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tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Program stuck at [IndexRegistry]: Chunking VCF(s) for days #4274

Open Jokendo-collab opened 2 months ago

Jokendo-collab commented 2 months ago

I am having a problem running vg mpmap. It has stuck on the [IndexRegistry]: Chunking VCF(s) for days. Is there a solution for this problem?

[IndexRegistry]: Checking for phasing in VCF(s).
[IndexRegistry]: Provided: VCF w/ Phasing
[IndexRegistry]: Chunking inputs for parallelism.
[IndexRegistry]: Chunking FASTA(s).
[IndexRegistry]: Chunking VCF(s).
jeizenga commented 2 months ago

Did you provide the variants as a single VCF file for the entire genome? If so, one thing you can do to speed it up is to separate the single VCF into chromosome-level VCFs. That will let vg autoindex use more parallelism during this step. I would also recommend using approximately as many threads as chromosomes if you have them available.

Jokendo-collab commented 2 months ago

Hi,

My genome assembly was highly fragmented. I only extracted chromosomal scale contigs and it now running.

On Thu, Apr 25, 2024 at 8:51 PM Jordan Eizenga @.***> wrote:

Did you provide the variants as a single VCF file for the entire genome? If so, one thing you can do to speed it up is to separate the single VCF into chromosome-level VCFs. That will let vg autoindex use more parallelism during this step. I would also recommend using approximately as many threads as chromosomes if you have them available.

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