test example failed

[igortru]

PhageBoost -f example/data/NC_000907.fasta.gz -o results processing: NC_000907 time after genecalls: 2.24992036819458 time after feature calculations: 8.712299346923828 [22:44:13] WARNING: ../src/learner.cc:1040: If you are loading a serialized model (like pickle in Python, RDS in R) generated by older XGBoost, please export the model by calling Booster.save_model from that version first, then load it back in current version. See:

https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html

for more details about differences between saving model and serializing.

[22:44:13] WARNING: ../src/learner.cc:749: Found JSON model saved before XGBoost 1.6, please save the model using current version again. The support for old JSON model will be discontinued in XGBoost 2.3. [22:44:13] WARNING: ../src/tree/./updater_quantile_hist.h:248: Attempted to load internal configuration for a model file that was generated by a previous version of XGBoost. A likely cause for this warning is that the model was saved with saveRDS() in R or pickle.dump() in Python. We strongly ADVISE AGAINST using saveRDS() or pickle.dump() so that the model remains accessible in current and upcoming XGBoost releases. Please use xgb.save() instead to preserve models for the long term. For more details and explanation, see https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html [22:44:13] WARNING: ../src/learner.cc:438: If you are loading a serialized model (like pickle in Python, RDS in R) generated by older XGBoost, please export the model by calling Booster.save_model from that version first, then load it back in current version. See:

https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html

for more details about differences between saving model and serializing.

Traceback (most recent call last): File "/home/tolstoy/.local/bin/PhageBoost", line 8, in sys.exit(main()) File "/home/tolstoy/.local/lib/python3.7/site-packages/PhageBoost/main.py", line 223, in main model, feats, feats_, limit = read_model_from_file(model_file) File "/home/tolstoy/.local/lib/python3.7/site-packages/PhageBoost/main.py", line 65, in read_model_fromfile feats = [i.replace('-delta', '') for i in feats] TypeError: 'NoneType' object is not iterable

[wangdi2016]

I had the same issue. I figured it out after downgrading xgboost from 2.1.1 to 1.1.1. I can run the test case successfully.

here is the output

processing: NC_000907 time after genecalls: 2.1909637451171875 time after feature calculations: 10.072350263595581 time after predictions: 11.75052547454834 {'phage6': 51, 'phage5': 26}

Here is my requirments.txt

biopython==1.76 joblib more-itertools numpy pandas pickleshare pyrodigal==0.6.4 scipy tables xgboost==1.1.1 cachier