Hi all,

I am running GSNAP version 2025-07-31 on macOS Sonoma 14.4.1 on an Intel Mac Pro with 128 GB of memory.

I'm aligning paired-end data against HG38, I'll attach the run parameters below

On two occasions now I see a core dump with the error

rungsnap.sh: line 4: 73620 Illegal instruction: 4

So far I can find no useful discussion threads about this problem

I 'solved' the problem the first time by dividing the input into ~50 paired files of a million reads each, and running them all separately. I discovered a single 'bad' file pair, and just discarded that data and merged the rest.

Now I have seen it happen a second time. This is in the course of processing dozens of files of similar size, so this is really an isolated problem.

Anyone else run into this? To really track this down I would need to build gsnap from source and run in the debugger, or else continue narrowing down the 'bad' file to identify the problematic content, would first like to verify that no one else has seen this.

Thanks in advance,

Randy

Settings :

-d hg38 --nthreads=16 --use-splicing=hg38.introns.iit -n 24 -Q --format=sam --force-xs-dir --gunzip