### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build mm10_cdna/kallisto_index` * Compute host: udc-ba25-17 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/kallisto_index/default/_refgenie_build/ * Pipeline started at: (04-08 21:46:22) 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`: `['mm10_cdna/kallisto_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/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/kallisto_index/default/_refgenie_build/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca_kallisto_index__default.flag` > `kallisto index -i /project/shefflab/deploy/rg.databio.org_full/genomes/data/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/kallisto_index/default/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca_kallisto_index.idx /project/shefflab/deploy/rg.databio.org_full/genomes/data/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/fasta/default/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca.fa` (27682)
[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 [build] loading fasta file /project/shefflab/deploy/rg.databio.org_full/genomes/data/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/fasta/default/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca.fa [build] k-mer length: 31 [build] warning: clipped off poly-A tail (longer than 10) from 645 target sequences [build] warning: replaced 3 non-ACGUT characters in the input sequence with pseudorandom nucleotides [build] counting k-mers ... done. [build] building target de Bruijn graph ... done [build] creating equivalence classes ... done [build] target de Bruijn graph has 736280 contigs and contains 100745897 k-mersCommand completed. Elapsed time: 0:03:59. Running peak memory: 3.935GB. PID: 27682; Command: kallisto; Return code: 0; Memory used: 3.935GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/kallisto_index/default/_refgenie_build/fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca_kallisto_index__default.flag` (28535)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.935GB. PID: 28535; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: a8653fdc5af32ebbb37eaf04385b4ca3 Default tag for 'fa159612d40b1bedea9a279eb24999b3d27145f9dd70dcca/kallisto_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:04:04 * Total elapsed time (all runs): 0:03:59 * Peak memory (this run): 3.9352 GB * Pipeline completed time: 2021-04-08 21:50:26 Finished building 'kallisto_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/mm10_cdna/kallisto_index/default