I'm running HapCUT2 on Oxford Nanopore Technology data for 1 chromosome (the 7) of the pig genome, on a pool seq sample of 4 individuals.
I tried running HapCUT2 without the --ont option and it seems to work nicely, at least I manage to reach a point where I can define haploblocks however when I tried the option --ont , to get better estimates for ONT data, I face a 'core dumped' error.
Here is what I run:
extractHAIRS --ont 1 --bam ${bam_file_out} --VCF ${vcf_file_out_modif} --out ${out_dir}/${sample_id}.fragment
HAPCUT2 --fragments ${out_dir}/${sample_id}.fragment --VCF ${vcf_file_out_modif} --output ${out_dir}/${sample_id}.haplotype
python3 ${hapcut2}/utilities/prune_haplotype.py -i ${out_dir}/${sample_id}.haplotype -o ${out_dir}/${sample_id}.haplotype.pruned --min_mismatch_qual 30 --min_switch_qual 30
extractHAIRS works but when reaching the HAPCUT2 command I get the error message "/var/spool/slurmd/job3756032/slurm_script: line 4: 97288 Segmentation fault (core dumped) HAPCUT2 --fragments 7_sample3.ont.fragment --VCF 7_sample3_modif.vcf --output7_sample3.ont.haplotype"
I checked my job and the allocated memory is not a limitation (I asked for 500Gb and only used 7.42Gb, so only 1.5%).
Do you have any idea of where this error is coming from?
Thanks in advance for your help.
Hi,
I'm running HapCUT2 on Oxford Nanopore Technology data for 1 chromosome (the 7) of the pig genome, on a pool seq sample of 4 individuals. I tried running HapCUT2 without the --ont option and it seems to work nicely, at least I manage to reach a point where I can define haploblocks however when I tried the option --ont , to get better estimates for ONT data, I face a 'core dumped' error. Here is what I run: extractHAIRS --ont 1 --bam ${bam_file_out} --VCF ${vcf_file_out_modif} --out ${out_dir}/${sample_id}.fragment HAPCUT2 --fragments ${out_dir}/${sample_id}.fragment --VCF ${vcf_file_out_modif} --output ${out_dir}/${sample_id}.haplotype python3 ${hapcut2}/utilities/prune_haplotype.py -i ${out_dir}/${sample_id}.haplotype -o ${out_dir}/${sample_id}.haplotype.pruned --min_mismatch_qual 30 --min_switch_qual 30 extractHAIRS works but when reaching the HAPCUT2 command I get the error message "/var/spool/slurmd/job3756032/slurm_script: line 4: 97288 Segmentation fault (core dumped) HAPCUT2 --fragments 7_sample3.ont.fragment --VCF 7_sample3_modif.vcf --output7_sample3.ont.haplotype" I checked my job and the allocated memory is not a limitation (I asked for 500Gb and only used 7.42Gb, so only 1.5%).
Do you have any idea of where this error is coming from? Thanks in advance for your help.