Hello,
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.
Thanks.
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.
Indeed, regenerating my index fixed this (though there was no apparent error while it was being made). Thanks for the clarity here!