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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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run with hifi and Hi-C data get Segmentation fault #206

Open yiqijiang17 opened 3 years ago

yiqijiang17 commented 3 years ago

Hi, I run hifiasm with ~20G hifi reads with paired Hi-C read (50G for read1, 49G for read2), the genome size is around 3G. I had test hifiasm with the test data you provide, it worked well. While when I use the data I mentioned with -t128, it got Segmentation fault after

[M:ha_print_ovlp_stat] # reverse overlaps: 1096485
Writing read to disk...

I also tried to extract 10k reads from each file to do a test, it got Segmentation fault at the same step.

not sure what causes that, if you need more info, I could upload the log file.

chhylp123 commented 3 years ago 
[M:ha_print_ovlp_stat] # reverse overlaps: 1096485
Writing read to disk...

It means the correction step has been done and hifiasm crashed during wring bin files to disk. Probably you should check if there is enough space in disk or if your server has enough RAM.

yiqijiang17 commented 3 years ago

Thanks for your reply. I rerun with 2000gb RAM and with >1T disk space, it still get error. I wonder which direction will hifiasm write to? I run on a cluster, I don't have permission to some directions, may this cause this error?

chhylp123 commented 3 years ago

It will write all bin files into the same folder as hifiasm itself.