Not able to run example data with most of the algorithm

[Hsu-Che-Wei]

Hello,

I followed your instructions and have successfully installed BEELINE. Yet when I run python BLRunner.py --config config-files/config.yaml, only two algorithm, PIDC and GRNVBEM are successfully run. The others have error messages such as:

(BEELINE) raphael830102@beeline-cwh:~/Beeline$ python BLRunner.py --config=config-files/new_config.yaml Skipping PIDC Skipping GRNVBEM Skipping GRNBOOST2 Skipping PPCOR Skipping SCODE Skipping SCNS Skipping LEAP Skipping GRISLI Skipping SINGE Skipping SCRIBE <BLRun.BLRun object at 0x7f29f320a080> Evaluation started docker run --rm -v /home/raphael830102/Beeline:/data/ --expose=41269 arboreto:base /bin/sh -c "time -v -o data/outputs/example/GSD/GENIE3/time.txt python runArboreto.py --algo=GENIE3 --inFile=data/inputs/example/G SD/GENIE3/ExpressionData.csv --outFile=data/outputs/example/GSD/GENIE3/outFile.txt " Traceback (most recent call last): File "runArboreto.py", line 43, in <module> main(sys.argv) File "runArboreto.py", line 32, in main network = genie3(inDF, client_or_address = client) File "/opt/conda/lib/python3.7/site-packages/arboreto/algo.py", line 73, in genie3 limit=limit, seed=seed, verbose=verbose) File "/opt/conda/lib/python3.7/site-packages/arboreto/algo.py", line 115, in diy expression_matrix, gene_names, tf_names = _prepare_input(expression_data, gene_names, tf_names) File "/opt/conda/lib/python3.7/site-packages/arboreto/algo.py", line 214, in _prepare_input expression_matrix = expression_data.as_matrix() File "/opt/conda/lib/python3.7/site-packages/pandas/core/generic.py", line 5130, in __getattr__ return object.__getattribute__(self, name) AttributeError: 'DataFrame' object has no attribute 'as_matrix' docker run --rm -v /home/raphael830102/Beeline:/SINCERITIES/data/ sincerities:base /bin/sh -c "time -v -o data/outputs/example/GSD/SINCERITIES/time0.txt Rscript MAIN.R data/inputs/example/GSD/SINCERITIES/Expressio nData0.csv data/outputs/example/GSD/SINCERITIES/outFile0.txt " Loading required package: SuppDists Loading required package: Matrix Loaded glmnet 4.0-2 Loading required package: MASS [1] "data/inputs/example/GSD/SINCERITIES/ExpressionData0.csv" [2] "data/outputs/example/GSD/SINCERITIES/outFile0.txt" Error in coef.cv.glmnet(CV_results, s = "lambda.min") : could not find function "coef.cv.glmnet" Calls: SINCERITITES In addition: There were 21 warnings (use warnings() to see them) Execution halted docker run --rm -v /home/raphael830102/Beeline:/SINCERITIES/data/ sincerities:base /bin/sh -c "time -v -o data/outputs/example/GSD/SINCERITIES/time1.txt Rscript MAIN.R data/inputs/example/GSD/SINCERITIES/Expressio nData1.csv data/outputs/example/GSD/SINCERITIES/outFile1.txt " Loading required package: SuppDists Loading required package: Matrix Loaded glmnet 4.0-2 Loading required package: MASS [1] "data/inputs/example/GSD/SINCERITIES/ExpressionData1.csv" [2] "data/outputs/example/GSD/SINCERITIES/outFile1.txt" Error in coef.cv.glmnet(CV_results, s = "lambda.min") : could not find function "coef.cv.glmnet" Calls: SINCERITITES In addition: There were 21 warnings (use warnings() to see them) Execution halted Traceback (most recent call last): File "BLRunner.py", line 77, in <module> main() File "BLRunner.py", line 71, in main evaluation.runners[idx].parseOutput() File "/home/raphael830102/Beeline/BLRun/runner.py", line 90, in parseOutput OutputParser[self.name](self) File "/home/raphael830102/Beeline/BLRun/genie3Runner.py", line 60, in parseOutput OutDF = pd.read_csv(outDir+'outFile.txt', sep = '\t', header = 0) File "/home/raphael830102/anaconda3/envs/BEELINE/lib/python3.7/site-packages/pandas/io/parsers.py", line 678, in parser_f return _read(filepath_or_buffer, kwds) File "/home/raphael830102/anaconda3/envs/BEELINE/lib/python3.7/site-packages/pandas/io/parsers.py", line 440, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/raphael830102/anaconda3/envs/BEELINE/lib/python3.7/site-packages/pandas/io/parsers.py", line 787, in __init__ self._make_engine(self.engine) File "/home/raphael830102/anaconda3/envs/BEELINE/lib/python3.7/site-packages/pandas/io/parsers.py", line 1014, in _make_engine self._engine = CParserWrapper(self.f, **self.options) File "/home/raphael830102/anaconda3/envs/BEELINE/lib/python3.7/site-packages/pandas/io/parsers.py", line 1708, in __init__ self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 384, in pandas._libs.parsers.TextReader.__cinit__ File "pandas/_libs/parsers.pyx", line 695, in pandas._libs.parsers.TextReader._setup_parser_source FileNotFoundError: File b'outputs/example/GSD/GENIE3/outFile.txt' does not exist

I wonder if I have missed out any critical step, would be nice if you would provide some suggestions. Thanks a lot.

[Hsu-Che-Wei]

For your convenience, here is the screen shot of the error message.

[adyprat]

Hey, Sorry for the late reply. The GENIE3 and GRNBoost2 errors are because of an issue with Arboreto as discussed here: https://github.com/Murali-group/Beeline/issues/37. I updated the files to fix that issue now.

Looks like most of the SINCERITIES fails due to a recent update to glmnet to 4.0, I fixed this by downgrading it to 2.0-13 (used at the time of publication). I cannot seem to figure out what the other Algorithms are not working from your error message. Please update your Dockers and let me know if you still have issues. Thanks, -Aditya

[Hsu-Che-Wei]

Hello Aditya,

Thanks for the update! I have reinstalled BEELINE, but ran into this Error, seems to do with Aboreto again.

Do you have any ideas what could cause this?

Thank you! -Che-Wei

[adyprat]

Hi, Looks like it is some Arboreto related issue (see here). I did not encounter this issue when I ran it with the new Docker setup yesterday. Perhaps I will need more information than just that error. What OS are you trying to run this on?

Anyway, form what I see it should still run the algorithms and produce an output using a different setup internally. Was there no output produced? Can you check in your outputs/example/GSD/GENIE3 or GRNBOOST2 to see if there's a rankedEdges.csv or an outFile.txt? Best, Aditya

[Hsu-Che-Wei]

Hello,

After reinstalling Docker, Anaconda and Beeline from scratch, now it works. All 12 algorithms can be successfully run on the example data.

Thanks a lot.

Best, Che-Wei