simonfqy
commented
4 years ago I am very sorry that I did not get back to you earlier. Thank you for your kind words!
The .sh files are independent of each other, you don't need to run them according to any certain order.
As for the versions, I don't remember exactly, and I no longer have access to the GPU cluster I used for running this project. I was likely using TensorFlow 1.4, which was released in late 2017. The DeepChem version was likely the one available in Dec 2017 or Jan 2018, the exact version is 1.3.1, this line shows the version number.
Some code can be buggy, yes. If you still want to ask, please give me a bit more info, thanks~
If you have any more queries, please don't hesitate to ask me. I will try my best to assist you. Again, many apologies for not replying to you sooner.
Running on dataset: tc_full_kinase
Traceback (most recent call last): File "driver.py", line 831, in
tf.compat.v1.app.run(main=run_analysis, argv=[sys.argv[0]] + unparsed)
File "/home/pharma1/anaconda3/envs/DeepChem/lib/python3.7/site-packages/tensorflow/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "/home/pharma1/anaconda3/envs/DeepChem/lib/python3.7/site-packages/absl/app.py", line 299, in run
_run_main(main, args)
File "/home/pharma1/anaconda3/envs/DeepChem/lib/python3.7/site-packages/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "driver.py", line 374, in run_analysis
remove_val_set_entries=remove_val_set_entries)
TypeError: load_tc_full_kinases() got an unexpected keyword argument 'cold_drug_cluster'
When I run drivw2.sh, I got
import pandas.util.testing as tm Traceback (most recent call last): File "driver.py", line 831, in
tf.compat.v1.app.run(main=run_analysis, argv=[sys.argv[0]] + unparsed)
File "/home/pharma1/anaconda3/envs/DeepChem/lib/python3.7/site-packages/tensorflow/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "/home/pharma1/anaconda3/envs/DeepChem/lib/python3.7/site-packages/absl/app.py", line 299, in run
_run_main(main, args)
File "/home/pharma1/anaconda3/envs/DeepChem/lib/python3.7/site-packages/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "driver.py", line 274, in run_analysis
assert len(set(aggregate)) == len(aggregate)
TypeError: 'NoneType' object is not iterable
You listed many .sh files. Do they need to be run at the certain series? such as first run **.sh, then run ***.sh? It will be great to list the version of the libraries you used in your code. Many thanks for your great work.