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.
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
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