Comments (10)
ctokheim
commented on June 2, 2024
It's most likely that the 2020plus.py script is not found on your PATH. Please see: https://2020plus.readthedocs.io/en/latest/installation.html#check-your-path-variable .
from 2020plus.
a00101
commented on June 2, 2024
Thanks. it works partially.
But another error occurred
rule predict_test:
input: data/2020plus_10k.Rdata, output_bladder/features.txt, output_bladder/simulated_summary/simulated_features.txt
output: output_bladder/pretrained_output/results/r_random_forest_prediction.txt
jobid: 1
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
Version: 1.2.3
Command: /addData01/01_Program_to_install/63.2020plus/2020plus-master/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 . . .
Type: <class 'ValueError'>
Exception: Buffer for this type not yet supported.
Traceback:
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py", line 275, in <module>
args.func() # run function corresponding to user's command
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py", line 37, in _classify
src.classify.python.classifier.main(opts) # run code
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/classifier.py", line 180, in main
seed=cli_opts['random_seed'])
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/r_random_forest_clf.py", line 314, in __init__
other_sample_ratio=other_sample_ratio)
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/r_random_forest_clf.py", line 40, in __init__
ro.r("suppressPackageStartupMessages(library(randomForest))") # load randomForest library
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/__init__.py", line 353, in __call__
return conversion.ri2py(res)
File "/root/anaconda2/envs/2020plus/lib/python3.6/functools.py", line 807, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/pandas2ri.py", line 139, in ri2py_vector
res = numpy2ri.ri2py(obj)
File "/root/anaconda2/envs/2020plus/lib/python3.6/functools.py", line 807, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/numpy2ri.py", line 159, in ri2py_sexp
res = numpy.asarray(obj)
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/numpy/core/_asarray.py", line 85, in asarray
return array(a, dtype, copy=False, order=order)
****************************************
AN ERROR HAS OCCURRED: check the log file
****************************************
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 /addData01/01_Program_to_install/63.2020plus/2020plus-master/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 "/addData01/01_Program_to_install/63.2020plus/2020plus-master/Snakefile", line 342, in __rule_predict_test
File "/root/anaconda2/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
below is my package version each.
- numpy
- scipy=1.2.1
- matplotlib
- pandas=0.25.3
- scikit-learn<0.20.0
- pyyaml
- pysam
- snakemake
- tzlocal
scipy=1.2.1 and pandas=0.25.3
because - logsum error and other errors
from 2020plus.
ctokheim
commented on June 2, 2024
I think this might be a version-specific numpy/rpy2 problem: https://stackoverflow.com/questions/58561333/r-magic-input-argument-not-working-properly-in-jupyter-notebook
from 2020plus.
ctokheim
commented on June 2, 2024
I'm also finding that it might be better to stick with pandas version that is less than 1.0.0.
from 2020plus.
a00101
commented on June 2, 2024
Unfortunately I got another error with pandas==0.25.3
Version: 1.2.3
Command: /addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --nul
Running Random forest . . .
Type: <class 'AttributeError'>
Exception: module 'rpy2.robjects.pandas2ri' has no attribute 'py2ri'
Traceback:
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py", line 275, in <module>
args.func() # run function corresponding to user's command
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py", line 37, in _classify
src.classify.python.classifier.main(opts) # run code
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/classifier.py", line 190, in main
result_df = trained_rand_forest_pred(rrclf, df, None, null_pvals, is_cv)
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/classifier.py", line 104, in trained_rand_forest_pred
onco_prob, tsg_prob, other_prob = clf.predict_cv()
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/generic_classifier.py", line 139, in predict_cv
tmp_prob = self.clf.predict_proba(test_feat)
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/r_random_forest_clf.py", line 272, in predict_proba
r_xtest = pandas2ri.py2ri(xtest)
****************************************
AN ERROR HAS OCCURRED: check the log file
****************************************
Error in job predict_test while creating output file output_lung/pretrained_output/results/r_random_forest_prediction.txt.
