### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg19/cellranger_reference` * 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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/_refgenie_build/ * Pipeline started at: (04-07 20:46:16) 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`: `['hg19/cellranger_reference']` * `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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_cellranger_reference__default.flag` > `gunzip /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/gencode_gtf/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.gtf.gz -c > /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.gtf` (19876)

Command completed. Elapsed time: 0:00:19. Running peak memory: 0.002GB.  
  PID: 19876;	Command: gunzip;	Return code: 0;	Memory used: 0.002GB


> `cellranger mkgtf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.gtf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_filtered.gtf` (20042)
/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin
cellranger mkgtf (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

Writing new genes GTF file (may take 10 minutes for a 1GB input GTF file)...
...done

Command completed. Elapsed time: 0:04:17. Running peak memory: 0.078GB. PID: 20042; Command: cellranger; Return code: 0; Memory used: 0.078GB > `rm /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.gtf` (21237)

Command completed. Elapsed time: 0:00:01. Running peak memory: 0.078GB.  
  PID: 21237;	Command: rm;	Return code: 0;	Memory used: 0.001GB


> `cd /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default; cellranger mkref --genome=ref --fasta=/project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa --genes=/project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_filtered.gtf --nthreads=8` (21239)
/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin
cellranger mkref (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

Apr 07 21:01:00 ..... Started STAR run
Apr 07 21:01:00 ... Starting to generate Genome files
Apr 07 21:02:46 ... starting to sort  Suffix Array. This may take a long time...
Apr 07 21:02:55 ... sorting Suffix Array chunks and saving them to disk...
Apr 07 22:02:18 ... loading chunks from disk, packing SA...
Apr 07 22:02:56 ... Finished generating suffix array
Apr 07 22:02:56 ... Generating Suffix Array index
Apr 07 22:05:53 ... Completed Suffix Array index
Apr 07 22:05:53 ..... Processing annotations GTF
Apr 07 22:06:29 ..... Inserting junctions into the genome indices
Apr 07 22:20:54 ... writing Genome to disk ...
Apr 07 22:21:10 ... writing Suffix Array to disk ...
Apr 07 22:21:54 ... writing SAindex to disk
Apr 07 22:22:03 ..... Finished successfully
Creating new reference folder at /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/ref
...done

Writing genome FASTA file into reference folder...
...done

Computing hash of genome FASTA file...
...done

Indexing genome FASTA file...
...done

Writing genes GTF file into reference folder...
...done

Computing hash of genes GTF file...
...done

Writing genes index file into reference folder (may take over 10 minutes for a 3Gb genome)...
...done

Writing genome metadata JSON file into reference folder...
...done

Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
...done.

>>> Reference successfully created! <<<

You can now specify this reference on the command line:
cellranger --transcriptome=/project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/ref ...
Command completed. Elapsed time: 1:31:12. Running peak memory: 21.187GB. PID: 21239; Command: cd; Return code: 0; Memory used: 21.187GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_cellranger_reference__default.flag` (2810)

Command completed. Elapsed time: 0:00:00. Running peak memory: 21.187GB.  
  PID: 2810;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: 7dc30c8d468b8617d309118d7be59eaa
Default tag for 'baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/cellranger_reference' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  1:37:03
*  Total elapsed time (all runs):  1:35:49
*         Peak memory (this run):  21.187 GB
*        Pipeline completed time: 2021-04-07 22:23:19
Finished building 'cellranger_reference' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19/cellranger_reference/default