Just when I thought my issues with

fasterq-dump

were done. It's not a problem with the module but

sra-toolkit

basically when I try and use the

--outfile

in

$args

for files (e.g. ERR1109373 as above) which have paired-end and single-end reads the single-end reads get lost due to the absence of a

.fastq

extension before the

pigz

step. The issue here https://github.com/ncbi/sra-tools/issues/388