shilpagarg/pstools

Segmentation fault (core dumped)

Opened this issue · 3 comments

ljchueca commented

Hi,

I was interested in running pstools with Omni-C data but I had the next error segementation fault error running hic_mapping_haplo.

... [M::tb_pipeline::10452.864*42.22] processed 1333334 sequences; [M::tb_pipeline::10462.076*42.23] processed 1333334 sequences; [M::tb_pipeline::10470.184*42.24] processed 1333334 sequences; [M::tb_pipeline::10474.139*42.25] processed 671892 sequences; /var/spool/slurmd/job106890/slurm_script: line 11: 12235 Segmentation fault (core dumped) ./pstools_1 hic_mapping_haplo -t64 02.4_Nypro_Flye_sspace_lr1_gc1_SLRr1_gc1.scaff_seqs <(zcat /cluster/home/shared/nypro/08.8_ALLHiC/fastq/RacoonDogHiC_EKDL200002762-1a_R1.fastq.gz) <(zcat /cluster/home/shared/nypro/08.8_ALLHiC/fastq/RacoonDogHiC_EKDL200002762-1a_R2.fastq.gz) -o scaff_connections.txt /var/spool/slurmd/job106890/slurm_script: line 12: 48458 Killed

"hic_mapping_haplo" ran out of RAM with a 1 TB server. I tried to follow shilpagarg/DipAsm#16 like you suggested in a previous issue but it didn't work.

Do you know how could I solve it?

Cheers,
Luis

shilpagarg commented

Thank you for the issue. I will be happy to help if you could share Omni-C data and graph.

ljchueca commented

Many thanks for your help. I would be happy to share the data with you. How could I do it?

Best,

shilpagarg commented

Any links to download data will be useful to help you.