Trouble running

[sinaghadermarzi]

Hi,
Thanks for your work on DTI-VOODOO.

I am trying to run DTI-VOODOO on my computer and I followed below steps as mentioned in in the src/README.md :
first created an enviornment which looks like this env.txt
then

1. went to the folders data/STITCH_data , data/STRING_data , data/PhenomeNET_data and ran download.sh command: successfully finished
2. went to src/ and ran DTI_data_preparation.py:
   there were errors with from sklearn.metrics import jaccard_similarity_score in similarity_measurement.py but I fixed that.
   got this output data_prep_output.txt

After this finished successfully, I went to the DL2vec directory and ran the command produced by the previous step
python runDL2vec.py -embedsize 200 -ontology ../../data/PhenomeNET_data/phenomenet.owl -associations ../../data/PhenomeNET_data/drugassociation_file -outfile ../../data/PhenomeNET_data/drugembedding_model -entity_list ../../data/PhenomeNET_data/drugentity_list -num_workers 48

and got this error: error.txt

Could you please help me figure out what's going on?

[THinnerichs]

Dear Sina,
it seems like there are still some issues with data preparation pipeline.

As your last error message states by sh: groovy: command not found, it seems like you didn't install groovy previously, leading to the axioms not being generated. See here for more information.

Feel free to reach out, if you encounter any more issues.

[sinaghadermarzi]

Thank you @THinnerichs for your response.

I installed groovy and tried again. Got the following error.
error_filename.txt

Apparently the filename the program is looking for (drugassociation_file) should have an extra underscore in it.

[THinnerichs]

Thanks a lot! I actually tested the pipeline quite thoroughly, but apparently my changes were lost somewhere in the ether. I will have more time next week to fix the whole pipeline. Thank you very much once again for your feedback!

Also resolved the underscore issue.

[sinaghadermarzi]

thank you! Yaya I understand.
looking forward to try again once you are done.

[sinaghadermarzi]

Hi @THinnerichs,

Any update on this request?