### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build rn6_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/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/kallisto_index/default/_refgenie_build/ * Pipeline started at: (04-08 21:51:02) 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`: `['rn6_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/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/kallisto_index/default/_refgenie_build/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89_kallisto_index__default.flag` > `kallisto index -i /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/kallisto_index/default/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89_kallisto_index.idx /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/fasta/default/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89.fa` (28728)
WARNING: 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/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/fasta/default/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89.fa
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
        from 57 target sequences
[build] warning: replaced 2710 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 153611 contigs and contains 49915185 k-mers 

Command completed. Elapsed time: 0:01:50. Running peak memory: 1.823GB. PID: 28728; Command: kallisto; Return code: 0; Memory used: 1.823GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/kallisto_index/default/_refgenie_build/d982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89_kallisto_index__default.flag` (29017)

Command completed. Elapsed time: 0:00:00. Running peak memory: 1.823GB.  
  PID: 29017;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: 8beb628953400ab94363249640fe157e
Default tag for 'd982f0b1888504cccc131d5fa2c11eb3522b9a8e95e0ea89/kallisto_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:01:53
*  Total elapsed time (all runs):  0:01:50
*         Peak memory (this run):  1.8229 GB
*        Pipeline completed time: 2021-04-08 21:52:54
Finished building 'kallisto_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rn6_cdna/kallisto_index/default