by_ST PhyML Failure when all samples are identical, same ST

[nvlachos]

Description of the bug

Ran into issue creating files for validation where using ST caused failure in PhyML because of the 5 isolates in the ST, they all had 0 SNPs between them and thus made no files to continue downstream.
All files needed to recreate situation are located at /scicomp/groups-pure/OID/NCEZID/DHQP/CEMB/Nick_DIR/Phylophoenix_validation/2017-49/PHYLO_PHX

Command used and terminal output

nextflow run /scicomp/groups-pure/OID/NCEZID/DHQP/CEMB/Nick_DIR/scripts/phylophoenix -profile singularity,scicomp_rosalind --input /scicomp/groups-pure/OID/NCEZID/DHQP/CEMB/Nick_DIR/Phylophoenix_validation/2017-49/PHX/Directory_samplesheet.csv --outdir /scicomp/groups-pure/OID/NCEZID/DHQP/CEMB/Nick_DIR/Phylophoenix_validation/2017-49/PHYLO_PHX -config /scicomp/groups-pure/OID/NCEZID/DHQP/CEMB/Alyssa_DIR/phoenix/PHoeNIx/script/scicomp.config --by_st

Command error:
  . The number of taxa cannot be negative.
  . Type enter to exit.

Relevant files

No response

System information

No response