NucleoATAC
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Published
20 hours ago •
GreenleafLab
GreenleafLab
Cython compilation errors, 'CompileError: command 'gcc' failed with exit status 1\n'
I've installed the package with python 2.7.14 as recommend. Using gcc (GCC) 6.2.0
Processing /path/location/NucleoATAC
Requirement already satisfied (use --upgrade to upgrade): NucleoATAC==0.3.2 from file://path/location/NucleoATAC in /path/python-2.7.14/lib/python2.7/site-packages
Requirement already satisfied: cython>=0.22 in /path/python-2.7.14/lib/python2.7/site-packages (from NucleoATAC==0.3.2)
Requirement already satisfied: numpy>=1.9.1 in /path/python-2.7.14/lib/python2.7/site-packages (from NucleoATAC==0.3.2)
Requirement already satisfied: scipy>=0.16.0 in /path/python-2.7.14/lib/python2.7/site-packages (from NucleoATAC==0.3.2)
Requirement already satisfied: pysam>=0.8.1 in /path/python-2.7.14/lib/python2.7/site-packages (from NucleoATAC==0.3.2)
Requirement already satisfied: matplotlib in /path/python-2.7.14/lib/python2.7/site-packages (from NucleoATAC==0.3.2)
Requirement already satisfied: backports.functools-lru-cache in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
Requirement already satisfied: six>=1.10 in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
Requirement already satisfied: pytz in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
Requirement already satisfied: subprocess32 in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
Requirement already satisfied: cycler>=0.10 in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
Requirement already satisfied: python-dateutil>=2.0 in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /path/python-2.7.14/lib/python2.7/site-packages (from matplotlib->NucleoATAC==0.3.2)
The specific versions of the libraries I'm using:
>>> cython.__version__
'0.27.3'
>>> numpy.__version__
'1.14.0'
>>> scipy.__version__
'1.0.0'
>>> pysam.__version__
'0.13'
>>> matplotlib.__version__
'2.1.1'
Here is the error I'm getting. Trouble-shooting ideas?
$ ./python-2.7.14/bin/python ./nucleoatac/run_nuc.py --bed nucleoATAC.bed --bam myfile.bam --fasta ./human_g1k_v37_decoy.decoy.fasta --out NucATAC
Error compiling Cython file:
------------------------------------------------------------
...
#### Import needed modules #####
import pyatac.seq as seq
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignmentFile, AlignedSegment
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:6:0: 'pysam/calignmentfile.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
#### Import needed modules #####
import pyatac.seq as seq
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignmentFile, AlignedSegment
^
------------------------------------------------------------
/path/python2.7/site-packages/pyatac/fragments.pyx:6:0: 'pysam/calignmentfile/AlignmentFile.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
#### Import needed modules #####
import pyatac.seq as seq
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignmentFile, AlignedSegment
^
------------------------------------------------------------
/path/python2.7/site-packages/pyatac/fragments.pyx:6:0: 'pysam/calignmentfile/AlignedSegment.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
import pyatac.seq as seq
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignmentFile, AlignedSegment
from pysam.cfaidx cimport FastaFile
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:7:0: 'pysam/cfaidx.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
import pyatac.seq as seq
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignmentFile, AlignedSegment
from pysam.cfaidx cimport FastaFile
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:7:0: 'pysam/cfaidx/FastaFile.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def makeFragmentMat(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int nrow = upper - lower
cdef int ncol = end - start
cdef np.ndarray[DTYPE_t, ndim=2] mat = np.zeros( (nrow, ncol), dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:21:9: 'AlignmentFile' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
def makeFragmentMat(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int nrow = upper - lower
cdef int ncol = end - start
cdef np.ndarray[DTYPE_t, ndim=2] mat = np.zeros( (nrow, ncol), dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
cdef AlignedSegment read
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:22:9: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getInsertions(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int npos = end - start
cdef np.ndarray[DTYPE_t, ndim=1] mat = np.zeros(npos, dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:46:9: 'AlignmentFile' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getInsertions(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int npos = end - start
cdef np.ndarray[DTYPE_t, ndim=1] mat = np.zeros(npos, dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
cdef AlignedSegment read
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:47:9: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getStrandedInsertions(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int npos = end - start
cdef np.ndarray[DTYPE_t, ndim=1] matplus = np.zeros(npos, dtype = DTYPE)
cdef np.ndarray[DTYPE_t, ndim=1] matminus = np.zeros(npos, dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:75:9: 'AlignmentFile' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
def getStrandedInsertions(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int npos = end - start
cdef np.ndarray[DTYPE_t, ndim=1] matplus = np.zeros(npos, dtype = DTYPE)
cdef np.ndarray[DTYPE_t, ndim=1] matminus = np.zeros(npos, dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
cdef AlignedSegment read
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:76:9: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getAllFragmentSizes(str bamfile, int lower, int upper, int atac = 1):
cdef np.ndarray[DTYPE_t, ndim =1] sizes = np.zeros(upper - lower, dtype= np.float)
# loop over samfile
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:104:9: 'AlignmentFile' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getAllFragmentSizes(str bamfile, int lower, int upper, int atac = 1):
