Traceback (most recent call last):
File "/usr/local/bin/OptiType/OptiTypePipeline.py", line 304, in <module>
table, features = ht.load_hdf(ALLELE_HDF, False, 'table', 'features')
File "/usr/local/bin/OptiType/hlatyper.py", line 88, in load_hdf
to_return = tuple((store[table] for table in args))
File "/usr/local/bin/OptiType/hlatyper.py", line 88, in <genexpr>
to_return = tuple((store[table] for table in args))
File "/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py", line 483, in __getitem__
return self.get(key)
File "/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py", line 671, in get
return self._read_group(group)
File "/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py", line 1349, in _read_group
return s.read(**kwargs)
File "/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py", line 2904, in read
start=_start, stop=_stop)
File "/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py", line 2459, in read_array
ret = node[0][start:stop]
File "/usr/local/lib/python2.7/dist-packages/tables/vlarray.py", line 671, in __getitem__
return self.read(start, stop, step)[0]
File "/usr/local/lib/python2.7/dist-packages/tables/vlarray.py", line 811, in read
listarr = self._read_array(start, stop, step)
File "tables/hdf5extension.pyx", line 2106, in tables.hdf5extension.VLArray._read_array (tables/hdf5extension.c:24649)
ValueError: cannot set WRITEABLE flag to True of this array
Closing remaining open files:/usr/local/bin/OptiType/data/alleles.h5...done
I am using fred2/optitype:release-v1.3.1 and fred2/optitype:latest and getting the same problem. here is my usage:
I am trying your dockers and running into errors:
I am using
fred2/optitype:release-v1.3.1
andfred2/optitype:latest
and getting the same problem. here is my usage:Could you help to solve this issue?