Description
Description of the bug
Creating issue as requested. This was over a year ago now but I had trouble with the QUAST_BINS process failing when running on very large numbers of bins.
My thought at the time was that this has something to do with the fact that it is implemented as a loop over each input FASTA file: https://github.com/nf-core/mag/blob/master/modules/local/quast_bins.nf, and that it's doing some kind of ORF calling for each bin.
edit: MetaQUAST calls genes using MetaGeneMark according to the paper: https://academic.oup.com/bioinformatics/article/32/7/1088/1743987
"In contrast with regular QUAST which uses GeneMarkS, MetaQUAST uses MetaGeneMark ([Zhu et al., 2010]) for gene prediction, which is developed specially for metagenomes."
edit 2:
The local module has --rna-finding --gene-finding set, so gene finding is turned on (this is disabled by default). A quick fix (ignoring SeqKit stuff) is to just remove these arguments - the pipeline profiles genes using Prodigal and Prokka anyway
Command used and terminal output
Relevant files
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System information
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