AssertionError: When I run clockwork remove_contam command about clockwork HOT 5 CLOSED

Thanks for reporting, I've reproduced the error. I know how to fix, will do it next week. In the meantime, a workaround would be to run the mapping and decontam separately on each pair of fastq files. Then cat the two decontam forwards fastqs into one file, and similarly for the reverse fastqs (catting in the same order!)

from clockwork.

Thank you very much for your reply!
I'm not sure about the workaround you mentioned. Take the sample SAMEA104027390 (including two runs: ERR1950064 and ERR1950065) as an example. What you mean is that I do mapping and decontam for ERR1950064 and ERR1950065 respectively, assuming that a total of 4 files are generated ERR1950064.decontam_1.fq.gz, ERR1950064.decontam_2.fq.gz, ERR1950065.decontam_1. fq.gz, ERR1950065.decontam_2.fq.gz. Subsequently, ERR1950064.decontam_1.fq.gz and ERR1950065.decontam_1.fq.gz are merged to produce a new file, and ERR1950064.decontam_2.fq.gz and ERR1950065.decontam_2.fq.gz are merged to produce a new file, producing two files as input to the next clockwork variant_call_one_sample?

from clockwork.

yes, what you've described is exactly what I was thinking

from clockwork.

Thank you so much!

from clockwork.

You're welcome :)

The fix is now in the new clockwork release version 0.12.2, so should all work now as intended.

from clockwork.