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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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ERROR: Tag "transcript_id" not found in attributes (line 145). #4264

Open 08li20 opened 2 months ago

08li20 commented 2 months ago

When I run this command, it will report an error indicating that the tag transcript_id cannot be found in a certain line.

vg autoindex --threads 5 --gff-feature exon --gff-tx-tag transcript_id --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattlecattle.gff5

ERROR: Tag "transcript_id" not found in attributes (line 145).

jeizenga commented 2 months ago

According to the sample of the GTF you supplied at https://github.com/vgteam/vg/issues/4256, line 145 isn't an exon line, so I'm not sure why it expects to find a transcript ID. If you can supply the inputs for this vg rna command, I can look into the issue.

08li20 commented 2 months ago

Run this command vg autoindex --threads 5 --gff-feature exon --gff-tx-tag transcript_id --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattlecattle.gff5 Why are we still looking for lines without transcript_id and exon after setting --gff-tx-tag to transcript_id?

jeizenga commented 2 months ago

It could be a bug, but it will be difficult for me to check what's going wrong in this specific instance unless you can supply the files that you used for inputs.