karel-brinda / rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
http://karel-brinda.github.io/rnftools
MIT License
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[dwgsim] 0 reads error for low coverage and short genomes #64

Closed simonepignotti closed 6 years ago

simonepignotti commented 6 years ago

When simulating reads for very short genomes (in this case 220bp) and very low coverage (1) the resulting number of reads to simulate is 0, which is not accepted by dwgsim.

"dwgsim" -1 150 -2 150 -z 1 -y 0 -N 0 -e 0.02 -E 0.02 -r 0.001 -R 0.15 -X 0.3 -d 500 -s 50.0 "viral/GCF_000839085.1_ViralProj14152_genomic/001/reference.fa" "viral/GCF_000839085.1_ViralProj14152_genomic/001/dwgsim_files.pe.1" > /dev/null
Error: command line option -N was out of range

To replicate this issue: Genome https://www.ncbi.nlm.nih.gov/assembly/GCF_000839085.1/ Coverage 1

rnftools.mishmash.DwgSim(
        fasta='viral/GCF_000839085.1_ViralProj14152_genomic.fna',
        coverage=1,
        read_length_1=150,
        read_length_2=150,
)
simonepignotti commented 6 years ago

Duplicate #53