File not found during bowtie2 step

databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing

http://pepatac.databio.org

BSD 2-Clause "Simplified" License

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File not found during bowtie2 step #142

Closed hugokitano closed 4 years ago

hugokitano commented 4 years ago

I ran pepatac on mouse bulk atac seq for the first time, and I'm running into an issue where a file is not found in an intermediate step.

Warning: Could not open read file "/oak/stanford/groups/satpathy/users/hkitano/atacseq/atacseq_ctr_r1/fastq/atacseq_ctr_r1_R1_trim.fastq.gz" for reading; skipping...
Error: No input read files were valid

I took a look in this directory, and saw that the trimmed fastq does exist, but it is not gzipped.

My log is attached. Thank you!

PEPATAC_log.txt

jpsmith5 commented 4 years ago

Hi @hugokitano . Found what I believe is the issue. Give the updated version a try. It should resolve your error. If not, let us know and I'll dive back in. Thanks for working with us!

jpsmith5 commented 4 years ago

Presumably this is resolved as expected. Closing for now.