search

quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data
MIT License
60 stars 9 forks source link

SIGSEGV: Illegal storage access. (Attempt to read from nil?) #96

Closed hchetia closed 2 years ago

hchetia commented 2 years ago

Facing error SIGSEGV: Illegal storage access. (Attempt to read from nil?) while running "strling merge". STRling version 0.5.0

Command used- nohup strling merge --output-prefix strling/strling_joint/joint -f GRCh38.primary_assembly.genome.fa 1.sorted.bam.bin 2.sorted.bam.bin

Error snapshot- image

hdashnow commented 2 years ago

Hi @hchetia would you mind trying with strling_debug, available here: https://github.com/quinlan-lab/STRling/releases

It may gives us a little more output to go off.

Any ideas @brentp ?

brentp commented 2 years ago

Hi, I just pushed a check for this. The bin files given in your command must not be correct (or readable) and we did not have a check for that. The linked PR should give a more informative message, but meanwhile, double-check your bin paths.

hchetia commented 2 years ago

The same bin files were used to generate single sample calls.

I did a chmod 755 * in the working directory and the command worked this time.

Thanks.