Unrecognized tax ID, tax name or tax_scope mode: 'auto'.

[leeun67]

Dear author, when i run emapper.py with the command line:

"emapper.py -i q2.fa --output diamond_bact_ -m hmmer -d ~/soft/eggnog-mapper/data/

I receive the error "Unrecognized tax ID, tax name or tax_scope mode: 'auto'."

[Cantalapiedra]

Hi @leeun67 ,

How did you install eggnog-mapper and which version are you using?

[leeun67]

hi

Hi @leeun67 ,

How did you install eggnog-mapper and which version are you using?

Hi , i am just clone the software by git , may be version is the newest.

[Cantalapiedra]

Hi @leeun67 ,

Did you paste the whole command raising the error? How did you exactly install the software? I cannot try to reproduce the error unless I know exactly what you did. You did git clone, and what was next? I guess you installed some python packages, downloaded eggnog-mapper databases, ...

Also, if you don't really need the git version, I would recommend you to install the latest conda version, or the latest release.

Best, Carlos

[leeun67]

Hi @leeun67 ,

Did you paste the whole command raising the error? How did you exactly install the software? I cannot try to reproduce the error unless I know exactly what you did. You did git clone, and what was next? I guess you installed some python packages, downloaded eggnog-mapper databases, ...

Also, if you don't really need the git version, I would recommend you to install the latest conda version, or the latest release.

Best, Carlos

Thank your very much. As you say ,i downloaded eggnog-mapper databases. I will try conda again.

[Cantalapiedra]

ok! let me know if you find any problem

Thank you.

Best, Carlos

[migueldc1]

Hi, I am having a similar issue. When I run the emmaper with the command:

"emapper.py -m diamond --itype CDS -i ORF/M-CONV-Control/M-CONV-Control.lst.fnn -o ORF/Annotation/M-CONV-Control --data_dir Databases/eggnog/"

I get: "Unrecognized tax ID, tax name or tax_scope mode: 'all'."

I do not understand what this error mean, or if it is an issue of the database (I downloaded it with "download_eggnog_data.py --data_dir Databases/eggnog -y" or just the input is not correct. I am using as input the ORFs obtained with GeneMarkS-T from an assembled metatranscriptome. I also tried annotating the assembled metatranscriptome but I get the very same error.

Any tip to solve this error?

Thank you in advance.

Miguel

[Cantalapiedra]

Hi @Migueldc1 ,

I would need more info to try to reproduce the issue.

Which OS are you using? How did you install eggnog-mapper? Which version of eggnog-mapper is it?

Thanks

Carlos

[migueldc1]

Hi @Migueldc1 ,

I would need more info to try to reproduce the issue.

Which OS are you using? How did you install eggnog-mapper? Which version of eggnog-mapper is it?

Thanks

Carlos

Oh sorry.

I am working in a cluster with conda (v 4.13.0), sorry I don't have much more info. I installed through pip install because wasn't able to install it through conda. But installing it from the release files gives the same error. The versions are "emapper-2.1.8 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: unknown / Diamond version found: diamond version 0.9.36 / MMseqs2 version found: 113e3212c137d026e297c7540e1fcd039f6812b1"

I hope this is enough information.

[Cantalapiedra]

Hi @Migueldc1 ,

sorry to bother you, but I am unable to reproduce it yet.

What version of python are you using? If you are using a conda environment, what packages and versions are currently active?

Best, Carlos

[migueldc1]

I am using python version 3.7.4

I have a really huge list of packages installed, could be any incompatibility? I tried to create a new environment and install again eggnog, and now it seems that is working properly. At least it is not giving me this error!

Thank you for your help, Miguel

[Cantalapiedra]

Hi @Migueldc1 ,

Great that you were able to resolve it! Yes, maybe it was due to some incompatibility. Maybe it is the same issue @leeun67 is undergoing. I am not an expert no environments, but I tend to create tiny, rather specific environments to avoid that kind of issues. If it is giving you a different error don't hesitate to ask.

Thank you for your patience and sorry for the inconveniences.

