Python: function get_cmscan_gff3_task.cmd
TaskError - taskid:cmscan-gff3:Trinity.fasta.x.rfam.gff3
PythonAction Error
Traceback (most recent call last):
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/doit/action.py", line 424, in execute
returned_value = self.py_callable(*self.args, *kwargs)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/tasks/gff.py", line 178, in cmd
for group in InfernalParser(input_filename):
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/fileio/infernal.py", line 67, in iter
yield self._build_df(data)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/fileio/infernal.py", line 73, in _build_df
convert_dtypes(df, dict(self.columns))
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/dammit/fileio/base.py", line 45, in convert_dtypes
df[c] = df[c].astype(dtypes[c])
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/util/_decorators.py", line 178, in wrapper
return func(args, kwargs)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/core/generic.py", line 5001, in astype
kwargs)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/core/internals.py", line 3714, in astype
return self.apply('astype', dtype=dtype, kwargs)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/core/internals.py", line 3581, in apply
applied = getattr(b, f)(kwargs)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/core/internals.py", line 575, in astype
**kwargs)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/core/internals.py", line 664, in _astype
values = astype_nansafe(values.ravel(), dtype, copy=True)
File "/home/mashanovlab/miniconda3/envs/dammit/lib/python3.6/site-packages/pandas/core/dtypes/cast.py", line 709, in astype_nansafe
return lib.astype_intsafe(arr.ravel(), dtype).reshape(arr.shape)
File "pandas/_libs/lib.pyx", line 456, in pandas._libs.lib.astype_intsafe
File "pandas/_libs/src/util.pxd", line 142, in util.set_value_at_unsafe
ValueError: invalid literal for int() with base 10: 'query'
Hi dammit fails at the cmscan-gff3 step. Any help is greatly appreciated. Below is the error message. Thanks.
rm -f /home/mashanovlab/Ob_NotchInhibitionDAPT_RNAseq/Dammit/Trinity.fasta.dammit/Trinity.fasta.x.rfam.gff3######################################## TaskError - taskid:cmscan-gff3:Trinity.fasta.x.rfam.gff3 cmscan-gff3:Trinity.fasta.x.rfam.gff3:
cmscan-gff3:Trinity.fasta.x.rfam.gff3: