search

vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
Other
1.07k stars 191 forks source link

a problem about vg autoidex (v1.56.0) #4271

Open dongdongdong0203 opened 2 months ago

dongdongdong0203 commented 2 months ago

1. What were you trying to do? Preparing for the mpmap workflow using vg autoindex.

2. What did you want to happen?

3. What actually happened?

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

No, but see log file

vg_autoindex_17385.log

5. What data and command can the vg dev team use to make the problem happen? We tried to analyse a mammalian fasta, VCF, GTF file using vg autoindex. Among them, GTF files are transcripts and exons predicted by isoquant software and merge by AGAT. The run process reported an error in log file.

vg autoindex --workflow mpmap --ref-fasta toplevel.fa --vcf phase.vcf.gz --tx-gff mergeRefGTF.gtf --threads 18 --target-mem 35G

6. What does running vg version say?

vg 1.56.0 - Collalto
jeizenga commented 2 months ago

The error output that you got probably means that your GTF includes transcripts where exons are annotated on both strands of the reference sequence. This is not something that vg currently supports. You will have to filter out those transcripts if you want to use this GTF as input.