cactus-pangenome in 2.6.4: "error: the following arguments are required jobStore, seqFile", even though they're given.

[TomHarrop]

I'm having some trouble with cactus-pangenome in 2.6.4. I'm using the Docker container via Singularity/Apptainer. The same command was working with cactus-pangenome in 2.5.1.

cactus-pangenome \
    --outDir out \
    --outName alignment \
    --reference simCow_chr6 \
    jobStore \
    seqfile.txt

gives me

cactus-pangenome: error: the following arguments are required: jobStore, seqFile

The seqfile is working OK with interspecies cactus.

Apptainer> ls -lh

total 3.1M
-rw-r--r-- 1 tom tom  158 Jul  4 09:56 seqfile.txt
-rw-rw-r-- 1 tom tom 601K Jul  4 09:57 simCow_chr6.fasta
-rw-rw-r-- 1 tom tom 592K Jul  4 09:57 simDog_chr6.fasta
-rw-rw-r-- 1 tom tom 600K Jul  4 09:57 simHuman_chr6.fasta
-rw-rw-r-- 1 tom tom 634K Jul  4 09:57 simMouse_chr6.fasta
-rw-rw-r-- 1 tom tom 645K Jul  4 09:57 simRat_chr6.fasta

Apptainer> cat seqfile.txt 

simCow_chr6 simCow_chr6.fasta
simDog_chr6 simDog_chr6.fasta
simHuman_chr6 simHuman_chr6.fasta
simMouse_chr6 simMouse_chr6.fasta
simRat_chr6 simRat_chr6.fasta

I feel like I'm missing something very obvious here - apologies if that's the case :)

[glennhickey]

Huh, that's kind of annoying.

The issues is that --reference can now accept multiple arguments. So it's gobbling up jobStore, and leading to this error.

To work around this, you need to change the order of your arguments. You can either move jobStore and seqFile.txt before --reference. Or move --outDir out and/or --outName alignment after --reference.

[TomHarrop]

Thanks, that workaround fixes it.