search

jts / nanopolish

Signal-level algorithms for MinION data
MIT License
568 stars 159 forks source link

Segmentation fault in nanopolish eventalign #1141

Open lyj95618 opened 6 months ago

lyj95618 commented 6 months ago

Hi,

I got the following error when I ran nanopolish eventalign. There isn't any other error message. I have run nanopolish eventalign with my other samples and it was fine.

/var/spool/slurm/d/job10023903/slurm_script: line 25: 1654969 Segmentation fault (core dumped) nanopolish eventalign --reads /largeprojects/nanopore/nanopore/merged_fastq/${sample}_merged.fastq.gz --bam /largeprojects/nanopore/nanopore/lauren_test/cdna_bam_for_xpore/$sample/$sample.bam --genome /largeprojects/nanopore/nanopore/lauren_test/annotationfile/Mus_musculus.GRCm38.cdna.all.fa --signal-index --scale-events --summary /largeprojects/nanopore/nanopore/lauren_test/nanopolish_output/$sample.nanopolish_summary.txt --threads 32 > /largeprojects/nanopore/nanopore/lauren_test/nanopolish_output/$sample.eventalign.txt

I am not sure if this is related to some of the error messages I got during the nanopolish index step which is telling me it can't open some of the fast5 files. However, the index step finished at the end and I got the index files.

I requested 90G memory for this and the job got killed after 15 hours due to this error. I have the eventalign.txt and nanopolish_summary.txt output but its a lot smaller than I expected. The nanopolish version I use is 0.13.3

Thanks for the help! Laur

Dongchengzhi commented 1 month ago

I encountered the same error when running nanopolish index on the ERR9834011 FAST5 files. However, it worked fine for other samples (ERR9834013 and ERR9834015). I've searched through all the issues, but couldn't find a specific solution.