OSError: SavedModel file does not exist

[die hu]

Hi, Thanks for your nice tool: iphop.

I got a error message from step 8 when I use iphop predict --fa_file Data_test_add_to_db/Input_viral_contigs.fasta --db_dir ../iphop_db/Sept_2021_pub_rw --out_dir iphop_test_results/ .

[8] Running the convolution networks...
[8/1] Loading data as tensors..
[8/1.1] Getting blast-based scores..
[8/1.2] Run blast classifier Model_blast_Conv-87 (by batch)..
Traceback (most recent call last):
File "/home/hudi/.conda/envs/iphop/bin/iphop", line 8, in <module>
sys.exit(cli())
File "/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/iphop.py", line 128, in cli
args"func"
File "/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/modules/master_predict.py", line 106, in main
runmodels.run_individual_models(args)
File "/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/modules/runmodels.py", line 58, in run_individual_models
full_predicted = run_single_classifier(classifier,tensors,args)
File "/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/modules/runmodels.py", line 229, in run_single_classifier
best_model = keras.models.load_model(h5_file, compile=False)
File "/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 67, in error_handler
raise e.with_traceback(filtered_tb) from None
File "/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/tensorflow/python/saved_model/loader_impl.py", line 118, in parse_saved_model
raise IOError(
OSError: SavedModel file does not exist at: /home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/classifiers/Model_blast_Conv-87.h5/{saved_model.pbtxt|saved_model.pb}

‌

How can I fix it?

Thanks in advance

[Simon Roux]

Hi,

Can you check (and put here) the content of the folder “/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/classifiers/” ? It seems like the installation was maybe not complete, and some files are missing (according to the error log).

Best,

Simon

[die hu]

Hi, Simon

There are the files in “/home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/classifiers/.

Thanks

[Simon Roux]

So that is strange, the program complains about “SavedModel file does not exist”, but we can see the file here (“Model_blast-Conv-87.h5”). I could think of two reasons for this, one would be permissions issues (i.e. you should double-check that all the files in “classifiers” have the correct permissions to be readable by the script), and the other would be something specific happening with your OS/system and h5 files (I know some systems need to load some custom python module to be able to read h5 correctly) ?