Minimap2 giving 2 TB sam file as an output

Question

[Inquisitive8995]

Hello,

I have been trying to run Minimap2 with fasta files of ~200Mb. I have 3 such files which I am trying to map onto a reference genome. The output sam file of first 2 files are about 500MB. But the third file gives a 2TB sam file and it has not completed running. Is there any reason of why this could be happening ? Any help would be appreciated.

The command I used is as follows:

minimap2 -a reference.mmi query.fasta -o output.sam -t 20

[WouterDeCoster]

You could consider avoiding creating a sam intermediate:

minimap2 -a -t 20 reference.mmi query.fasta | samtools sort -o output.bam

[Inquisitive8995]

Thanks for your answer. But I am still confused as the other 2 files of the same size gave the output of around 500Mb and this gives 2TB.

[GenoMax]

Perhaps you have a lot of multi-mapping or secondary alignments?

[Inquisitive8995]

Thanks for your reply. Is there anyway with which I can restrict the mapping to only the top hit or something like that ? Are there any parameters in Minimap to do so ?

[GenoMax]

You can set -N 0 to not retain secondary alignments.

[WouterDeCoster]

Why do you tag this as "assembly" while you are aligning? Why do you think this is a "software error"? Wouldn't "minimap2" be the best tag here?

[Inquisitive8995]

Noted. Thank you for mentioning this