ERROR in train module : #41
Description
Hi,
I'm pretty new to fungi and I discovered funannotate with a recent pangenome study on Aspegullus fumigatus (https://pubmed.ncbi.nlm.nih.gov/36395320/).
I'm starting to work with A. fumigatus and I have to annotated some genomes.
so, i installed funannotate2 yesterday (CET time) -> funannotate2 v25.11.1
I'm on a linux cluster and i installed the conda env following the installation instructions in https://funannotate2.readthedocs.io/en/latest/installation.html
mambacreate -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite conda activate funannotate2 python -m pip install git+https://github.com/nextgenusfs/funannotate2.git
I did not install GeneMark and i proceeded to test the different modules:
1- I defined a specific FUNANNOTATE-DB folder
2- I installed the databases (had to install mibig, go and dbCAN manually)
3 - test funannotate2 clean -> OK
4 - dowloaded BUSCO aspergillus_odb12.2025-07-01.tar.gz to FUNANNOTATE-DB/BUSCO
5 - funannotate2 train
and here I have an error.
this is the command I used
funannotate2 train -f /home/martinssimoes/bac_a_sable/analyses/funnnotate2/test_2025-02-13/Assemblies_cleaned/10_S10_cleaned_renamed.fasta -s "Aspergillus fumigatus" -o /home/martinssimoes/bac_a_sable/analyses/funnnotate2/test_2025-02-13 -t 24 --busco-lineage /path_folder_to_FUNANNOTATE2_DB/aspergillus_odb12
Here is the error :
[Feb 13 05:50 PM] Python v3.12.12; funannotate2 v25.11.1; gfftk v25.6.10; buscolite v26.1.26
[Feb 13 05:50 PM] Loading genome assembly and running QC checks
[Feb 13 05:50 PM] Genome stats:
{
"n_contigs": 777,
"size": 28346551,
"n50": 145342,
"n90": 31443,
"l50": 58,
"l90": 212,
"avg_length": 36482
}
[Feb 13 05:50 PM] Filtered genome for training: kept 309 contigs (27,486,431 bp), filtered 468 contigs (860,120 bp) shorter than 10,000 bp
ERROR in taxonomy lookup: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
[Feb 13 05:50 PM] Getting taxonomy information
false
Traceback (most recent call last):
File "/home/martinssimoes/miniconda3/envs/funannotate2/bin/funannotate2", line 6, in
sys.exit(main())
^^^^^^
File "/home/martinssimoes/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/main.py", line 28, in main
train(args)
File "/home/martinssimoes/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/train.py", line 129, in train
aug_species = choose_best_augustus_species(taxonomy)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/martinssimoes/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/utilities.py", line 391, in choose_best_augustus_species
return best_taxonomy(query_tax, augustus_species)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/martinssimoes/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/utilities.py", line 480, in best_taxonomy
score = similarity_score(query, attributes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/martinssimoes/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/utilities.py", line 431, in similarity_score
return sum(
^^^^
File "/home/martinssimoes/miniconda3/envs/funannotate2/lib/python3.12/site-packages/funannotate2/utilities.py", line 434, in
if level in query
^^^^^^^^^^^^^^
TypeError: argument of type 'bool' is not iterable
It seems that it tries to connect to an external DB to check the taxonomy. But i thought that the augustus species was already downloaded ( miniconda3/envs/funannotate2/config/species).
I verified augustus --species=help and Aspergillus fumigatus (as many other groups) appear listed.
I am sure I'm doing something wrong and it's in front of my eyes... but i can't see it. do I need to set an AUGUSTUS path variable ? I didn't see it in the manual ...
Thanks in advance for your help !!
Best regards,
Patricia