Input File Error with Singularity/Apptainer

[whottel]

Hello,

I am running into an error when trying to run gubbins on the PMEN1 dataset described here: https://github.com/nickjcroucher/gubbins/tree/master/example_data/PMEN1

When running the command:
run_gubbins.py --prefix PMEN1 --first-tree-builder rapidnj --first-model JC --tree-builder raxmlng --model GTR PMEN1.aln

I get the following error:

Checking dependencies and input files...

Checking input alignment file...
Unexpected error: <class 'RuntimeError'>
Error with the input FASTA file: It is in the wrong format, check it is an alignment
Each sequence must be the same length
The input alignment file /Shared/SHL-BUG/workspaces/whottel/scratch/pipeline_tool_maintenance_tests/Gubbins/v3.3.5/tmpovc5sigo/PMEN1.aln is invalid

I am using singularity/apptainer to run the container file for v.3.3.5 pulled from here:
https://hub.docker.com/r/staphb/gubbins/tags

[nickjcroucher]

Could the alignment file be corrupted - have you compared the md5 sums?

[whottel]

I do not think the alignment file is corrupted. I get the same md5 sum value for the alignment I was using and from redownloading and gunzipping the alignment.
Also I was able to run gubbins 2.4.1 using this file with the following command:
run_gubbins.py --prefix PMEN1 --tree_builder raxml PMEN1.aln