Open OZTaekOppa opened 2 months ago
It looks like you are trying to provide #
as an argument to -a
, but that option doesn't take an argument. Because of that, #
is being interpreted as a positional argument. The only positional argument that vg deconstruct
takes is the graph itself, so it's trying to open #
as the graph instead of ${OUTPUT_DIR}/chm13_t2tctg_mgout.gfa
.
@jeizenga
Thank you for your reply.
Following your suggestions, I used these two commands:
Command 1: vg deconstruct -e -a -t 4 --snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.gfa > ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf
Command 2: vg deconstruct -e -a -t 4 -P chm13 --snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.gfa > ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf
Both commands only generated meta-information lines. From the header and data lines, only the first header line was produced in the chm13_t2tctg_mgout.sv.lv.vcf file.
Did I miss something?
Kind regards,
Taek
I think I'll redirect this question to @glennhickey
You can't run vg deconstruct
on minigraph
output because it doesn't have the (non-reference) paths embedded in it. vg deconstruct
needs the path information to work.
@glennhickey, thanks for your reply. I will get back to you after testing it again with the PGGB gfa files.
1. What were you trying to do?
Dear vg team,
Thank you for the great program.
FYI, minigraph v0.21 (https://github.com/lh3/minigraph) vg v1.56.0 (https://github.com/vgteam/vg) vcfbub (https://github.com/pangenome/vcfbub) Input file: Followed PanSN-spec: Pangenome Sequencing Naming (https://github.com/pangenome/PanSN-spec)
I encountered an issue while testing the minigraph GFA file using HPRC in the vg deconstruct step.
2. What did you want to happen? Ensure LV annotations using vg deconstruct
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:5. What data and command can the vg dev team use to make the problem happen? Human pangenome minigraph
6. What does running
vg version
say? v1.56.0