RuleException:
CalledProcessError in line 342 of /addData01/01_Program_to_install/63.2020plus/2020plus-master/Snakefile:
Command '
python `which 2020plus.py` --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution output_lung/simulated_null_dist.
python `which 2020plus.py` --out-dir output_lung/pretrained_output --log-level=INFO classify -n 200 --trained-classifier data/2020plus_10k.Rdata -d .7
' returned non-zero exit status 1.
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/Snakefile", line 342, in __rule_predict_test
File "/root/anaconda2/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
from 2020plus.
ctokheim
commented on June 2, 2024
Can you check your rpy2 version? I did not get this error in rpy2 version 2.9.4. I suspect rpy2 version 3 or higher result in this error.
from 2020plus.
a00101
commented on June 2, 2024
rpy2==2.9.4
pandas==0.25.3
I got error again.
I'm too tired to fix numerous errors if I thank you for your generous support.
Can you give me docker image?
Version: 1.2.3
Command: /addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution output_lung/simulated_null_dist.txt --features output_lung/simulated_summary/simulated_features.txt --simulated --cv
Running Random forest . . .
Type: <class 'ValueError'>
Exception: Buffer for this type not yet supported.
Traceback:
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py", line 275, in <module>
args.func() # run function corresponding to user's command
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/2020plus.py", line 37, in _classify
src.classify.python.classifier.main(opts) # run code
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/classifier.py", line 180, in main
seed=cli_opts['random_seed'])
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/r_random_forest_clf.py", line 314, in __init__
other_sample_ratio=other_sample_ratio)
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/src/classify/python/r_random_forest_clf.py", line 40, in __init__
ro.r("suppressPackageStartupMessages(library(randomForest))") # load randomForest library
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/__init__.py", line 353, in __call__
return conversion.ri2py(res)
File "/root/anaconda2/envs/2020plus/lib/python3.6/functools.py", line 807, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/pandas2ri.py", line 139, in ri2py_vector
res = numpy2ri.ri2py(obj)
File "/root/anaconda2/envs/2020plus/lib/python3.6/functools.py", line 807, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/rpy2/robjects/numpy2ri.py", line 159, in ri2py_sexp
res = numpy.asarray(obj)
File "/root/anaconda2/envs/2020plus/lib/python3.6/site-packages/numpy/core/_asarray.py", line 85, in asarray
return array(a, dtype, copy=False, order=order)
****************************************
AN ERROR HAS OCCURRED: check the log file
****************************************
Error in job predict_test while creating output file output_lung/pretrained_output/results/r_random_forest_prediction.txt.
RuleException:
CalledProcessError in line 342 of /addData01/01_Program_to_install/63.2020plus/2020plus-master/Snakefile:
Command '
python `which 2020plus.py` --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution output_lung/simulated_null_dist.txt --features output_lung/simulated_summary/simulated_features.txt --simulated --cv
python `which 2020plus.py` --out-dir output_lung/pretrained_output --log-level=INFO classify -n 200 --trained-classifier data/2020plus_10k.Rdata -d .7 -o 1.0 --features output_lung/features.txt --null-distribution output_lung/simulated_null_dist.txt --random-seed 71 --cv
' returned non-zero exit status 1.
File "/addData01/01_Program_to_install/63.2020plus/2020plus-master/Snakefile", line 342, in __rule_predict_test
File "/root/anaconda2/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
from 2020plus.
ctokheim
commented on June 2, 2024
There currently are no docker images. You might want to see a related issue about installing the correct package versions: #13
from 2020plus.
stroke1989
commented on June 2, 2024
I got the same error
55 of 57 steps (96%) done
rule predict_test:
input: data/2020plus_10k.Rdata, output_bladder/features.txt, output_bladder/simulated_summary/simulated_features.txt
output: output_bladder/pretrained_output/results/r_random_forest_prediction.txt
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
Version: 1.2.3
Command: /home/ug0416/software/2020plus/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 . . .
