vg paths returns no results and no error when using -S and -G together

[hui-liu]

1. What were you trying to do? I am trying to use vg to extract the non-reference paths from the Minigraph-Cactus (version 2.6.7) pangenome.

I used the command

vg paths -S SDTS1 -L -G -x MC.gbz

2. What did you want to happen?

I was expecting the run to list the path names of non-reference samples.

3. What actually happened?

Nothing was printed on the screen.

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:

Place stacktrace here.

5. What data and command can the vg dev team use to make the problem happen?

Here is the command I used to generate the MC pangenome.

cactus-pangenome \
${dir}/js \
${dir}/seqfile \
--workDir ${dir}/temp \
--reference SDTS1 SDTS2 \
--vcfReference SDTS1 SDTS2 \
--outDir ${dir}/MC \
--outName MC \
--mgCores 64 \
--mapCores 24 \
--consCores 64 \
--indexCores 64 \
--filter 2 \
--gbz clip filter full \
--gfa clip full \
--giraffe clip filter \
--vcf \
--odgi \
--viz \
--chrom-og \
--chrom-vg clip filter \
--logFile mc_SDTS.log

6. What does running vg version say?

version v1.50.1 "Monopoli"