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hifiasm crashes with segfault on a toy Hi-C dataset #152
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Let me have a look at it. But for this example, the coverage is too low for assembly. |
Thank you @chhylp123 ! In terms of coverage, do you mean the HiFi reads or Hi-C reads? HiFi reads I selected so that they map to the same contig, so I hoped that they could be assembled? |
The k-mer plot looks weird. The normal HiFi data should have a k-mer plot like: #49 (comment) |
How do they look like? Maybe, it's just because these are only 204 HiFi reads mapping to a particular HG002 contig, and on the whole HG002 PacBio HiFi run the kmer profile would be different? |
Yes, I think so. So the coverage looks not enough. But hifiasm shouldn't crash even in this rare case, I will have a look at it. I just recommend you to have a try with enough coverage for testing. |
@sidorov-si You can assembly the whole HG002 HiFi reads or just one chromosome, and then grep the HiFi reads in the |
Thank you @chhylp123 ! So, I'm using 204 reads that map to one conting from the whole HG002 assembly produced in your paper. How do you estimate the coverage? |
Sorry for the delay. This bug has been fixed in v0.15.5 (see: https://github.com/chhylp123/hifiasm/releases/tag/0.15.5). |
Dear hifiasm team,
I'm developing an nf-core module for hifiasm, and I've tested haplotype phasing with hifiasm using a toy set of PacBio HiFi reads and a small set of Hi-C reads (please find attached). The HiFi reads come from a child genome (GIAB's HG002, SRR10382244), and the Hi-C reads come from a normal human lung tissue (SRR13061060) and are selected so that they map to the HiFi reads.
When I run the following command with hifiasm
v0.15.4-r343
in a conda env on my Mac, it fails in a short time with
Segmentation fault: 11
(please see the full run log attached).However, it still produces some output:
What could be the reason for the segfault?
Thank you,
Slava
hifiasm_output.tar.gz
SRR10382244_subset.fastq.gz
SRR13061060_10000reads_mapped_1.fastq.gz
SRR13061060_10000reads_mapped_2.fastq.gz
hifiasm_run_log.txt
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