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schneebergerlab / fixchr

MIT License
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Installation error #1

Closed aaannaw closed 5 months ago

aaannaw commented 1 year ago

When I install the software running "python setup.py install", the error occurs: Traceback`(most recent call last):

File "/data/01/user157/software/fixchr/setup.py", line 18, in <module>
    long_description=open('README.rst').read(),
FileNotFoundError: [Errno 2] No such file or directory: 'README.rst'

I can not find the file "README.rst". Could you give me any suggestions?

aaannaw commented 1 year ago

I modify the "README.rst" to "README.md" in the setup.py. It successfuly! I can run the ./fixchr -h" . But when I run "/data/01/user157/software/fixchr/bin/dotplot -o 05.1.fixchr -c 03.A-B.coord -F T -r 00.A.Chr.2210.fasta -q 00.B.Chr.2210.fasta -o 05.1.pdf" to draw the plot, I got the error:

Traceback (most recent call last):
  File "/data/01/user157/software/fixchr/bin/dotplot", line 6, in <module>
    main(sys.argv[1:])
  File "/data/00/user/user157/miniconda3/lib/python3.9/site-packages/fixchr-0.1-py3.9.egg/fixchr/scripts/dotplot.py", line 185, in main
  File "/data/00/user/user157/miniconda3/lib/python3.9/site-packages/fixchr-0.1-py3.9.egg/fixchr/scripts/dotplot.py", line 156, in dotplot
  File "/data/00/user/user157/miniconda3/lib/python3.9/site-packages/fixchr-0.1-py3.9.egg/fixchr/scripts/func.py", line 448, in readcoords
  File "/data/00/user/user157/miniconda3/lib/python3.9/site-packages/pandas/core/generic.py", line 5478, in __setattr__
    return object.__setattr__(self, name, value)
  File "pandas/_libs/properties.pyx", line 66, in pandas._libs.properties.AxisProperty.__set__
  File "/data/00/user/user157/miniconda3/lib/python3.9/site-packages/pandas/core/generic.py", line 670, in _set_axis
    self._mgr.set_axis(axis, labels)
  File "/data/00/user/user157/miniconda3/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 220, in set_axis
    raise ValueError(
ValueError: Length mismatch: Expected axis has 11 elements, new values have 12 elements

I guess it is due to my coord file. Because the--maxmatch parameter costs too much memory. I run the following command to get the coors file: nucmer --mum --mincluster 500 -t 30 01.AonlyChr.fasta 01.B.onlyChr.fasta -p 02.A-B; /data/01/user157/software/MUMmer/mummer-4.0.0rc1/bin/delta-filter -m -i 90 -l 100 02.A-B.delta> 03.A-B.filter.delta;/data/01/user157/software/MUMmer/mummer-4.0.0rc1/bin/show-coords -THrd 02.A-B.delta > 03.A-B.coord. Does the deletion of the--maxmatch parameter have influence to syri identify SVs? And about the above error, could you give me any suggestions? Looking forward with your reply!