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ijuric / MAPS

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MAPS won't trigger bwa mem #13

Closed mblanche closed 4 years ago

mblanche commented 4 years ago

Hey guys, looking into your pipeline, I really like your treatment of the HiChIP data. I'm trying to run it on data we generated but I can't seem to figure out why feather won't start the alignments. Traced back the issue to line 206 of feather_filter_chr.py

proc = subprocess.Popen(["bwa", "mem", "-t", str(threads), bwa_index, fastq], stdout = output_file, stderr = open(output_filename + ".log", 'w'))

the subprocess never start and I'm not sure why.

Any suggestions?

thanks

mblanche commented 4 years ago

Ok,

mblanche commented 4 years ago

Ok, disregard this issue. Was able to find the alignment log and my index was not parametrize properly.