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?
It worked! Thank you. b.t.w can I use .gbz in "vg find"?
Awesome! Yeah, you should be able to use the .gbz file with the
vg find -x
flag, even though it's not an xgMichal : Please accept this answer (green checkmark) to provide closure to this thread.