Cannot include both --query_cover and --subject_cover in my search.

[KPapac]

Hi there,

I have installed eggnog through conda and I have made a custom database with Drosophilidae proteins to annotate against. To do that I execute:

emapper.py --output_dir . -o testing_unclustered --decorate_gff yes --go_evidence non-electronic --itype CDS -i unclustered.fna --cpu 30 --dmnd_db /space/Software/eggnog_5.0_drosophilids_DB/myDrosophila.dmnd --decorate_gff longest_func_annotI15_noWil_noLowGCAllIsoforms.gff3 --evalue 0.000001,

which works as expected. Now I want to make this search more strict by requiring that both the query and the subject coverages are more than 80%.

If I run: emapper.py --output_dir . -o testing_unclustered --decorate_gff yes --go_evidence non-electronic --itype CDS -i unclustered.fna --cpu 30 --dmnd_db /space/Software/eggnog_5.0_drosophilids_DB/myDrosophila.dmnd --decorate_gff longest_func_annotI15_noWil_noLowGCAllIsoforms.gff3 --evalue 0.000001 --query_cover 80.0,

I get outputs as expected. I also get outputs if I use --subject_cover 80.0 instead of the --query_cover 80.0.

But when I add both flags in my command, like: emapper.py --output_dir . -o testing_unclustered --decorate_gff yes --go_evidence non-electronic --itype CDS -i unclustered.fna --cpu 30 --dmnd_db /space/Software/eggnog_5.0_drosophilids_DB/myDrosophila.dmnd --decorate_gff longest_func_annotI15_noWil_noLowGCAllIsoforms.gff3 --evalue 0.000001 --query_cover 80.0 --subject_cover 80.0

I get this error: Error running diamond: Error: vector::_M_range_check: __n (which is 8547) >= this->size() (which is 4095)

4095 is the number of fasta sequences I have in my query file "unclustered.fna", but I don't recognise the 8547 number.

I googled a bit and this error shows up in programs written in C++, which I am not familiar with. Does anyone have any idea what is going on?

I have Python 3.12.3, diamond v2.1.9.163, emapper-2.1.12.