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halPhyloPTrain error #184

Closed minjinhan closed 3 years ago

minjinhan commented 3 years ago

Hello guys,

We encountered the same problem with #129 (No module named 'sonLib.bioio'). According to the suggestion, we setup Python 3.6+ virtualenv and pip install sonLib. Finally, sonLib-1.1.0 was successfully installed in our server (centos6.5). But when we run halPhyloPTrain.py again, there are new errors as follows:

Traceback (most recent call last): File "./hal/bin/hal2mafMP.py", line 19, in from sonLib.bioio import system File "./python3.6/site-packages/sonLib/bioio.py", line 431 os.chmod(dirName, 0777)

SyntaxError: invalid token Traceback (most recent call last): File "./hal/bin/halPhyloPTrain.py", line 260, in sys.exit(main()) File "./hal/bin/halPhyloPTrain.py", line 257, in main computeModel(args) File "./hal/bin/halPhyloPTrain.py", line 133, in computeModel extractGeneMAFs(options) File "./hal/bin/halPhyloPTrain.py", line 60, in extractGeneMAFs bedFile4d, options.refGenome)) File "./hal/hal/stats/halStats.py", line 28, in runShellCommand (command, sts)) RuntimeError: Command: hal2mafMP.py evolver.hal ..... exited with non-zero status 1

Anybody can help me to fix this error?

Thanks!

diekhans commented 3 years ago

It looks like you have a python 2.7 version of sonlib. The current code uses python 3 syntax of:

   os.chmod(dirName, 0o777)

minjinhan notifications@github.com writes:

Hello guys,

We encountered the same problem with #129 (No module named 'sonLib.bioio'). According to the suggestion, we setup Python 3.6+ virtualenv and pip install sonLib. Finally, sonLib-1.1.0 was successfully installed in our server (centos6.5). But when we run halPhyloPTrain.py again, there are new errors as follows:

Traceback (most recent call last): File "./hal/bin/hal2mafMP.py", line 19, in from sonLib.bioio import system File "./python3.6/site-packages/sonLib/bioio.py", line 431 os.chmod(dirName, 0777)

SyntaxError: invalid token Traceback (most recent call last): File "./hal/bin/halPhyloPTrain.py", line 260, in sys.exit(main()) File "./hal/bin/halPhyloPTrain.py", line 257, in main computeModel(args) File "./hal/bin/halPhyloPTrain.py", line 133, in computeModel extractGeneMAFs(options) File "./hal/bin/halPhyloPTrain.py", line 60, in extractGeneMAFs bedFile4d, options.refGenome)) File "./hal/hal/stats/halStats.py", line 28, in runShellCommand (command, sts)) RuntimeError: Command: hal2mafMP.py evolver.hal ..... exited with non-zero status 1

Anybody can help me to fix this error?

Thanks!

minjinhan commented 3 years ago

@diekhans Thanks for your suggestion. We have solved that problem.