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
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