emapper - Error: Invalid output field: scovhsp

Question

[N.D.Hubot]

Hi everyone,

I am fighting with an error using emapper and I am running out of ideas to try to solve it.

It is the first time that I am running emapper but the installation and the download of the databases seemed to go well. I am running the following command:

emapper.py --data_dir /scratch/ndh1n17/eggnog_db/ -m diamond --cpu 32 -i JM-A.prot.orf.fasta -o Emapper

I directly receive the following error:

emapper-2.1.3 emapper.py --data_dir /scratch/ndh1n17/eggnog_db/ -m diamond --cpu 32 -i JM-A.prot.orf.fasta -o Emapper ESC[1;33m /home/ndh1n17/.conda/envs/bioinformatics/bin/diamond blastp -d /mainfs/scratch/ndh1n17/eggnog_db/eggnog_proteins.dmnd -q /mainfs/scratch/ndh1n17/megahit/JM-A_assembly/JM-A.prot.orf.fasta --threads 32 -o /mainfs/scratch/ndh1n17/megahit/JM-A_assembly/Emapper.emapper.hits --sensitive -e 0.001 --top 3 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhspESC[0m Error running diamond: Error: Invalid output field: scovhsp

If I understand correctly, it appears that by default emapper is adding the option --outfmt and the following arguments "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp". I think these are the supported format for the output data and it seems that "scovhsp" is not supposed to be there and is considered invalid.

So I have tried to change the command and add the --outfmt option its arguments except for scovhsp, as follow:

emapper.py --data_dir /scratch/ndh1n17/eggnog_db/ -m diamond --cpu 32 -i JM-A.prot.orf.fasta -o Emapper --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp

Does someone have an idea how to solve this, please? Thank you in advance for your help.

Nathan

[N.D.Hubot]

Sorry, I forgot to say that of course the last command was not working and all the arguments of --outfmt are considered unexpected arguments...

[zorbax]

upgrade your emapper-diamond versions

Answer 1

[zorbax]

Install an updated version using a conda environment:

conda create -n eggnog -c bioconda -c conda-forge eggnog-mapper

conda activate eggnog

emapper.py --data_dir /scratch/ndh1n17/eggnog_db/ -m diamond --cpu 32 -i JM-A.prot.orf.fasta -o Emapper

conda deactivate

[N.D.Hubot]

Thank you so much Zorbax!