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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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stops at idr2 #119

Closed ahorn720 closed 6 years ago

ahorn720 commented 6 years ago

Hello, I have 3 samples im trying to run and although one of them runs completely, for some reason, the next 2 samples both stop at the idr2 step. Any suggestions would be very helpful.

Thank you, Aaron

NBM_55stderror.txt NBM_55stdout.txt

ahorn720 commented 6 years ago

I've repeated the run a few times now and I keep getting the same errors. Any suggestions?

leepc12 commented 6 years ago

Run the following for more info: $ zcat /labs/ccurtis2/aaron/data_miseq_omniATACseq_NBM15-55-40/Files/Analysis/Fastqs/NBM_55_Peaks_pipeline_out/peak/macs2/idr/pseudo_reps/rep1/NBM_55_rep1-pr.IDR0.1.13-col.bed.gz | wc -l

It looks like no peak passed the IDR threshold?

ahorn720 commented 6 years ago

yep... it returns 0. Ok thank you for your time and the suggestion. I'll try raising the threshold and just removing that step possibly.