I was mapping some poorly annotated RNA-seq data using subread and incorrectly understood it to be paired end data.
Supplying the fastq files as PE reads to
subread-align caused a near-instant segfault. Should it provide a clearer error message?
I can supply some offending files if you like, but I suspect this behaviour will be reproducible with any data you have lying around.
E: just to add, this is on version 1.6.4, the command would have been something very much like:
subread-align -r $file -R $file2 -i $index -t 0 -P 3 -T 1 -o $out. It wasn't very clear to the user exactly why this segfault was happening, either, hence my suggestion here.