human repeats --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/human_repeats-fasta-fasta` * Compute host: udc-ba26-34c0 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:25:54) 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`: `['human_repeats/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/human_repeats-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `test description human repeats` * `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 exists: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/7319f9237651755047bc40d7f7a9770d42a537e840f4e105_fasta__default.flag` Asset digest: 4a749d4e74b057d0efa0c8398ebcb871 ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:00 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0 GB * Pipeline completed time: 2021-04-07 15:25:54 Finished building 'fasta' asset Removed existing flag: '/project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/refgenie_completed.flag' ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_repeats/fasta --genome-description test description human repeats --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/human_repeats-fasta-fasta` * Compute host: udc-aw34-18c0 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:29:58) 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`: `['human_repeats/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/human_repeats-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `test description human repeats` * `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 exists: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/7319f9237651755047bc40d7f7a9770d42a537e840f4e105_fasta__default.flag` Asset digest: 4a749d4e74b057d0efa0c8398ebcb871 ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:00 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0 GB * Pipeline completed time: 2021-04-07 15:29:58 Finished building 'fasta' asset Removed existing flag: '/project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/_refgenie_build/refgenie_completed.flag'