Open lerminin opened 1 year ago
Hi,
I have encountered a similar problem when running POLCA (MaSuRCA v4.1.0) on a Flye assembly in a second round of polishing.
In my case, it turned out that the .vcf file was not generated because FreeBayes did not call any variants and outputted empty .vcf files for each batch. When trying to create the final .vcf file, the grep command in line 178 of polca.sh exited with exit status 1 and prevented it from being created:
seq 1 $BATCHES | xargs -I % ls $BASM.vc/%.vcf |xargs cat | grep -v '^#' > $BASM.vcf.body.tmp && mv $BASM.vcf.body.tmp $BASM.vcf.body
There probably is a better to way to fix this, but as a workaround I have changed that line to:
seq 1 $BATCHES | xargs -I % ls $BASM.vc/%.vcf |xargs cat | { grep -v '^#' || true; } > $BASM.vcf.body.tmp && mv $BASM.vcf.body.tmp $BASM.vcf.body
I guess there might be a similar problem in your case in that chained command for generating the final .vcf file. Did you check the presence of the temporary files, like assembly_polished.fasta.vcf.header.tmp? Might help to understand at which step it fails.
Thanks for the reply, modifying that line as you suggested worked for me in v4.0.9
I had the same issue, corrected line 178, and it works perfectly in v4.1.0.
Hi there,
I'm running Masurca v4.0.9 and am having an issue using POLCA to polish a Flye assembly with Illumina reads where it prints the following error:
From what I can tell, the .vcf file is not being generated and this causes the fix_consensus_from_vcf.pl script to crash? I've run this command in this workflow many times and have not had any issues except for this one assembly file. There's 6 contigs in this assembly file and I can run POLCA on each contig individually without issue. I'm not sure how to diagnose the problem from this error message; it's not clear to me if there is a problem with my assembly file or a bug in the program and would appreciate any help.
May be related to #308