Running error with Singularity image

[shilinti]

Hello, thanks for the great work!

I am trying to run PGGB with Singularity image, and I strictly followed the example commands line as below:

1. Pull the docker file:
   git clone --recursive https://github.com/pangenome/pggb.git

2. clone the repo and cd:
   git clone --recursive https://github.com/pangenome/pggb.git
   cd pggb

3. run pggb:
   singularity run -B ${PWD}/data:/data ../pggb_latest.sif pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -n 10 -t 16 -V 'gi|568815561' -o /data/out
   which gives me:
   [pggb] warning: there are sequence names (like 'gi|568815592:32578768-32589835') that do not match the Pangenome Sequence Naming (PanSN).
   [pggb] ERROR: -V/--vcf-spec cannot be used if the Pangenome Sequence Naming (PanSN) is not respected.

I did checked the solution in issue#388, I am little confused, do I have to installed all other components individually (wfmash, seqwish...) and pull the docker image at the same time? is there anything I did wrong?

FYI, I did:
./pggb --version
pggb v0.7.2-0-g0e9c9e1

Thanks for the help!
-S.

[AndreaGuarracino]

We should probably update the README and/or the input datasets. Currently, PanSN is mandatory in vg, the tool we used to project the graph into a VCF file format, but DRB1-3123.fa.gz's sequences do not follow PanSN convention. If you remove -V 'gi|568815561' from pggb's command line, so you skip the GFA->VCF projection, it should work.

A lazy way to fix the error and keep the VCF in output is to just hack sequence names in DRB1-3123.fa.gz:

zcat DRB1-3123.fa.gz | sed 's/:/#1#/g' > DRB1-3123.pansn.fa
samtools faidx DRB1-3123.pansn.fa # index the new FASTA file

and run pggb with DRB1-3123.pansn.fa.

[shilinti]

Thanks for the fast response!

I tried both ways, which gave me same error:
singularity run -B ${PWD}/data:/data ../pggb_latest.sif pggb -i /data/HLA/DRB1-3123.pansn.fa -p 70 -s 3000 -n 10 -t 16 -V 'gi|568815561' -o /data/out Illegal option --

I also tried the solutions in #291 and #404, all ended up with showing same error info.

As the suggestions from these two notes, I tried below commands:
singularity run -B ${PWD}/data:/data ../pggb_latest.sif /bin/bash -c "pggb -i /data/HLA/DRB1-3123.pansn.fa -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m" Illegal option --
singularity exec -B ${PWD}/data:/data ../pggb_latest.sif /bin/bash -c "pggb -i /data/HLA/DRB1-3123.pansn.fa -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m" Illegal option --
singularity exec -B ${PWD}/data:/data ../pggb_latest.sif /bin/bash -c "pggb -i /data/HLA/DRB1-3123.pansn.fa -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561' -o /data/out -M -m"

I am running on HPC, so I don't have docker access to run pggb with docker commands.

Thanks,
-S.

[AndreaGuarracino]

Have you tried also https://github.com/pangenome/pggb?tab=readme-ov-file#resolving-the-illegal-option----error-with-singularity-on-hpc-thanks-to-rachel-rusholme-pilcher?

[shilinti]

unset -f which does the trick!

Many thanks!
-S.