Error running diamond: Length sorting reference

[royercj]

Error running diamond: Length sorting reference

[Cantalapiedra]

Dear @royercj ,

How did you install eggnog-mapper?
Which is the version of diamond that its being run?

Best,
Carlos

[royercj]

Hi Carlos, thanks for the reply. I created a conda env to run eggnog, and installed it with conda install bioconda::eggnog-mapper (version 2.1.12). Diamond 2.1.9 was installed in this env, as was python 3.12.3.

[Cantalapiedra]

Hi @royercj ,

Thank you for your follow up. Do you have any other diamond version installed? What is the output of
which diamond
diamond --version
?

[royercj]

The results of which diamond just shows the env path (~/envs/eggnog/bin/diamond) and diamond --version returns 2.1.9.

[Cantalapiedra]

OK. No clue there. Could you please try running the diamond command from your first post alone, without eggnog-mapper?
Just to see if it gives us any other clue.

envs/eggnog/bin/diamond blastp -d 'scratch/eggnog_db/eggnog_proteins.dmnd' -q '/storage/scratch/faa/GCA_00342195.faa' --threads 4 -o 'eggnog/GCA_00342195.emapper.hits' --tmpdir 'scratch/eggnog/emappertmp_dmdn_7r_et45u' --sensitive --iterate -e 0.001 --id 70.0 --query-cover 70.0 --top 3 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp