Running mapping

[Acribbs]

When trying to run the help for mapping I get the following error, any suggestions?

cgatflow mapping --help
Traceback (most recent call last):
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/bin/cgatflow", line 11, in <module>
    load_entry_point('CGATPipelines', 'console_scripts', 'cgatflow')()
  File "/ifs/projects/adam/cgat-developers-v1/cgat-flow/CGATPipelines/cgatflow.py", line 86, in main
    module = imp.load_module(pipeline, file, pathname, description)
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/ifs/projects/adam/cgat-developers-v1/cgat-flow/CGATPipelines/pipeline_mapping.py", line 219, in <module>
    import CGATPipelines.PipelineWindows as PipelineWindows
  File "/ifs/projects/adam/cgat-developers-v1/cgat-flow/CGATPipelines/PipelineWindows.py", line 28, in <module>
    import CGAT.Expression as Expression
  File "/ifs/projects/adam/cgat-developers-v1/cgat-apps/CGAT/Expression.py", line 57, in <module>
    import ggplot
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/__init__.py", line 21, in <module>
    from .qplot import qplot
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/qplot.py", line 6, in <module>
    from .geoms import geom_point, geom_bar, geom_boxplot, geom_histogram, geom_line
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/geoms/__init__.py", line 4, in <module>
    from .geom_abline import geom_abline
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/geoms/geom_abline.py", line 6, in <module>
    from .geom import geom
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/geoms/geom.py", line 10, in <module>
    import ggplot.stats
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/stats/__init__.py", line 7, in <module>
    from .stat_density import stat_density
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ggplot/stats/stat_density.py", line 5, in <module>
    from scipy.stats import gaussian_kde
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/stats/__init__.py", line 345, in <module>
    from .stats import *
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/stats/stats.py", line 171, in <module>
    from . import distributions
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/stats/distributions.py", line 10, in <module>
    from ._distn_infrastructure import (entropy, rv_discrete, rv_continuous,
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py", line 16, in <module>
    from scipy.misc import doccer
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/misc/__init__.py", line 68, in <module>
    from scipy.interpolate._pade import pade as _pade
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/interpolate/__init__.py", line 175, in <module>
    from .interpolate import *
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/interpolate/interpolate.py", line 32, in <module>
    from .interpnd import _ndim_coords_from_arrays
  File "interpnd.pyx", line 1, in init scipy.interpolate.interpnd
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/spatial/__init__.py", line 94, in <module>
    from .kdtree import *
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/spatial/kdtree.py", line 8, in <module>
    import scipy.sparse
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/sparse/__init__.py", line 229, in <module>
    from .csr import *
  File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/sparse/csr.py", line 15, in <module>
    from ._sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
ImportError: /ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/matplotlib/../../../libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/scipy/sparse/_sparsetools.cpython-36m-x86_64-linux-gnu.so)

[sebastian-luna-valero]

Hi Adam,

Can you please paste the output of conda list scipy?

Best regards, Sebastian

[Acribbs]

It seems I dont have script installed. Should I give it a go? Only one version is available, v1.1.0

[Acribbs]

Installation of scipy worked. Thanks for your help @sebastian-luna-valero