Unexpected segmentation fault

Hi @hasindu2008,

I'm trying to run F5C on an sample of 16M direct RNA nanopore reads, but I'm getting a segmentation fault at the same point roughly 200k reads into the sample. I've gotten warning about too many threads, which I've tried reducing. I've tried allocating more memory, and I've tried removing the last read written to the output to try and get past this segmentation fault that is happening always at the same point. I would appreciate any help. here is the last few lines of the log

[sprintf_append::WARNING][1;33m Too long string got truncated: 88.1937,96.7707,113.925,88.1937,96.7707,96.7707,113.925,101.059,113.925,113.925,113.925,113.925,101.059,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,122.502,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,118.213,122.502,113.925,113.925,113.925,113.925,113.925,118.213,113.925,113.925,113.925,113.925,113.925,113.925,113.925,122.502,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,118.213,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.925,113.9

......

[0m [sig_handler::ERROR][1;31m I regret to inform that a segmentation fault occurred. But at least it is better than a wrong answer.[0m

Here is the command: f5c_x86_64_linux eventalign -t 12 --iop 12 -r basecalled.fastq -b mapped.bam -g ref.fa --rna --print-read-names --scale-events --samples --min-mapq 0 --secondary=yes -o f5c_eventalign.tsv

Thanks, Logan

hasindu2008 / f5c

Unexpected segmentation fault #138