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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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ERROR: Missing hic_results or bowtie_results files for H446-rep #73

Closed jlpulice closed 5 years ago

jlpulice commented 5 years ago

HI!

I'm getting this error: ERROR: Missing hic_results or bowtie_results files for H446-rep; either exclude the sample or manage the file architecture/input

Under hicpro-output/bowtie_results/bwt2/H446-rep/: H446-rep_hg19.bwt2pairs.bam H446-rep_hg19.bwt2pairs.pairstat H446-rep_R1_hg19.bwt2merged.bam H446-rep_R1_hg19.mapstat H446-rep_R2_hg19.bwt2merged.bam H446-rep_R2_hg19.mapstat

hicpro-output1/hic_results/data/H446-rep/: H446-rep_hg19.bwt2pairs.DEPairs H446-rep_hg19.bwt2pairs.FiltPairs H446-rep_hg19.bwt2pairs.REPairs H446-rep_hg19.bwt2pairs.SCPairs H446-rep_hg19.bwt2pairs.validPairs H446-rep_hg19.bwt2pairs.DumpPairs H446-rep_hg19.bwt2pairs_interaction.bam H446-rep_hg19.bwt2pairs.RSstat H446-rep_hg19.bwt2pairs.SinglePairs

Other directories have identical files and aren't throwing this error, and I can't trace back what file is missing.

I am using hichipper v0.7.7

caleblareau commented 5 years ago

did you run step 2 of HiC-Pro (assuming you ran in parallel mode) and the hichipper command? I think it's the _allValidPairs file that is missing

jlpulice commented 5 years ago

Yep that was it all set. Thanks!