How to use the error report in python mcscan operation
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Python mcscan running error report
The python version of mcscan analysis ends up drawing collinear graphics with the following error:
Run the command as follows:
/ biosoft/miniconda/miniconda2/bin/python-m jcvi.graphics.karyotype-- format=pdf-- figsize=15x5 mcscan_seqid mcscan_layout
The error message is as follows:
Ms.boundary' 'scipy.spatial.kdtree'] 12:29:39 [_ _ init__] CACHEDIR=/home/manager/.cache/matplotlib12:29:39 [font_manager] Using fontManager instance from / home/manager/.cache/matplotlib/fontList.json12:29:40 [_ _ init__] backend agg version v2.212 Load file `mcscan_ layout`12: 29:40 [base] Load file `HVI.bed`12: 29:41 [base] Load file `OSI.bed`Traceback (most recent call last): File " / biosoft/miniconda/miniconda2/lib/python2.7/runpy.py " Line 174, in_ run_module_as_main "_ main__", fname, loader, pkg_name) File "/ biosoft/miniconda/miniconda2/lib/python2.7/runpy.py", line 72, in_ run_code exec code in run_globals File "/ biosoft/miniconda/miniconda2/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 330, in main () File "/ biosoft/miniconda/miniconda2/lib/python2.7/site-packages/jcvi/graphics/karyotype.py" Line 318, in main Karyotype (fig, root, seqidsfile, layoutfile) File "/ biosoft/miniconda/miniconda2/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 269, in _ init__ layout = Layout (layoutfile, generank=generank) File "/ biosoft/miniconda/miniconda2/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 87 In _ _ init__ self.assign_colors () File "/ biosoft/miniconda/miniconda2/lib/python2.7/site-packages/jcvi/graphics/base.py", line 97, in assign_colors self.assign_array ("color", colorset) File "/ biosoft/miniconda/miniconda2/lib/python2.7/site-packages/jcvi/graphics/base.py", line 91, in assign_array if not getattr (x, attrib): AttributeError: 'LayoutLine' object has no attribute' color'
This is because there is an extra blank line in the second configuration file as follows, and the deletion of the blank line runs successfully; so there are no blank lines in the end.
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