through a pipeline and, sometimes, there are files with not that many reads. For those, I am getting the error:
Nonpareil v3.401
Fatal error:
Reduce the number of query reads (-X) to ≤ 10% of total reads
[ 0.0] Fatal error: Reduce the number of query reads (-X) to ≤ 10% of total reads
Looking at the code, it seems that nonpareil requires -X to be less than 10% of the total reads.
I am a bit confused with this options since, either:
nonpareil needs ONLY 10% of the reads; if so, why the -X option? nonpareil can just get the number of reads it needs.
nonpareil can sub-sample the input file (usually for speed purposes); if so, why does it fail? If input file has less than -X, then just use all the reads.
I am running
nonpareilas:through a pipeline and, sometimes, there are files with not that many reads. For those, I am getting the error:
Looking at the code, it seems that
nonpareilrequires-Xto be less than 10% of the total reads. I am a bit confused with this options since, either:nonpareilneeds ONLY 10% of the reads; if so, why the-Xoption?nonpareilcan just get the number of reads it needs.nonpareilcan sub-sample the input file (usually for speed purposes); if so, why does it fail? If input file has less than-X, then just use all the reads.