Error with download_eggnog_database.py

[desmodus1984]

Hi, I am trying to follow the instructions on the website for doing the annotations and I would appreciate some help. I am an amateur but trying to learn.

I am trying the following code to annotate and "decorate" a GFF that I developed using GeMoMa, the code is:

emapper.py -m diamond --itype proteins -i /fs/scratch/PHS0338/appz/annotation/6Ref+Homo-100/predicted_proteins.fasta -o myse0 \
        --decorate_gff /fs/scratch/PHS0338/appz/annotation/6Ref+Homo-100/final_annotation.gff --decorate_gff_ID_field GeneID \
        --dbmem --cpu 48 --temp_dir $TMPDIR --scratch_dir $TMPDIR

And I got the following error: [31mDIAMOND database /users/PHS0338/jpac1984/.conda/envs/eggnob/lib/python3.10/site-packages/data/eggnog_proteins.dmnd not present. Use download_eggnog_database.py to fetch it[0m

So then, I tried it, and it didn't work either. I got the following error: /var/spool/slurmd/job11952613/slurm_script: line 11: download_eggnog_database.py: command not found

I am using conda, and I created an environment just for eggnob. What do I need to do for the .py command to work?

Thanks;

[Cantalapiedra]

Hi @desmodus1984 ,

As the error says, it is not finding the doanload_eggnog_database.py script.

Could you please share the output of the following commands?

which emapper.py which download_eggnog_database.py

It is to check whether those scripts are in the current PATH.

Best, Carlos

[desmodus1984]

Hi Carlos,

I did as suggested and I got the following outputs:

which emapper.py~/.conda/envs/eggnob/bin/emapper.py which download_eggnog_database.py/usr/bin/which: no download_eggnog_database.py in (/users/PHS0338/jpac1984/.conda/envs/eggnob/bin:/usr/local/xalt/xalt/bin:/usr/local/python/3.6-conda5.2/bin:/users/PHS0338/jpac1984/.linuxbrew/bin:/users/PHS0338/jpac1984/.linuxbrew/sbin:/users/PHS0338/jpac1984/.cargo/bin:/users/PHS0338/jpac1984/perl5/bin:/opt/mvapich2/intel/19.0/2.3.3/bin:/usr/local/gnu/8.4.0/bin:/opt/intel/itac/2019.5.041/bin:/opt/intel/advisor_2019/bin64:/opt/intel/vtune_amplifier_2019/bin64:/opt/intel/inspector_2019/bin64:/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/usr/local/software_usage:/usr/lib64/qt-3.3/bin:/opt/osc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/ddn/ime/bin:/opt/puppetlabs/bin:/users/PHS0338/jpac1984/edirect) Hope that provide a suggestion of a potential solution.

Thanks;

Juan Pablo Aguilar Cabezas

Ecology and Evolutionary Biology Ph.D. Candidate

Department of Biological Sciences

Ohio University, Athens OH

---

From: Carlos P Cantalapiedra @.> Sent: Friday, July 8, 2022 2:49 AM To: eggnogdb/eggnog-mapper @.> Cc: Aguilar Cabezas, Juan Pablo @.>; Mention @.> Subject: [External] Re: [eggnogdb/eggnog-mapper] Error with download_eggnog_database.py (Issue #397)

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As the error says, it is not finding the doanload_eggnog_database.py script.

Could you please share the output of the following commands?

which emapper.py which download_eggnog_database.py

It is to check whether those scripts are in the current PATH.

Best, Carlos

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[Cantalapiedra]

Hi Juan Pablo,

I don't understand what is happening. I did a fresh conda install, and I can find both emapper.py and download_eggnog_database.py in the PATH.

What commands did you use to install it? What is the output of ls -l ~/.conda/envs/eggnob/bin/?

[shanexuuu]

Hi Juan Pablo,

I don't understand what is happening. I did a fresh conda install, and I can find both emapper.py and download_eggnog_database.py in the PATH.

What commands did you use to install it? What is the output of ls -l ~/.conda/envs/eggnob/bin/?

Hi Cantalapiedra, I have the same issue: cann't find download_eggnog_database.py. And I tried to conda install v2.1.7 to v2.1.9, which results the same issue. The code I used for installation is: sudo chown -R $USER:$USER /bin/miniconda3 conda create -y --name eggnog conda activate eggnog conda install eggnog-mapper #v2.1.9 #or conda install -c bioconda eggnog-mapper emapper.py --version #tried for other version conda install eggnog-mapper=2.1.8

I would like to ask for your help about this. Thanks very much and look forward to hearing you back.

[Cantalapiedra]

Hi @shanexuuu,

What is the output of the which command for both emapper.py and download_eggnog_data.py?

Just as a note, it seems weird to me that you are installing miniconda3 under /bin, and then change all the permissions. Why didn't you install it under your home?

[shanexuuu]

Hi @shanexuuu,

What is the output of the which command for both emapper.py and download_eggnog_data.py?

Just as a note, it seems weird to me that you are installing miniconda3 under /bin, and then change all the permissions. Why didn't you install it under your home?

Hi Carol,

Thanks for reply!

I have fixed this problem by manually downloading all database and put them inside /data. Hope this can help others.

About miniconda3, it is bc every group member can use the same conda env without installing on their own home.

[Cantalapiedra]

Hi @shanexuuu,

Thank you for your reply and for the explanation about miniconda3 use.

Glad that you solved by downloading the data (I guess that from here http://eggnog5.embl.de/download/emapperdb-5.0.2/).

Best, Carlos

[alephreish]

The issue is that the script is called download_eggnog_data.py and not download_eggnog_database.py. Pre-downloading the data with download_eggnog_data.py avoids the error (and is more flexible in a pipeline context).