Comments (5)
heuermh
commented on August 11, 2024
Not the only problem
...
Argument 'N' received invalid value type
'DRB1-3123.pggb-s1000-p90-n10-a90-K16-k8-w10000-j5000-W0-e5000.smooth.maf'
smoothxg {OPTIONS}from pggb.
ekg
commented on August 11, 2024
I think the option may not be synced in to the docker image yet. Hold on.
Will be syncing everything in the coming days.
…On Mon, Nov 23, 2020, 00:30 Michael L Heuer ***@***.***> wrote:
Not the only problem
...
Argument 'N' received invalid value type
'DRB1-3123.pggb-s1000-p90-n10-a90-K16-k8-w10000-j5000-W0-e5000.smooth.maf'
smoothxg {OPTIONS}
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subwaystation
commented on August 11, 2024
I just ran your example @heuermh including -N -M and it ran through successfully.
I suspect you still have an old version of the docker image. Please try docker pull ghcr.io/pangenome/pggb:latest and then run your commands again.
We are already planning to release docker images with the current pggb GitHub hash to make debugging more efficient. This will also help us to build a better Dockerfile for the nf-core/pangenome pipeline.
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subwaystation
commented on August 11, 2024
We now have snapshots of our docker images :)
https://github.com/orgs/pangenome/packages/container/package/pggb
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heuermh
commented on August 11, 2024
Works for me with a new pull of the :latest tag, thanks!
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Related Issues (20)
- seqwish std::invalid_argument error HOT 11
- Error with the __glibc package when installing HOT 5
- Mapping k-mers and contigs to pangenome graph HOT 1
- Flag could not be matched: temp-dir HOT 3
- How to understand the long range links? HOT 5
- smoothxg: Command terminated by signal 4 HOT 3
- PGGB discarding SNPs and Small InDels HOT 4
- add version HOT 1
- Sample command from README.md fails and fix? HOT 2
- Command terminated by signal 4 HOT 8
- Error following tutorial for PGGB VCF evaluation HOT 5
- Building a genus pangenome case HOT 1
- Setting -n to number of genomes, or number of genomes minus one? HOT 3
- empty VCF after running PanGenIe on the pggb assembly HOT 1
- GFA with no P lines HOT 5
- DRB1-3123 example not producing a nice graph anymore after `biwflambda` update. HOT 5
- PGGB use case with hexaploidy genomes HOT 1
- force reference output in VCF HOT 2
- Three chromosome take too long time HOT 16
- High heterogeneity in sequences identity HOT 2
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