issue using emapper.py: "Error running diamond: Loading reference sequences..."

[AMosca96]

Hi,

I'm using emapper in order to obtain functional annotation of my fasta file which contains proteins strings retrieved from prodigal. The script that I'm running is the following:

emapper.py -i prodigal.proteins.fa -o eggnog --output_dir eggnog_dir/ --database bact -m diamond --target_orthologs all --seed_ortholog_evalue 0.001 --seed_ortholog_score 60 --override

However, after less than a minute I obtain the following messages:

#  emapper-2.1.10
# emapper.py  -i prodigal.proteins.fa -o eggnog --output_dir eggnog_dir/ --database bact -m diamond --target_orthologs all --seed_ortholog_evalue 0.001 --seed_ortholog_score 60 --override
  /mnt/shared/scratch/user/apps/conda/envs/eggnog/bin/diamond blastp -d '/mnt/shared/scratch/user/apps/conda/envs/eggnog/lib/python3.11/site-packages/data/eggnog_proteins.dmnd' -q '/mnt/shared/scratch/user/plant_JA/2308_fastq_filtered/repair/abundo/drep_out/dereplicated_genomes/prova_prodigal/prodigal.proteins.fa' --threads 1 -o '/mnt/shared/scratch/user/plant_JA/2308_fastq_filtered/repair/abundo/drep_out/dereplicated_genomes/prova_prodigal/eggnog_dir/eggnog.emapper.hits' --tmpdir '/mnt/shared/scratch/user/plant_JA/2308_fastq_filtered/repair/abundo/drep_out/dereplicated_genomes/prova_prodigal/emappertmp_dmdn_ms2prym4' --sensitive --iterate -e 0.001 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp
Error running diamond: Loading reference sequences...

I highlighted in bold the last message. I tried to run the script within a job in the slurm cluster I'm currently using, but it seems freezed even if it goes for more than 10 hours. In these jobs I set higher memory as suggested to users that had a similar problem to mine, but nothing happens.

Any ideas about this error?

P.S. the current versions of eggnog and other DBs in my conda environment are the following: emapper-2.1.10 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: 5.0.2 / Diamond version found: diamond version 2.1.6 / MMseqs2 version found: 13.45111

[YuanwenGuo]

Has this issue been solved? I encountered the similar issue, stucking with "Error running diamond: Masking reference..."

[Cantalapiedra]

Dear all,

How did you install eggnog-mapper? I notice that your diamond version is 2.1.6 despite your emapper version being 2.1.10. Note that eggnog-mapper uses Diamond version 2.0.11 since version 2.1.5.

Best, Carlos