Type: <class 'ValueError'>
Exception: Buffer for this type not yet supported.
Traceback:
File "/home/ug0416/software/2020plus/2020plus.py", line 275, in
args.func() # run function corresponding to user's command
File "/home/ug0416/software/2020plus/2020plus.py", line 37, in _classify
src.classify.python.classifier.main(opts) # run code
File "/home/ug0416/software/2020plus/src/classify/python/classifier.py", line 184, in main
rrclf.clf.load_cv(cli_opts['trained_classifier'])
File "/home/ug0416/software/2020plus/src/classify/python/r_random_forest_clf.py", line 176, in load_cv
self.cv_folds = com.convert_robj(ro.r["cvFoldDf"])
File "/home/ug0416/.conda/envs/2020plus/lib/python3.5/site-packages/pandas/rpy/common.py", line 226, in convert_robj
return converter(obj)
File "/home/ug0416/.conda/envs/2020plus/lib/python3.5/site-packages/pandas/rpy/common.py", line 142, in _convert_DataFrame
rows = np.array(rdf.rownames)
AN ERROR HAS OCCURRED: check the log file
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/ug0416/software/2020plus/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/ug0416/software/2020plus/Snakefile", line 342, in __rule_predict_test
File "/home/ug0416/.conda/envs/2020plus/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
the following is modules version of my python
- numpy==1.17.0
- scipy==0.19.1
- matplotlib==3.0.3
- pandas==0.19.0
- scikit-learn==0.19.1
- pyyaml==3.12
- pysam==0.18.0
- snakemake==3.7.1
- tzlocal==2.1
- pip==20.3.4
- pip:
- probabilistic2020==1.2.3
the following is the required dependecies recorded in build-in file "environment_python.yml"
name: 2020plus
channels:
- probabilistic2020==1.2.3
- bioconda
- defaults
dependencies: - numpy
- scipy<1.0.0
- matplotlib
- pandas<1.0.0
- scikit-learn<0.20.0
- pyyaml
- pysam
- snakemake
- tzlocal
- pip
- pip:
- probabilistic2020
could someone who operate successfully provide his/her version of required modules? Appreciate!
from 2020plus.
stroke1989
commented on June 2, 2024
finally, I get out this mud and run sucessfully. the version of python moduls I install were as following:
python 3.6.9
matplotlib 3.1.1
numpy 1.15.4
pandas 0.25.2
pip 21.3.1
probabilistic2020 1.2.3
pysam 0.15.0
PyYAML 6.0
rpy2 2.9.4
scikit-learn 0.19.1
scipy 0.19.1
snakemake 4.3.0
tzlocal 4.1
from 2020plus.
Related Issues (20)
- Error in rule simMaf HOT 16
- Error in rule simFeatures HOT 5
- Error in job simMAf : Called processor error : HOT 7
- rpy2 may need a specified version HOT 4
- Can't open file 'features': [Errno 2] No such file or directory HOT 2
- error while executing 2020plus.py command " python 2020plus.py" HOT 1
- Is grch38 supported? HOT 1
- Error in rule SimSummary: /bin/bash: mut_annotate: command not found HOT 5
- Should I train a new model ? HOT 1
- CalledProcessorError in Line 342
- Not enough Mutated Oncogenes or TSGs Found in Your Data HOT 5
- Error in load("data/2020plus_10k.Rdata") : error reading from connection HOT 1
- Errors: libicuuc.so.54 not found HOT 1
- Require snvboxGenes.fa file HOT 1
- Dependencies problem HOT 3
- can not find download page
- pandas.errors.EmptyDataError: No columns to parse from file HOT 5
- OSError: file `data//snvboxGenes.fa` not found HOT 5
- Keep getting error : Error in job simMaf while creating output file HOT 1
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from 2020plus.