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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Segfault from latest version #735

Open jetrz opened 7 hours ago

jetrz commented 7 hours ago

Hello, when trying to use the latest --ont feature, I am getting a segfault.

I am trying to perform diploid and haploid assembly respectively on:

  1. HG002: https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC_PLUS/HG002/raw_data/nanopore/HG002_ONT_PAD64459_Guppy_3.2.fastq.gz
  2. Fruit Fly: https://www.ncbi.nlm.nih.gov/sra/SRR23215007

Are these datasets not suitable? Thank you.

chhylp123 commented 7 hours ago

The public data we tested including: HG002 from https://github.com/paoloshasta/shasta/issues/28 and a tomato from https://obj.umiacs.umd.edu/marbl_publications/duplex/Solanum_lycopersicum_heinz1706/UL/R10.4_40x.noduplex.fastq.gz. I haven't test your datasets yet. I will have a try to find the issue. Thanks!

jetrz commented 7 hours ago

The exact commands I used for each are: HG002: hifiasm --prt-raw --write-paf --write-ec --dual-scaf --ont -o hg002_ont -t16 -1 /path/to/pat.yak -2 /path/to/mat.yak /path/to/dataset Fruit Fly: hifiasm --prt-raw --write-paf --write-ec --ont -o fruitfly_ont -t16 /path/to/dataset

Also, can I check is the tomato dataset above haploid or diploid? Would like to test it myself as well. Thanks again!

chhylp123 commented 7 hours ago

You can double check tomato here: https://genome.cshlp.org/content/early/2024/11/04/gr.279334.124.abstract

jetrz commented 6 hours ago

Will give it a look. Thanks!