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Hi, I ran pggb to build pangenomes for 10 bacterial genomes (Ecoli). The command is `pggb -i merged.fa.gz -o 10n95p -t 20 -p 95 -n 10 -S -m` and it can work well. But i have some confused with the par…
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**1. What were you trying to do?**
Call variants from read support.
**2. What did you want to happen?**
Generate a VCF file.
**3. What actually happened?**
The command have been running…
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I'm trying to run cactus-pangenome to construct a pangenome of 6 different samples of the same species (including a reference). My invocation is below:
`cactus-pangenome ./js seqFile.txt --outDir ./o…
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Sorry guys,
I'm trying to visualize the output of a my cactus pangenome analysis using sequenceTubeMap but it is not straightforward to do it.
I would like to visualize the gbz files but, even if I…
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I was running through an analysis of 174 genbank files and have this error at the partitioning step:
`zsh: segmentation fault ppanggolin partition -p pangenome.h5 --draw_ICL`
`/opt/homebrew/an…
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Hi,
I am running the step-by-step pangenome pipeline and failed at `filter_paf_deletions` in `cactus-graphmap`
Based on this log `Exit reason: MEMLIMIT`, it should be caused by insufficient memo…
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I created [this issue over on the Cactus Git page](https://github.com/ComparativeGenomicsToolkit/cactus/issues/1106#issue-1818858818). You can see the errors using gcc 10.3 and 13.0.1. Is there a fix …
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Hi,
I am getting error when running job with multiple processors.
`-[Arcadia-Science/prehgt] Pipeline completed with errors-ERROR ~ Error executing process > 'ARCADIASCIENCE_PREHGT:PREHGT:build_genu…
onbio updated
4 months ago
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Hello,
As an experiment, I've tried take the vcf of the draft human pangenome, use bcftools +setGT to unphase the pangenome vcf, and then rephase the vcf using different reference panels. I am usin…
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**1. What were you trying to do?**
I was trying to performe the augmentation step before variant calling to call variants from a set of illumina WGS reads that I've aligned to my vg graph. I'm runn…