AssertionError: When I run clockwork remove_contam command

[Huicen01]

I use the 'Walkthrough: scripts only.' option, and my command is:

singularity exec clockwork_v0.11.3.img clockwork map_reads --unsorted_sam ./SAMEA104027390 ./Ref.remove_contam/ref.fa SAMEA104027390.sam ./SAMEA104027390/ERR1950064_1.fastq.gz ./SAMEA104027390/ERR1950064_2.fastq.gz ./SAMEA104027390/ERR1950065_1.fastq.gz ./SAMEA104027390/ERR1950065_2.fastq.gz
when I ran clockwork map_reads command, it worked properly!

singularity exec clockwork_v0.11.3.img clockwork remove_contam ./Ref.remove_contam/remove_contam_metadata.tsv ./SAMEA104027390.sam ./SAMEA104027390.decontam.counts.tsv ./SAMEA104027390.decontam_1.fq.gz ./SAMEA104027390.decontam_2.fq.gz
When I ran clockwork remove_contam command, I have encountered the following error, how can I solve it?
Traceback (most recent call last):
File "/usr/local/bin/clockwork", line 4, in
import('pkg_resources').run_script('clockwork==0.11.3', 'clockwork')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/EGG-INFO/scripts/clockwork", line 1019, in
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/tasks/remove_contam.py", line 17, in run
File "/usr/local/lib/python3.8/dist-packages/clockwork-0.11.3-py3.8.egg/clockwork/contam_remover.py", line 173, in run
AssertionError

PS: For some reason, I have to choose 'Walkthrough: scripts only', and 'Walkthrough: database and nextflow' cannot be selected! Thank you all for your help!

[martinghunt]

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!)

[Huicen01]

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?

[martinghunt]

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

[Huicen01]

Thank you so much!

[martinghunt]

You're welcome :)

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