funannotate compare fails at diamond

[jsimba-99]

I have tried to fix this but looks like funannotate compare needs .faa files that doesnt recognise even when I place them in the same directory

/pangenome_out# more funannotate-compare.log
[08/22/24 12:40:38]: /root/miniforge3/envs/funannotate_env/bin/funannotate compare -i ../proteins/updated_ATCC.gbk ../proteins/updated_
S11.gbk -o pangenome_out --cpus 16

[08/22/24 12:40:38]: OS: Ubuntu 22.04, 32 cores, ~ 41 GB RAM. Python: 3.12.3
[08/22/24 12:40:38]: Running 1.8.5
[08/22/24 12:40:39]: Input files/folders: ['../proteins/updated_ATCC.gbk', '../proteins/updated_S11.gbk']

[08/22/24 12:40:39]: Now parsing 2 genomes
[08/22/24 12:40:50]: working on .
[08/22/24 12:41:36]: working on .
[08/22/24 12:42:06]: No secondary metabolite annotations found
[08/22/24 12:42:06]: Summarizing PFAM domain results
[08/22/24 12:42:06]: Summarizing InterProScan results
[08/22/24 12:42:06]: Loading InterPro descriptions
[08/22/24 12:42:06]: Summarizing MEROPS protease results
[08/22/24 12:42:06]: Summarizing CAZyme results
[08/22/24 12:42:07]: found 0 CAZy familes
[08/22/24 12:42:07]: No COG annotations found
[08/22/24 12:42:07]: SignalP raw data:
[{}, {}]
[08/22/24 12:42:07]: No SignalP annotations found
[08/22/24 12:42:07]: [{}, {}]

[08/22/24 12:42:07]: Summarizing fungal transcription factors
[08/22/24 12:42:07]: No transcription factor IPR domains found
[08/22/24 12:42:07]: Running GO enrichment for each genome
[08/22/24 12:42:08]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...
[08/22/24 12:42:08]: proteinortho -project=funannotate -synteny -cpus=16 -singles -selfblast ..faa .-1.faa
[08/22/24 12:42:09]: CMD ERROR: proteinortho -project=funannotate -synteny -cpus=16 -singles -selfblast ..faa .-1.faa
[08/22/24 12:42:09]: *****************************************************************
Proteinortho with PoFF version 6.3.2 - An orthology detection tool

---

Using 16 CPU threads (1 threads per processes each with 16 threads), Detected 'diamond' version 2.1.8
Checking input files.
Checking ..faa... ok
Checking .-1.faa... ok

Step 19%)
The database for '.-1.faa' is present and will be used
The database for '..faa' is present and will be used

Step 2 using diamond with : synteny selfblast

Parameter-vector : (version=6.3.2,step=0,verbose=1,debug=1,synteny=1,duplication=2,cs=3,alpha=0.5,connectivity=0.1,cpus=16,evalue=1e-05
,purity=-1,coverage=50,identity=25,blastmode=diamond,sim=0.95,report=3,keep=0,force=0,selfblast=1,twilight=0,core=0,coreMinSpecies=0,co
reMaxProts=10,pseudo=1,omni=0,identical=0,range=-1,singles=1,clean=0,blastOptions=,makeBlastOptions=,nograph=0,xml=0,desc=0,tmp_path=./
proteinortho_cache_funannotate/,blastversion=2.1.8,binpath=,makedb=diamond makedb -p 16 --in,blast=,jobs_todo=3,project=funannotate,in
project=funannotate,po_path=/root/miniforge3/envs/funannotate_env/bin/,run_id=,threads_per_process=5,um=0)

[Error] diamond failed
return error code = 256
full error command = diamond blastp --tmpdir . --parallel-tmpdir . --threads 5 --db '/home/jaime2/Synteny_analysis/prot_compar
ison/pangenome_out/protortho/.-1.faa.diamond' --query '/home/jaime2/Synteny_analysis/prot_comparison/pangenome_out/protortho/.-1.faa' -
e 1e-05 --outfmt 6 --quiet --sensitive --ignore-warnings >'.-1.faa.vs..-1.faa.diamond.tmp'
return error message = No such file or directory

Please visit the proteinortho-wiki, where the most common errors are documented:
https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes

If you cannot solve this error, please file a report (including the input files, the error code and the above 'Parameter-vector'):
incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com

Further more all mails to [email protected] are welcome.

Perl exited with active threads:
15 running and unjoined
0 finished and unjoined
0 running and detached

[hyphaltip]

might help to show your command-line options here. I cannot see the folder you refer to.

Alternatively just generate the protein files for all your strains and run OrthoFinder on the dataset?

[jsimba-99]

This is the command I used:
/prot_comparison$ funannotate compare -i ../proteins/updated_ATCC.gbk ../proteins/updated_S11.gbk -o pangenome_out --cpus 16