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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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issue using emapper.py: "Error running diamond: Loading reference sequences..." #493

Open AMosca96 opened 11 months ago

AMosca96 commented 11 months ago

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 commented 6 months ago

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

Cantalapiedra commented 6 months ago

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