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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg pack error #4114

Closed Lucio-Yang closed 1 year ago

Lucio-Yang commented 1 year ago

Hi ! I used PGGB software to get a graph of one chromosome of 10 genomes, and then wanted to align the WGS data to the graph and perform SV calling.

Command: vg autoindex --workflow giraffe -t 60 -g combined.paf.417fcdf.42e55e5.smooth.final.gfa -p pangenome_chr14

vg giraffe -t 60 -Z pangenome_chr14.giraffe.gbz -m pangenome_chr14.min -d pangenome_chr14.dist -f T2-1_good_1.fastp.fq.gz -f T2-1_good_2.fastp.fq.gz > pangenome_chr14.gam

vg pack -x pangenome_chr14.giraffe.gbz -a pangenome_chr14.gam -o pangenome_chr14.pack -Q 5 ,

But the following error occurred in "vg pack",

_[E::hts_hopen] Failed to open file pangenome_chr14.gam [E::hts_open_format] Failed to open file "pangenome_chr14.gam" : Exec format error [vg::alignment.cpp] couldn't open pangenomechr14.gam

I checked the path and size of the gam file and there is no problem. What could be the cause of this problem? Is it because the chromosome is too large (~713 Mb) or WGS data cannot be used to align a single chromosomes in vg?

Thanks for your help!

glennhickey commented 1 year ago

Use vg pack -g

    -g, --gam FILE         read alignments from this GAM file (could be '-' for stdin)
    -a, --gaf FILE         read alignments from this GAF file (could be '-' for stdin)
Lucio-Yang commented 1 year ago

Thank you very much! I referred to the code of this web page. It seems that it needs to be updated. https://github.com/vgteam/vg/wiki/SV-Genotyping-and-variant-calling