nonpareil failing with too few reads

[fgvieira]

I am running nonpareil as:

nonpareil -T kmer -s input.fastq -f fastq -F -o out.npo -a out.npa -C out.npc

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.