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cfce / chilin

ChIP-seq DC and QC Pipeline
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Not generating .bam files #7

Closed darrylyan46 closed 5 years ago

darrylyan46 commented 7 years ago

Hi, I was trying to run chilin on a new sample with the following command:

chilin simple -s hg38 --threads 8 -i BCL3_t00 -o BCL3_t00 -t ${sample} 
-c ${ctrl} --dont_remove -p narrow 2>&1

The program runs through but only completes the FastQC steps. I looked at the log and found the following:

image

This happens occurs every instance where there is a .bam file attempted to be read where there is an empty line followed by:

Missing inputs ['/gpfs/fs0/data/reddylab/Darryl/BCL3_t00/BCL3_t00_treat_rep1mycoplasma.bam']

Perhaps there is an issue generating the .bam files? I believe I have the correct dependencies and version of *samtools (version 1.3.1). If you could shed some light on this issue I would appreciate it.

qinqian commented 5 years ago

The bwa genome index for mycoplasma should be filled in the conf file section.