ValueError: need at least one array to concatenate

[ofleitas]

Hello

I am trying to run InterLabelGO but when I run python prepare_data.py --make_db --ia I get the following output:

(InterLabelGO) ofm@ofm-Nitro-AN515-58:~/Documents/Programs/InterLabelGO+$ python prepare_data.py --make_db --ia
Loading the obo.pkl file from /home/ofm/Documents/Programs/InterLabelGO+/utils/obo.pkl
The obo file version is releases/2024-11-03
creating diamond_db...
diamond v2.1.8.162 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: /home/ofm/Documents/Programs/InterLabelGO+/Data/alignment_database/BPO/AlignmentKNN.fasta
Opening the database file... [0s]
Loading sequences... [0s]
Masking sequences... [0.003s]
Writing sequences... [0s]
Hashing sequences... [0s]
Loading sequences... [0s]
Writing trailer... [0s]
Closing the input file... [0s]
Closing the database file... [0s]

Database sequences 34
Database letters 18594
Database hash fca40b3ef5d3e65bd542fb25c475f7f1
Total time 0.004000s
creating diamond_db...
diamond v2.1.8.162 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: /home/ofm/Documents/Programs/InterLabelGO+/Data/alignment_database/CCO/AlignmentKNN.fasta
Opening the database file... [0s]
Loading sequences... [0s]
Masking sequences... [0.001s]
Writing sequences... [0s]
Hashing sequences... [0s]
Loading sequences... [0s]
Writing trailer... [0s]
Closing the input file... [0s]
Closing the database file... [0s]

Database sequences 41
Database letters 21046
Database hash de7bcba5c2ba38f134dbb939001b1544
Total time 0.002000s
creating diamond_db...
diamond v2.1.8.162 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: /home/ofm/Documents/Programs/InterLabelGO+/Data/alignment_database/MFO/AlignmentKNN.fasta
Opening the database file... [0s]
Loading sequences... [0s]
Masking sequences... [0.002s]
Writing sequences... [0s]
Hashing sequences... [0s]
Loading sequences... [0s]
Writing trailer... [0s]
Closing the input file... [0s]
Closing the database file... [0s]

Database sequences 29
Database letters 12873
Database hash d195fd627b5e9684579c55d54a604d0e
Total time 0.002000s
database created

proteins in BPO aspect with terms frequency greater than 50: 0
proteins in CCO aspect with terms frequency greater than 20: 8
proteins in MFO aspect with terms frequency greater than 20: 3

Traceback (most recent call last):
File "/home/ofm/Documents/Programs/InterLabelGO+/prepare_data.py", line 371, in
main(train_terms_tsv, train_seqs_fasta, Data_dir, make_alignment_db, min_count_dict, seed, stratifi, test_terms_tsv, test_seqs_fasta)
File "/home/ofm/Documents/Programs/InterLabelGO+/prepare_data.py", line 271, in main
aspect_train_term_matrix = np.vstack([goset2vec(aspect_train_term_grouped_dict[aspect][entry], aspect_go2vec_dict[aspect], fixed_len=True) for entry in aspect_train_seq_list])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<array_function internals>", line 200, in vstack
File "/home/ofm/Documents/Programs/InterLabelGO+/conda/envs/InterLabelGO/lib/python3.11/site-packages/numpy/core/shape_base.py", line 296, in vstack
return _nx.concatenate(arrs, 0, dtype=dtype, casting=casting)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<array_function internals>", line 200, in concatenate
ValueError: need at least one array to concatenate