atac_dnase_pipelines icon indicating copy to clipboard operation
atac_dnase_pipelines copied to clipboard

Published 20 hours ago • verified publisher icon kundajelab

Fatal error: atac.bds, line 1200, pos 2. Task/s failed....during peakcalling

Open grrompala opened this issue 6 years ago • 1 comments

pipe_out_unfilt.txt

Hi, I am encountering the errors described in the log at the macs2 step of the pipeline. I am starting with BAM files-- I have tried both filtered and unfiltered. Moreover, I tried boosting the mem_macs2 and I still have the issue.

Let me know if I can provide any more insight and thanks for the help!!

-Greg

grrompala avatar Jul 16 '18 15:07 grrompala

You have irregular chromosomes (chr20_GL383577v2_alt), which is not covered our default chromosome sizes file, in your BAM file. Please use your own chromosome sizes file (define it with -chrsz) or start from FASTQs.

Chromosome chr20_GL383577v2_alt isn't in /sc/orga/work/rompag01/genome_data/hg38/hg38.chrom.sizes line 1 of stdin: chr20_GL383577v2_alt:0-101601

leepc12 avatar Jul 16 '18 18:07 leepc12