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KarchinLab / 2020plus

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
http://2020plus.readthedocs.org
Apache License 2.0
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CalledProcessorError in Line 342 #20

Closed yasirniazi closed 3 years ago

yasirniazi commented 4 years ago

I have faced the following issue after 96% job done and started Random Forest.... Version: 1.2.3 Command: /home/yasirniazi/2020plus-1.2.3/2020plus.py --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution output_bladder/simulated_null_dist.txt --features output_bladder/simulated_summary/simulated_features.txt --simulated --cv Running Random forest . . .

AN ERROR HAS OCCURRED: check the log file

Type: <class 'rpy2.rinterface.RRuntimeError'> Exception: Error in load("data/2020plus_10k.Rdata") : error reading from connection

Traceback: File "/home/yasirniazi/2020plus-1.2.3/2020plus.py", line 275, in args.func() # run function corresponding to user's command File "/home/yasirniazi/2020plus-1.2.3/2020plus.py", line 37, in _classify src.classify.python.classifier.main(opts) # run code File "/home/yasirniazi/2020plus-1.2.3/src/classify/python/classifier.py", line 184, in main rrclf.clf.load_cv(cli_opts['trained_classifier']) File "/home/yasirniazi/2020plus-1.2.3/src/classify/python/r_random_forest_clf.py", line 164, in load_cv ro.r('load("{0}")'.format(path)) File "/home/yasirniazi/anaconda3/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/init.py", line 352, in call res = self.eval(p) File "/home/yasirniazi/anaconda3/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/functions.py", line 178, in call return super(SignatureTranslatedFunction, self).call(*args, *kwargs) File "/home/yasirniazi/anaconda3/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/functions.py", line 106, in call res = super(Function, self).call(new_args, **new_kwargs)

Error in job predict_test while creating output file output_bladder/pretrained_output/results/r_random_forest_prediction.txt. RuleException: CalledProcessError in line 342 of /home/yasirniazi/2020plus-1.2.3/Snakefile: Command ' python which 2020plus.py --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution output_bladder/simulated_null_dist.txt --features output_bladder/simulated_summary/simulated_features.txt --simulated --cv python which 2020plus.py --out-dir output_bladder/pretrained_output --log-level=INFO classify -n 200 --trained-classifier data/2020plus_10k.Rdata -d .7 -o 1.0 --features output_bladder/features.txt --null-distribution output_bladder/simulated_null_dist.txt --random-seed 71 --cv ' returned non-zero exit status 1. File "/home/yasirniazi/2020plus-1.2.3/Snakefile", line 342, in __rule_predict_test File "/home/yasirniazi/anaconda3/envs/2020plus/lib/python3.6/concurrent/futures/thread.py", line 56, in run Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message