CPhasing runs successfully but .hg file is missing after hyperpartition

[yt619]

Hi,

I encountered an issue when running CPhasing. The pipeline finishes normally without any error messages, but the expected .hg file is not generated.

Specifically, after running the hyperpartition step, the following file is missing:

3.hyperpartition/*.pairs.q1.e5m.hg

I checked the output directory 3.hyperpartition/, and other intermediate files were generated as expected, but the .hg file does not exist. I am not sure why this file was not produced.

Command used:
cphasing pipeline -f SMT.hic.hap12.p_ctg.fa -hic1 SMT.hic_R1.fq.gz -hic2 SMT.hic_R2.fq.gz -t 100 -n 7:4

[wangyibin]

Hi,
Thank you for reporting this bug. We have just submitted a new commit to resolve the issue. You will need to update the file CPhasing/cphasing/cli.py.

Best,
Yibin

[yt619]

Hi,
Thank you for your timely response. At the current stage, the .hg file can be generated normally. However, when executing cphasing collapse rescue, CPhasing encounters a msgspec.ValidationError while loading the input hypergraph (*.hg).

Command used:
cphasing collapse from-gfa merged.gfa
cphasing collapse rescue ../3.hyperpartition/SMT.hic.corrected.pairs.q1.e5m.hg ../SMT.hic.hap12.p_ctg.contigsizes ../3.hyperpartition/output.clusters.txt ./contigs.collapsed.contig.list -n 4 -at ../3.hyperpartition/SMT.hic.hap12.p_ctg.corrected.allele.table

[wangyibin]

Hi,
I'm very sorry for the late reply.

We have also just submitted a new commit to resolve the issue. You will need to update the file CPhasing/cphasing/cli.py.

Best,
Yibin

[yt619]

Hi,

Thank you for the timely update. I have reanalyzed the previously generated data and found that no collapsed contigs could be identified using either HiFi reads or GFA files. However, our previous results clearly indicated the presence of partially collapsed regions. Could this be caused by the use of the --chimeric-correct parameter, which may have corrected the sequences in the .corrected.fasta file?

Command used:
cphasing collapse rescue ../3.hyperpartition/SMT.hic.corrected.pairs.q1.e5m.hg ../SMT.hic.hap12.p_ctg.contigsizes ../3.hyperpartition/output.clusters.txt ./contigs.collapsed.contig.list -n 4 -at ../3.hyperpartition/SMT.hic.hap12.p_ctg.corrected.allele.table

Best,

[Xiaofengbro]

Hello, it appears that when running CPhasing.v0.2.10.r308.linux-64.tar.gz, the file 3.hyperpartition/*.pairs.q1.e5m.hg is still missing. We then tried running versions v0.2.9 and v0.2.8, and only v0.2.8 was able to generate the file correctly.