ERROR when running RAXML-NG with partition on CIpres Grateway

[Vanina Castroagudin]

Hello Dr Lozlov,

I have some issues running Raxml-NG on Cipres. I am unsure if this is the correct place to write and ask for help, but I didn't find another option.

I used the format given in the manual of RaxML-NG for running the program on CIPRES Gateway, which gave me an error. Can it be possible that different models for DNA alignments with partition can be run on the RaxML lab website (https://raxml-ng.vital-it.ch/#/) but not in the cypres portal with the RanxMl-NG Black Box tool?
Should the format of the files to indicate the alignment partition be different when the software is run on the website or CIPRES?

I used this syntax -entered as a txt file- to indicate my partition
KY+I+G4, ITS = 1-561
TrNef+I+G4, TUB = 562-1053
HKY+I+G4, TEF = 1054-1565

And it gave me this error on CIPRES:

srun: error: exp-1-06: tasks 0-9: Exited with exit code 255
srun: launch/slurm: _step_signal: Terminating StepId=18453233.0

It did work on the website.
I really appreciate any help you can provide.
Thanks in advance,

Vanina

[Mark Miller]

Hi Vanina,

I recovered your job from our repository.

Although the stderr.txt file was uninformative, the stdout.txt file had more information. 

The error message says:

NOTE: Following symbols are not allowed in taxa names to ensure Newick compatibility:
NOTE: " " (space), ";" (semicolon), ":" (colon), "," (comma), "()" (parentheses), "'" (quote).
NOTE: Please either correct the names manually, or use the reduced alignment file
NOTE: generated by RAxML-NG (see above).

There are about 20 tax names with parens in your input file.

If you remove them with an editor, I am sure you job will run.

Let me know if you have further issues at CIPRES.

Best,

Mark