Best, Carlos

[1525513874]

Hi, @Cantalapiedra I am having a similar issue. When I run the emmaper with the command: Unrecognized tax ID, tax name or tax_scope mode: 'all'. python3.7.13 eggnog2.1.8 and 2.1.9 data 5.0.2 I can use command --no_annot to get partial results.

Thank you for your help, Jackson

[Cantalapiedra]

Hi Jackson,

How did you install eggnog-mapper and which exact command are you running which raises the error? As you can see, Miguel apparently fixed his issue by installing a fresh environment. Is it you environment a very large one, or is it a fresh one for eggnog-mapper?

Best, Carlos

[1525513874]

Hi Jackson,

How did you install eggnog-mapper and which exact command are you running which raises the error? As you can see, Miguel apparently fixed his issue by installing a fresh environment. Is it you environment a very large one, or is it a fresh one for eggnog-mapper?

Best, Carlos

I use the simplest command. python emapper.py -i seqs.fa --output result/out --data_dir /data/5.0.2/ My environments are all newly created. My data are all from 5.0.2. There are two ways to install software. 1.anaconda python3.7 with linux,It installs version 2.1.3 of eggnog-mapper by default,and I can use the database of 5.0.2 to run correctly. 2.python 3.10.6 with linux ，I tried eggnog-mapper 2.1.9, 2.1.8 and 2.1.3, None of them work properly.But I can use command --no_annot to get partial results(no results for out.emapper.annotations).

Thank, Jackson

[Cantalapiedra]

Thank for the info, but, how did you install eggnog-mapper? At least in point 2 you specify the versions and SO, but you don't specify how you installed it. Did you use pip directly on your linux environment, or are you using a conda environment? As you can see in Miguel's answers he was having the error probably due to some incompatibility which it seems it was solved by installing with a new conda environment.

[1525513874]

Thank for the info, but, how did you install eggnog-mapper? At least in point 2 you specify the versions and SO, but you don't specify how you installed it. Did you use pip directly on your linux environment, or are you using a conda environment? As you can see in Miguel's answers he was having the error probably due to some incompatibility which it seems it was solved by installing with a new conda environment.

At the beginning, I used Windows to configure some of the configurations. Now I use linux configuration completely and now can run normally.

Thank you for your help, Jackson

[leonhardt913]

Hi, I also encountered same issue when using downloaded eggnog-mapper in CMD of Windows:

C:\Python38\Lib\site-packages\eggnog-mapper-2.1.9>python emapper.py -i test.fasta -o out Unrecognized tax ID, tax name or tax_scope mode: 'all'.

My OS is Windows10 Home 10.0.19043 Build 19043

I download the source code of eggnog-mapper 2.1.9 directly and unzip them under Python38\Lib\site-packages\ (as you can see it from my command line above). And I installed them with the command:

pip install -r requirements.txt

However, I have installed the requrements already so this step went fast:

Requirement already satisfied: biopython==1.76 in c:\python38\lib\site-packages (from -r requirements.txt (line 1)) (1.76) Requirement already satisfied: psutil==5.7.0 in c:\python38\lib\site-packages (from -r requirements.txt (line 2)) (5.7.0) Requirement already satisfied: xlsxwriter==1.4.3 in c:\python38\lib\site-packages (from -r requirements.txt (line 3)) (1.4.3) Requirement already satisfied: numpy in c:\python38\lib\site-packages (from biopython==1.76->-r requirements.txt (line 1)) (1.23.4)

And I manually download the eggnog.db, eggnog.taxa.tar, and eggnog_proteins.dmnd. And put them under Python38\Lib\site-packages\eggnog-mapper-2.1.9\data

I install python using python-3.8.4-amd64.exe.

Could you please help me with the issue? Thanks, I will provide more information if you need.

[Cantalapiedra]

Hi @leonhardt913 ,

It seems that Jackson (user 1525513874) was able to run it by switching from windows to linux. Unfortunately, I don't know very well how to help you, since I don't use windows at all. Is using conda a possibility on windows? Maybe installing through conda could be of help. My personal advice would be installing the Ubuntu that can be installed within Windows.

Good luck!

Best, Carlos