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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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Problem in creating consensus ATAC peaks #236

Open gauriprasad08 opened 1 year ago

gauriprasad08 commented 1 year ago

Hi,

I used the project pipeline of PEPATAC to create consensus ATAC peaks for my samples.I get the combined summary stats for all samples (PEPATAC_tutorial_stats_summary.tsv). However, the pipeline fails to run the PEPATAC_collator and do not produce the consensus peaks. I have attached a PEPATAC_collator_log.md file for your reference.

The error does not seem to indicate that any component is missing from the installation, so most likely it is due to a certain feature in my data that the PEPATAC "does not like". But What is that feature is not clear to me?

Kindly help me out to solve this issue.

PEPATAC_collator_log.txt

nsheff commented 1 year ago

This script is choking when trying to read in a file. Could it be an empty file? Or is it possible one of your sample names has a space in it?

gauriprasad08 commented 1 year ago

Hi. Thanks for raising this point. I checked my files one by one. None of the files is empty or with space in its name.

nsheff commented 1 year ago

Ah, I think I see something. Do you have multiple genomes in this PEP?

You cannot call consensus peaks if the reference genome isn't identical across all samples.