cdef np.ndarray[DTYPE_t, ndim =1] sizes = np.zeros(upper - lower, dtype= np.float)
# loop over samfile
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
cdef AlignedSegment read
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:105:9: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getFragmentSizesFromChunkList(chunks, str bamfile, int lower, int upper, int atac = 1):
cdef np.ndarray[DTYPE_t, ndim =1] sizes = np.zeros(upper - lower, dtype= np.float)
# loop over samfile
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:126:9: 'AlignmentFile' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getFragmentSizesFromChunkList(chunks, str bamfile, int lower, int upper, int atac = 1):
cdef np.ndarray[DTYPE_t, ndim =1] sizes = np.zeros(upper - lower, dtype= np.float)
# loop over samfile
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
cdef AlignedSegment read
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:127:9: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def makeFragmentMat(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int nrow = upper - lower
cdef int ncol = end - start
cdef np.ndarray[DTYPE_t, ndim=2] mat = np.zeros( (nrow, ncol), dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:21:35: 'AlignmentFile' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getInsertions(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int npos = end - start
cdef np.ndarray[DTYPE_t, ndim=1] mat = np.zeros(npos, dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:46:35: 'AlignmentFile' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getStrandedInsertions(str bamfile, str chrom, int start, int end, int lower, int upper, int atac = 1):
cdef int npos = end - start
cdef np.ndarray[DTYPE_t, ndim=1] matplus = np.zeros(npos, dtype = DTYPE)
cdef np.ndarray[DTYPE_t, ndim=1] matminus = np.zeros(npos, dtype = DTYPE)
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:75:35: 'AlignmentFile' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getAllFragmentSizes(str bamfile, int lower, int upper, int atac = 1):
cdef np.ndarray[DTYPE_t, ndim =1] sizes = np.zeros(upper - lower, dtype= np.float)
# loop over samfile
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:104:35: 'AlignmentFile' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
@cython.boundscheck(False)
def getFragmentSizesFromChunkList(chunks, str bamfile, int lower, int upper, int atac = 1):
cdef np.ndarray[DTYPE_t, ndim =1] sizes = np.zeros(upper - lower, dtype= np.float)
# loop over samfile
cdef AlignmentFile bamHandle = AlignmentFile(bamfile)
^
------------------------------------------------------------
/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragments.pyx:126:35: 'AlignmentFile' is not a constant, variable or function identifier
/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
#error Do not use this file, it is the result of a failed Cython compilation.
^~~~~
Traceback (most recent call last):
File "./nucleoatac/run_nuc.py", line 17, in <module>
from nucleoatac.NucleosomeCalling import NucChunk, NucParameters
File "/path/python-2.7.14/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py", line 13, in <module>
from nucleoatac.Occupancy import OccupancyTrack
File "/path/python-2.7.14/lib/python2.7/site-packages/nucleoatac/Occupancy.py", line 12, in <module>
from pyatac.fragmentsizes import FragmentSizes
File "/path/python-2.7.14/lib/python2.7/site-packages/pyatac/fragmentsizes.py", line 10, in <module>
from pyatac.fragments import getAllFragmentSizes, getFragmentSizesFromChunkList
File "/path/python-2.7.14/lib/python2.7/site-packages/pyximport/pyximport.py", line 458, in load_module
language_level=self.language_level)
File "/path/python-2.7.14/lib/python2.7/site-packages/pyximport/pyximport.py", line 233, in load_module
exec("raise exc, None, tb", {'exc': exc, 'tb': tb})
File "/path/python-2.7.14/lib/python2.7/site-packages/pyximport/pyximport.py", line 215, in load_module
inplace=build_inplace, language_level=language_level)
File "/path/python-2.7.14/lib/python2.7/site-packages/pyximport/pyximport.py", line 191, in build_module
reload_support=pyxargs.reload_support)
File "/path/python-2.7.14/lib/python2.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "/path/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/path/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/path/python-2.7.14/lib/python2.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
_build_ext.build_ext.run(self)
File "/path/python2.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/path/python-2.7.14/lib/python2.7/site-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions
self.build_extension(ext)
File "/path/python2.7/distutils/command/build_ext.py", line 499, in build_extension
depends=ext.depends)
File "/path/python2.7/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/path/python2.7/distutils/unixccompiler.py", line 124, in _compile
raise CompileError, msg
ImportError: Building module pyatac.fragments failed: ["CompileError: command 'gcc' failed with exit status 1\n"]
I suspect one solution is to roll back dependencies to earlier versions, but the above is a bit odd
Sorry I don't really have much to offer in way of guidance or suggestions. It seems like the issue would be with pysam, so rolling back the version there would be first thing to try.
We were able to correct the module issue by cleaning up PYTHONPATH Tested the example workflow with pysam version 0.13
Python 2.7.14 (default, Dec 4 2017, 10:25:20)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>> pysam.__version__
'0.13'
Command run: bin/nucleoatac run --bed example/example.bed --bam example/example.bam --fasta example/sacCer3.fa --out testing/anotherTest
nucleoatac version 0.3.4
start run at: 2018-01-29 16:06
---------Step1: Computing Occupancy and Nucleosomal Insert Distribution---------
Making figure
---------Step2: Processing Vplot------------------------------------------------
---------Step3: Obtaining nucleosome signal and calling positions---------------
---------Step4: Making combined nucleosome position map ------------------------
---------Step5: Calling NFR positions-------------------------------------------
end run at: 2018-01-29 16:07
@Toseph
Tested the example workflow with pysam version 0.13
Excellent, thanks!