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I have wrapped tbpore-process and tbpore-cluster as separate modules
Could not do the same with tbpore-download (the download keeps failing urllib.error.URLError: <urlopen error [Errno -3] Temporary failure in name resolution. So decontamination db has to be passed using a Channel (fromPath)
Wrote tests for both processes (tbpore-process and tbpore-cluster)
The tests too keep failing (not becaus of the code but because of minimap2 runtime failure) Error calling minimap2 -aL2 -x map-ont -t 6 -o .tbpore/test.decontaminated.sam remove_contam.map-ont.mmi .tbpore/test.fq.gz (return code -9) This seems like a memory problem but I doubt it. I ran the test first on a 32GB RAM PC, and for the benefit of doubt on a 128GB Workstation. Spent about 15 hours of my precious time trying to debug to know avail.
Thanks for all your efforts here @ycode-sh , please allow me sometime to go through this PR especially the minimap2 issue 🤔
The tests too keep failing (not becaus of the code but because of minimap2 runtime failure)
Error calling minimap2 -aL2 -x map-ont -t 6 -o .tbpore/test.decontaminated.sam remove_contam.map-ont.mmi .tbpore/test.fq.gz (return code -9) This seems like a memory problem but I doubt it. I ran the test first on a 32GB RAM PC, and for the benefit of doubt on a 128GB Workstation. Spent about 15 hours of my precious time trying to debug to know avail.
Thanks for all your efforts here @ycode-sh , please allow me sometime to go through this PR especially the minimap2 issue 🤔
I'm not sure but I think there is a problem with how nextflow and tbpore interacts. minimap2 did not fail when running tbpore without nextflow. return code -9 indicates insufficient memory. I'm wondering how that's even possible since the process was run with a 128GB memory workstation and label 'process_high'
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Hi @abhi18av and @Mxrcon
urllib.error.URLError: <urlopen error [Errno -3] Temporary failure in name resolution. So decontamination db has to be passed using a Channel (fromPath)Error calling minimap2 -aL2 -x map-ont -t 6 -o .tbpore/test.decontaminated.sam remove_contam.map-ont.mmi .tbpore/test.fq.gz (return code -9)This seems like a memory problem but I doubt it. I ran the test first on a 32GB RAM PC, and for the benefit of doubt on a 128GB Workstation. Spent about 15 hours of my precious time trying to debug to know avail.