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Incompatibility issues with custom reference genome

See original GitHub issue

Incompatibility issues with custom reference genome

Macs2 peak calling fails if the FASTA file used to build a custom genome database does not follow the chr[\dXY] naming convention. For example, I am using the Ensembl masked version of the rat genome (rn6, release 94) found here ftp://ftp.ensembl.org/pub/release-94/fasta/rattus_norvegicus/dna/, which does not prepend ‘chr’ to chromosome names. The error is produced by the following call:

[2018-10-31 18:06:20,887 ERROR] Unknown exception caught. Killing process group 72093...
Traceback (most recent call last):
  File "/users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 224, in run_shell_cmd
    p.returncode, cmd)
CalledProcessError: Command 'cat /mnt/lab_data/montgomery/nicolerg/motrpac/atac/pipeline-output/cromwell-executions/atac/03a28d2a-f364-4ce1-bfd5-f10488cf42a9/call-macs2/shard-0/inputs/-78707573/rn6_masked.chrom.sizes | grep -P 'chr[\dXY]+[ \t]' > 20180725_2_Gastroc_002_powder_S1_L001_R1_001.trim.merged.nodup.tn5.pval0.01.300K.bfilt.chrsz.tmp' returned non-zero exit status 1

OS/Platform and dependencies

Platform: Ubuntu 16.04.4
Cromwell: cromwell-34
Conda version: conda 4.5.11

Issue Analytics

State:
Created 5 years ago
Comments:8 (3 by maintainers)

Top GitHub Comments

1reaction

leepc12commented, Nov 7, 2018

Sure, working on it and will be fixed in the next release.

0reactions

leepc12commented, Jan 22, 2019

Sure, I am working on parameterizing ``atac.mito_chr_name : "any_mito_chr_name" in an input JSON. This will be fixed in the next release.

BTW regex-filter-reads is sort of a wrapper variable for --regex-grep-v-ta in bam2ta.

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