Dear vg team,

Thank you for the great program. I encountered an issue while testing the minigraph GFA file using HPRC in the vg deconstruct step.

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)

Executed command:

Step 6: Ensure LV annotations using vg deconstruct

vg snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.gfa > ${OUTPUT_DIR}/chm13_t2tctg_mgout.snarls
vg deconstruct -e -a ‘#’ -P chm13 --snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.snarls ${OUTPUT_DIR}/chm13_t2tctg_mgout.gfa > ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf

Step 7: Convert bgzip of vcf

bgzip -c ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf > ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf.gz
tabix -p vcf  ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf.gz

Step 8: Remove large (> 10Mb) spurious DELsin MC & PGGB graphs

singularity exec /singularityimg/pggb_latest.sif vcfbub -l 0 -r 10000000 -i ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.vcf.gz > ${OUTPUT_DIR}/chm13_t2tctg_mgout.sv.lv.filterd.vcf.gz

In Step 6, although the -H option has been deprecated and that was fine, the issue lies with the # symbol. I tried using variations such as '#', "#", and "\#", but all failed. The error message I received was:

vg deconstruct -e -a '#' -P chm13 --snarls /data/minigraph_run/chm13_t2tctg_mgout.snarls /data/minigraph_run/chm13_t2tctg_mgout.gfa error:[get_input_file_name] unable to open input file: # error[VPKG::load_one]: Could not open # to determine file type

Do you have any suggestions for resolving this?

Kind regards,

Taek