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Hi, I runned roary on the example dataset and it was successful. On my personal dataset, instead, I get this error for roary out (find attached the specific log. It seems the pan_genome_reference.fa f…
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Just gathering up the changes I proposed to the [schedule](https://calyxir.org/tutorial/). The original comments are [here](https://github.com/cucapra/calyx/issues/1479#issuecomment-1559969787) and be…
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I am trying to start pggb user the user manual:
`https://github.com/pangenome/pggb#singularity`
with the command
`singularity run -B ${PWD}/data:/data ../pggb_latest.sif "pggb -i /data/HLA/DR…
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Dear @npch @prenderj @RenzoTale88 @prasundutta87
Your code shows us a clear way to constrcut a pangenome. When I came to detect non-reference sequence, I can't find a help documentation. I don't und…
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I have a dataset that was working fine on my old computer. I got a new computer and set everything up but now I keep having the these errors. I have not changed the datasets and did not experience t…
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Hi,
I was running the SqueezeMeta pipeline to create bins of each sample. All of them were running sperarately and by trying to combine the tables of each sample from a separate folder finally to jus…
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**1. What were you trying to do?**
I am trying to genotype short reads resequencing samples using `vg call`
**2. What did you want to happen?**
Get a VCF file including sample-specific va…
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Hi there I have two VCF files for HG002 benchmarked with `hap.py`
- one has been generated from a pangenome graph using GRCh38 as a reference
- the other is the product of a graph sub-sampling whi…
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## The need
Finally got anvi'o installed but now I'm seeing the following message when trying to export fasta:
```
Config Error: The database at 'CONTIGS.db' is outdated (this database is v9 a…
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Hi there, how r u? I'm getting an error while trying to run the script for comparing three genomes. I'm runnning the following code:
`./panX.py -cg 0.66 -fn data/AbSputum -sl "Acinetobacter baumanni…