Can't produce OrthoXML output file

[mpmeurville]

Dear David,

I would like to produce an Orthoxml output file from my analysis, and everything goes well until building the file. The data I use are private so not on an online database, could that be a problem? I have 15 species.

This is my command line : ./orthofinder -f GAGA_annotation_final_24092021/ -x GAGA_annotation_final_24092021/OrthoFinder/data_species_files.txt

my species file looks like this : GAGA-0004_final_annotation_representative_repfilt.pep.fasta Messor barbarus 87890 GAGA GAGA-0004_final_annotation_representative_repfilt.pep.fasta

where GAGA refers to my private database.

I also paste the end of the log here so you can see the error:

[... everything goes well ...] 2021-10-06 18:47:31 : Written final scores for species 15 to graph file 2021-10-06 18:47:46 : Ran MCL

Writing orthogroups to file

OrthoFinder assigned 211032 genes (95.8% of total) to 13652 orthogroups. Fifty percent of all genes were in orthogroups with 17 or more genes (G50 was 17) and were contained in the largest 4824 orthogroups (O50 was 4824). There were 7535 orthogroups with all species present and 3103 of these consisted entirely of single-copy genes. Traceback (most recent call last): File "orthofinder.py", line 7, in File "scripts_of/main.py", line 1775, in main File "scripts_of/main.py", line 1404, in DoOrthogroups NameError: global name 'speciesXML' is not defined [2668625] Failed to execute script orthofinder

I thank you in advance for your help!

Marie-Pierre

[eli1199]

Hi @mpmeurville! did you end up figuring this out? I'm getting a very similar error message to yours:

"NameError: name 'speciesXML' is not defined"

Thank you!

[amarosaco]

I ran into the same error. The species file seems to be fine however.

[mpmeurville]

Hi, no I never managed to have it working ...