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ekawaler / pyQUILTS

Rebuilding QUILTS in Python.
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read_chr_bed error #21

Open rsalz opened 4 years ago

rsalz commented 4 years ago

I already prepared the proteome and genome as instructed and tried to run quilts.py with the following command:

python2 quilts.py --output_dir ../databases/ --junction ../junctions/two_pass/test/ --junction_file_type star --germline ../vcf/test/ --genome genome/hg38/ --proteome proteome/

and then i get this error immediately, with no further explanation:

/bin/sh: 1: /mnt/xomics/renees/data/recognition/pyQUILTS/read_chr_bed: Exec format error ERROR: read_chr_bed didn't work - now we don't have a proteome.bed.dna file. Aborting program.

What's going on? why is it stopping

ekawaler commented 4 years ago

It seems your computer is having trouble running the C file. Have you tried recompiling read_chr_bed?

rsalz commented 4 years ago

right, that error is fixed now. but now when I run it i get "Error opening: genome/hg38/chr6.fa.cmp1" for all .cmp1 files in the genome

ekawaler commented 4 years ago

Did you check to see whether those files exist at that location?

rsalz commented 4 years ago

ah yes. they are named something else in the folder. the naming convention in my genome folder is 'Homo_sapiens.GRCh38.dna_rm.chromosome.21.fa.cmp1' while the quilts script looks for chr21.fa.cmp1. strange that this wasn't correct despite me following the steps in 'prepare_genome'. i'll rename the files and try again...

rsalz commented 4 years ago

now it found other files it can't open: 'Error opening: genome/hg38/chrCHR_HG1342_HG2282_PATCH.fa.cmp1' Is it possible the 'prepare_genome' portion isn't really preparing my genome for running quilts.py?

ekawaler commented 4 years ago

There are often some non-canonical chromosomes in the variant sets - you can usually safely ignore those errors. The vast majority of your variants should still come out fine.