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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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plot-vcfstats non-zero status 256 #624

Closed price333 closed 7 years ago

price333 commented 7 years ago

Hi,

I'm getting the following error running plot-vcfstats:

Plotting graphs: python plot.py Traceback (most recent call last): File "plot.py", line 219, in for i in range(n): col[i] = cm(1.*i/n) TypeError: 'range' object does not support item assignment The command exited with non-zero status 256: python plot.py

at /data/user/bin/plot-vcfstats line 76.

Any help would be greatly appreciated!

pd3 commented 7 years ago

Interesting error. Would you mind sharing the generated plot.py script? There is an email address on my profile page.

Also what version of python and matplotlib is this?

        python --version
        python 
        >>> import matplotlib
        >>> matplotlib.__version__
        '1.4.3'
price333 commented 7 years ago

Thank you for your reply. So I tried again with Python version 2.7.13 (matplotlib 2.0.2+4197.geb6e422ff) and get the following error:

Plotting graphs: python plot.py Traceback (most recent call last): File "plot.py", line 262, in ax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y') File "/data/borne/virtualenv/test/lib/python2.7/site-packages/matplotlib-2.0.2+4197.geb6e422ff-py2.7-linux-x86_64.egg/matplotlib/axes/_base.py", line 2610, in ticklabel_format "This method only works with the ScalarFormatter.") AttributeError: This method only works with the ScalarFormatter. The command exited with non-zero status 256: python plot.py

at /data/user/bin/plot-vcfstats line 76. main::error("The command exited with non-zero status 256:\x{a}\x{9}python plot.py\x{a}\x{a}") called at /data/user/bin/plot-vcfstats line 276 main::plot(HASH(0x22c0e70)) called at /data/user/bin/plot-vcfstats line 65

The previous error I posted was Python version 3.5.2 (matplotlib 2.0.2+4197.geb6e422ff). I'll email you both plot.py files now.

pd3 commented 7 years ago

Thank you for sharing the data. I can now confirm this is an issue with matplotlib differences between versions.

Editing the script like this might help (I don't have 2.x installed anywhere so cannot try it myself at this moment): http://matplotlib.1069221.n5.nabble.com/How-do-you-use-ticklabel-format-td11642.html

Alternatively, as a quick workaround you could comment out offending lines.