groopm refine error

[igsbma]

error log: Traceback (most recent call last): File "/home/bma/.local/bin/groopm", line 338, in GM_parser.parseOptions(args) File "/home/bma/.local/lib/python2.7/site-packages/groopm/groopm.py", line 160, in parseOptions plotFinal=pfx) File "/home/bma/.local/lib/python2.7/site-packages/groopm/refine.py", line 185, in refineBins self.plotterRefineBins(ignoreRanges=ignoreRanges) File "/home/bma/.local/lib/python2.7/site-packages/groopm/refine.py", line 192, in plotterRefineBins self.printRefinePlotterInstructions() File "/home/bma/.local/lib/python2.7/site-packages/groopm/refine.py", line 2196, in printRefinePlotterInstructions "****\n" EOFError: EOF when reading a line

output log:

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REFINING INSTRUCTIONS - PLEASE READ CAREFULLY

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You have chosen to refine in plotter mode. Congratulations! You will be shown a 3d plot of all the bins, colored by kmer profile. Bin Ids in close proximity and similar color may need to be merged. Conversely, you can split bins which appear chimeric Follow the instructions to merge or split these bins

Good Luck!

Press return to continue...Unexpected error: <type 'exceptions.EOFError'>

[igsbma]

Hi, minillinim I want to try GroopM, but the above error prevent me from going forward. I saw you closed this issue and thought that you have a solution for this??? I am not sure if you will read this since it is closed. I will open a new one if not response by Aug 1st, 2014 Thanks!

[minillinim]

Hey,

Sorry about that. I was cleaning up some other issues and I must have closed yours as well. So... Questions,

Are you running this command in a screen or some other type of background process. Looking on google I see that this happens when Python is waiting for user input and none comes. GroopM refine is supposed to be run interactively, is this the way you're running it.

It makes it easier for me to fix the issue if I know more about your system.

Could you open a python console window on the machine where the error occurs and run these commands and send back the results please.

import tables import pysam import numpy import scipy import matplotlib import platform import sys print platform.system(), platform.release() print(sys.version) print(sys.path) print "Numpy version: %s" % numpy.version print "Location: %s" % numpy.file print "Tables version: %s" % tables.version print "Location: %s" % tables.file print "Pysam version: %s" % pysam.version print "Location: %s" % pysam.file print "Scipy version: %s" % scipy.version print "Location: %s" % scipy.file print "MPL version: %s" % matplotlib.version print "Location: %s" % matplotlib.file