Error running diamond: Length sorting reference

[royercj]

I am running emapper.py on a cluster, and I tried to run a test on one .faa. I have exported the data dir to EGGNOG_DATA_DIR="/storage/scratch/eggnog_db". I ran the test using the following command (some path names truncated):

emapper.py --data_dir $EGGNOG_DATA_DIR -i faa/GCA_00342195.faa --itype proteins --cpu 4 --override --pident 70 --query_cover 70 --output $(basename GCA_00342195.faa .faa) --output_dir scratch/eggnog/ --scratch_dir scratch/eggnog/ --temp_dir scratch/eggnog/

This results in the following output with error message:

#  emapper-2.1.12
# emapper.py  --data_dir /storage/scratch/eggnog_db  -i faa/GCA_00342195.faa --itype proteins --cpu 4 --override --pident 70 --query_cover 70 --output GCA_00342195 --output_dir scratch/eggnog/ --scratch_dir scratch/eggnog/ --temp_dir scratch/eggnog/

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

Error running diamond: Length sorting reference...

I did not see this error mentioned before, so any help I could get would be greatly appreciated. Thanks!

[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

[royercj]

@Cantalapiedra I was able to run the command you gave me, and everything appeared to run normally. I did not get any error messages and I got the output file I expected.

[Cantalapiedra]

@royercj ,

Oh, it is a bit weird that diamond now was working fine. Maybe the first error was a one-time thing? Did you try to run the same eggnog-mapper command more than once?