nucleoatac not running

[da-bar]

Hello,

it seems I have a problem with running NucleoATAC. It seems that there is some problem with pysam and compilation of pyatac. We have pysam-0.11.2.2 and cython-0.26.1 installed. Here is the error message I get:

nucleoatac version 0.3.4
start run at: 2017-10-16 19:09
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /mnt/biggley/home/damir/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:485:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^~~~~~~
In file included from /mnt/biggley/home/damir/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:492:0:
/usr/lib/python2.7/dist-packages/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^~~
In file included from /usr/include/python2.7/Python.h:78:0,
                 from /mnt/biggley/home/damir/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:4:
/mnt/biggley/home/damir/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
/mnt/biggley/home/damir/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:2267:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
Traceback (most recent call last):
  File "/usr/local/bin/nucleoatac", line 33, in <module>
    nucleoatac_main(args)
  File "/usr/local/lib/python2.7/dist-packages/nucleoatac/cli.py", line 50, in nucleoatac_main
    from nucleoatac.run_occ import run_occ
  File "/usr/local/lib/python2.7/dist-packages/nucleoatac/run_occ.py", line 19, in <module>
    from nucleoatac.Occupancy import FragmentMixDistribution, OccupancyParameters, OccChunk
  File "/usr/local/lib/python2.7/dist-packages/nucleoatac/Occupancy.py", line 12, in <module>
    from pyatac.fragmentsizes import FragmentSizes
  File "/usr/local/lib/python2.7/dist-packages/pyatac/fragmentsizes.py", line 10, in <module>
    from pyatac.fragments import getAllFragmentSizes, getFragmentSizesFromChunkList
  File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 458, in load_module
    language_level=self.language_level)
  File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 233, in load_module
    exec("raise exc, None, tb", {'exc': exc, 'tb': tb})
  File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 216, in load_module
    mod = imp.load_dynamic(name, so_path)
  File "libcfaidx.pxd", line 51, in init pyatac.fragments
ImportError: Building module pyatac.fragments failed: ["AttributeError: 'module' object has no attribute 'FastxRecord'\n"]

Thank you for the answer in advance. Best regards, Damir