phyml command not found

[SeanSierra-Patev]

Description of the bug

terminated woth phyml command not found...

running with docker

I did get a "warn" on execution

` N E X T F L O W ~ version 25.10.4

Pulling cdcgov/phylophoenix ...
downloaded from https://github.com/CDCgov/phylophoenix.git
Launching https://github.com/cdcgov/phylophoenix [jovial_volhard] DSL2 - revision: 5c70948 [main]

WARN: Config setting docker.userEmulation is not supported anymore
`

Command used and terminal output

nextflow run cdcgov/phylophoenix -profile docker --outdir phylo_phx --indir ./phx_output/







-[dhqp/phylophoenix] Pipeline completed with errors-
ERROR ~ Error executing process > 'PHYLOPHOENIX_WF:PHYLOPHOENIX:SNVPHYL:PHYML (All_Isolates)'

Caused by:
  Process `PHYLOPHOENIX_WF:PHYLOPHOENIX:SNVPHYL:PHYML (All_Isolates)` terminated with an error exit status (127)


Command executed:

  phyml -i All_Isolates_snvAlignment.phy --datatype nt --model GTR -v 0.0 -s BEST --ts/tv e --nclasses 4 --alpha e --bootstrap -4 --quiet
  mv All_Isolates_snvAlignment.phy_phyml_stats.txt All_Isolates_TreeStats_SNVPhyl.txt
  mv All_Isolates_snvAlignment.phy_phyml_tree.txt pre_All_Isolates_SNVPhyl.newick
  
  cat <<-END_VERSIONS > versions.yml
  "PHYLOPHOENIX_WF:PHYLOPHOENIX:SNVPHYL:PHYML":
      phyml: $( phyml --version | grep -P -o '[0-9]+.[0-9]+.[0-9]+' )
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: phyml: command not found

Work dir:
  /home/sean/Workdir/Relatedness_Requests/2026/2026-2-17_KPn_Stillwater/work/fe/fce21c42e94361c811302f3761e28e

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response

[snallani-msdh]

I've had this same issue also. If I run only two samples with the same MLST, it's working. But more samples (even if they're the same MLST), I'm getting this exact error message.

[aginnimb]

Hi @SeanSierra-Patev, we've made some updates to the phyml container and adjusted the configuration, could you please pull the dev branch and give it another try?

[SeanSierra-Patev]

Sure thing! Which version of nextflow is preferred, I had to rollback from 26.04 the other day because of wonkiness for regular Phoenix. 25.10.4 is working fine so I assume I'd use that one.

[aginnimb]

yeah we had that issue with 26.04, but yes 25.10.4 works fine.