why does vg convert doesn't work?

Question

[Michal]

I am using vg version 1.49.0 on Ubuntu I am trying to convert a gam file to a gfa format and it is not working. I have the file hprc1004mapped.gam and I run the command:

./vg convert –G hprc1004mapped.gam > hprc1004mapped.gfa 

And I get the error:

error:[get_input_file_name] specify input filename, or "-" for standard input

When I try the command:

 ./vg convert -G -F hprc1004mapped.gam > hprc1004mapped.gaf

I get the error:

error[VPKG::load_one]: Correct input type not found in hprc1004mapped.gam while loading handlegraph::HandleGraph.

The same error I also get when I try to convert gbwt to xg file :

./vg convert -x hprc-v1.0-mc-grch38-minaf.0.1.gbwtx > hprc-v1.0-mc-grch38-minaf.0.1.gx
error:[get_input_file_name] unable to open input file: hprc-v1.0-mc-grch38-minaf.0.1.gbwtx
error[VPKG::load_one]: Could not open hprc-v1.0-mc-grch38-minaf.0.1.gbwtx while loading handlegraph::HandleGraph

Are these errors related? What am I doing wrong?

Answer 1

[Xian]

vg convert requires a graph as a positional argument at the end of the command, and when you use the -G flag, you need to include the GAM file immediately after the flag. In your first command, it couldn't find the graph and in the second, it tried to load -F as the GAM file and the GAM file as the graph. Your command should look something like ./vg convert –G hprc1004mapped.gam [graph_file] > hprc1004mapped.gfa

The second problem is that you can't convert a GBWT to an xg because the GBWT stores haplotpyes through a graph, while the xg is the graph itself. It looks like you're using the hprc graphs, so there should be a gbz file that you can convert to an xg. You should be able to use the gbz for most things you need the xg for though; I'd recommend checking here to see if xg is the format you want https://github.com/vgteam/vg/wiki/File-Types

[Michal]

It worked! Thank you. b.t.w can I use .gbz in "vg find"?

[Xian]

Awesome! Yeah, you should be able to use the .gbz file with the vg find -x flag, even though it's not an xg

[GenoMax]

Michal : Please accept this answer (green checkmark) to provide closure to this thread.

Answer 2

[colindaven]

Also, keep in mind that (it might have been a typo in your commands) than GFA (pangenome) and GAF (mapping format) formats are completely different in pangenomes.

I've listed the formats here:

https://github.com/colindaven/awesome-pangenomes