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TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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No module named 'PIL' #170

Open theo-allnutt-bioinformatics opened 1 year ago

theo-allnutt-bioinformatics commented 1 year ago

Installing pil / pillow / image, made no difference to this error.

kat hist -m27 test.fastq Kmer Analysis Toolkit (KAT) V2.4.2

Running KAT in HIST mode

Input 1 is a sequence file. Counting kmers for input 1 (test.fastq) ... done. Time taken: 6.7s

Bining kmers ... done. Time taken: 2.2s

Merging counts ... done. Time taken: 0.0s

Saving results to disk ... done. Time taken: 0.0s

Creating plot ...Traceback (most recent call last): File "//g/data/if89/apps/kat/2.4.2/share/kat/scripts/kat/plot/spectra_hist.py", line 6, in from misc import * File "/g/data/if89/apps/kat/2.4.2/share/kat/scripts/kat/plot/misc.py", line 2, in import matplotlib File "/home/554/ta0341/.local/lib/python3.9/site-packages/matplotlib/init.py", line 113, in from . import _api, _version, cbook, _docstring, rcsetup File "/home/554/ta0341/.local/lib/python3.9/site-packages/matplotlib/rcsetup.py", line 27, in from matplotlib.colors import Colormap, is_color_like File "/home/554/ta0341/.local/lib/python3.9/site-packages/matplotlib/colors.py", line 51, in from PIL import Image ModuleNotFoundError: No module named 'PIL'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "//g/data/if89/apps/kat/2.4.2/share/kat/scripts/kat/plot/spectra_hist.py", line 8, in from kat.plot.misc import * File "//g/data/if89/apps/kat/2.4.2/share/kat/scripts/kat/plot/misc.py", line 2, in import matplotlib File "/home/554/ta0341/.local/lib/python3.9/site-packages/matplotlib/init.py", line 113, in from . import _api, _version, cbook, _docstring, rcsetup File "/home/554/ta0341/.local/lib/python3.9/site-packages/matplotlib/rcsetup.py", line 27, in from matplotlib.colors import Colormap, is_color_like File "/home/554/ta0341/.local/lib/python3.9/site-packages/matplotlib/colors.py", line 51, in from PIL import Image ModuleNotFoundError: No module named 'PIL' Time taken: 0.3s

KAT HIST completed. Total runtime: 9.3s

../lib/include/kat/pyhelper.hpp(158): Throw in function void kat::PyHelper::execute(std::string, int, char*) Dynamic exception type: boost::exception_detail::clone_impl std::exception::what: std::exception [kat::KatPythonError] = Unexpected python error