### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38_noalt_decoy/star_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/star_index/default/_refgenie_build/ * Pipeline started at: (04-07 18:15:50) 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/star_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/star_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_star_index__default.flag` > `mkdir -p /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default` (22775)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 22775; Command: mkdir; Return code: 0; Memory used: 0.001GB > `STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default --genomeFastaFiles /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/fasta/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa` (22776)
[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 Apr 07 18:15:50 ..... started STAR run Apr 07 18:15:50 ... starting to generate Genome files Apr 07 18:17:08 ... starting to sort Suffix Array. This may take a long time... Apr 07 18:17:29 ... sorting Suffix Array chunks and saving them to disk... Apr 07 20:47:24 ... loading chunks from disk, packing SA... Apr 07 20:49:04 ... finished generating suffix array Apr 07 20:49:04 ... generating Suffix Array index Apr 07 20:54:09 ... completed Suffix Array index Apr 07 20:54:09 ... writing Genome to disk ... Apr 07 20:54:24 ... writing Suffix Array to disk ... Apr 07 20:56:31 ... writing SAindex to disk Apr 07 20:56:40 ..... finished successfullyCommand completed. Elapsed time: 2:40:51. Running peak memory: 33.369GB. PID: 22776; Command: STAR; Return code: 0; Memory used: 33.369GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_star_index__default.flag` (22226)
Command completed. Elapsed time: 0:00:00. Running peak memory: 33.369GB. PID: 22226; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: c7ff741217f4175af81bd133d6251247 Default tag for 'a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 2:41:54 * Total elapsed time (all runs): 2:40:51 * Peak memory (this run): 33.369 GB * Pipeline completed time: 2021-04-07 20:57:44 Finished building 'star_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_noalt_decoy/star_index/default