Hmm. Can you attach the contents of the '# Task 1' in the whitelist and non whitelist filter jobs, <job dir>/workflow/P_Filter/filter_001of0??.sh for a working whitelist it should look something like this:
Code:
filterPlsH5.py --debug --filter='MinReadScore=0.80,MinSRL=500,MinRL=100,ReadWhitelist=/home/rhall/projects/reads.list' --trim='True' --outputDir=/home/rhall/projects/data/filtered_regions --outputSummary=/home/rhall/projects/data/filtered_summary.chunk001of064.csv --outputFofn=/home/rhall/projects/data/filtered_regions.chunk001of064.fofn /home/rhall/projects/input.chunk001of064.fofn
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