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  • #1

    LSC-example test error

    Hi all, I am trying to use LSC to correct my pacbio reads with illumina reads. However, after installation, I ran into problems running LSC example data.
    I have the required modules available (python, numpy, scipy), but the following error occurred running the example data: the previous steps look fine.

    ===samParser SR.??.cps.nav:===
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    Exit Code: 256
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Exception in thread Thread-22:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ab temp/SR.fa.ab.cps.sam temp/SR.fa.ab.cps.nav 12 T > temp/SR.fa.ab.cps.samParser.log', exited with code 256

    Exit Code: 256
    Exception in thread Thread-30:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.aj temp/SR.fa.aj.cps.sam temp/SR.fa.aj.cps.nav 12 T > temp/SR.fa.aj.cps.samParser.log', exited with code 256

    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    Exit Code: 256
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Exception in thread Thread-28:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ah temp/SR.fa.ah.cps.sam temp/SR.fa.ah.cps.nav 12 T > temp/SR.fa.ah.cps.samParser.log', exited with code 256

    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    Exit Code: 256
    Exception in thread Thread-25:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ae temp/SR.fa.ae.cps.sam temp/SR.fa.ae.cps.nav 12 T > temp/SR.fa.ae.cps.samParser.log', exited with code 256

    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Exit Code: 256
    Exception in thread Thread-21:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.aa temp/SR.fa.aa.cps.sam temp/SR.fa.aa.cps.nav 12 T > temp/SR.fa.aa.cps.samParser.log', exited with code 256

    Exit Code: 256
    Exception in thread Thread-23:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ac temp/SR.fa.ac.cps.sam temp/SR.fa.ac.cps.nav 12 T > temp/SR.fa.ac.cps.samParser.log', exited with code 256

    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import multiarray
    import numpy
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    Exit Code: 256
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    Exception in thread Thread-24:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ad temp/SR.fa.ad.cps.sam temp/SR.fa.ad.cps.nav 12 T > temp/SR.fa.ad.cps.samParser.log', exited with code 256

    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    Traceback (most recent call last):
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py", line 6, in <module>
    import numpy.core.numeric as _nx
    import numpy
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>
    import add_newdocs
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    from numpy.lib import add_newdoc
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
    File "/software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module>
    import multiarray
    ImportError: /software/numpy/1.7.1/b1/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyOS_string_to_double
    Exit Code: 256
    Exception in thread Thread-29:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ai temp/SR.fa.ai.cps.sam temp/SR.fa.ai.cps.nav 12 T > temp/SR.fa.ai.cps.samParser.log', exited with code 256

    Exit Code: 256
    Exit Code: 256
    Exception in thread Thread-26:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.af temp/SR.fa.af.cps.sam temp/SR.fa.af.cps.nav 12 T > temp/SR.fa.af.cps.samParser.log', exited with code 256

    Exception in thread Thread-27:
    Traceback (most recent call last):
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
    File "/software/python/2.7.8/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run '/usr/bin/python /gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/samParser.py temp/LR.fa.cps temp/SR.fa.ag temp/SR.fa.ag.cps.sam temp/SR.fa.ag.cps.nav 12 T > temp/SR.fa.ag.cps.samParser.log', exited with code 256

    0:02:13.723077
    ===cat SR.??.cps:===
    0:02:14.437597
    ===cat SR.??.idx:===
    0:02:15.876772
    ===cat SR.??.cps.sam :===
    0:02:22.276569
    ===cat SR.??.cps.nav :===
    cat: temp/SR.fa.aa.cps.nav: No such file or directory
    Traceback (most recent call last):
    File "./bin/runLSC.py", line 532, in <module>
    log_command("cat " + temp_foldername + SR_filename + ext + ".cps.nav" + " >> " + temp_foldername + SR_filename + ".cps.nav", printcommand=False )
    File "/gpfs/fs1/home/bli16/package/LSC_1_beta/example/bin/commonLSC.py", line 13, in log_command
    raise Exception('Failed to run \'' + command + '\', exited with code ' + str(code));
    Exception: Failed to run 'cat temp/SR.fa.aa.cps.nav >> temp/SR.fa.cps.nav', exited with code 256
    Tags: error correction, illumina, lsc, pacbio
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