Error in conifer.py call: ValueError: Unknown keyword argument 'copy_args'

[Manuel Solís Moruno]

Hi,

I'm using CoNIFER v0.2.2 with Python 2.7.13, PyTables 2.4.0 and PySam 0.8.3.
I managed to create the RPKM files for my 5 samples and I also created the corresponding files using the command analyze. Here you have what I executed:

python $conifer rpkm --probes $probes --input $input/BQSR_S${i}.bam --output $input/BQSR_S${i}.rpkm.txt

mv $input/BQSR_S${i}.rpkm.txt $RPKMs

python $conifer analyze --probes $probes --rpkm_dir $RPKMs --output $results/analysis_BQSR_S${i}.hdf5 --svd 4 --write_svals $results/singular_values_BQSR_S${i}.txt --plot_scree $results/screenplot_BQSR_S${i}.png --write_sd $results/sd_values_BQSR_S${i}.txt

The thing is tthat, at that point, the files are created properly, but I see some things I don't like in the output file. For instance, you have here some lines:

/homes/users/msolis/scratch/bin/conifer_v0.2.2/conifer.py:157: VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0; dimension is 21679 but corresponding boolean dimension is 21678
  probeIDs = np.array(map(operator.itemgetter("probeID"),chr_probes))[probe_mask]
/homes/users/msolis/scratch/bin/conifer_v0.2.2/conifer.py:158: VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0; dimension is 21679 but corresponding boolean dimension is 21678
  probe_starts = np.array(map(operator.itemgetter("start"),chr_probes))[probe_mask]
/homes/users/msolis/scratch/bin/conifer_v0.2.2/conifer.py:159: VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0; dimension is 21679 but corresponding boolean dimension is 21678
  probe_stops = np.array(map(operator.itemgetter("stop"),chr_probes))[probe_mask]
/homes/users/msolis/scratch/bin/conifer_v0.2.2/conifer.py:160: VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0; dimension is 21679 but corresponding boolean dimension is 21678
  gene_names =  np.array(map(operator.itemgetter("name"),chr_probes))[probe_mask]
/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/tables/path.py:98: NaturalNameWarning: object name is not a valid Python identifier: 'sample_BQSR_S2.rpkm'; it does not match the pattern ``^[a-zA-Z_]
  NaturalNameWarning )
/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/tables/path.py:98: NaturalNameWarning: object name is not a valid Python identifier: 'sample_BQSR_S15-487.rpkm'; it does not match the pattern ``^[a-z
  NaturalNameWarning )

But the error comes when I try to actually call CNVs. This is my command:

python $conifer call --input $results/analysis_BQSR_S${i}.hdf5 --output $results/call_BQSR_S${i}.txt

And here you see the error:

Traceback (most recent call last):
File "/homes/users/msolis/scratch/bin/conifer_v0.2.2/conifer.py", line 683, in <module>
args.func(args)
File "/homes/users/msolis/scratch/bin/conifer_v0.2.2/conifer.py", line 344, in CF_call
data = r.getExonValuesByRegion(chr)
File "/gpfs42/robbyfs/scratch/lab_genresearch/msolis/bin/conifer_v0.2.2/conifer_functions.py", line 304, in getExonValuesByRegion
table_rows = probe_tbl.getWhereList('(start >= 0) & (stop <= 1000000000)')
File "/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/tables/table.py", line 1509, in getWhereList
self._where(condition, condvars, start, stop, step) ]
File "/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/tables/table.py", line 1405, in _where
compiled = self._compileCondition(condition, condvars)
File "/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/tables/table.py", line 1284, in _compileCondition
compiled = compile_condition(condition, typemap, indexedcols, copycols)
File "/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/tables/conditions.py", line 396, in compile_condition
func = NumExpr(expr, signature, copy_args=copycols)
File "/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/numexpr/necompiler.py", line 625, in NumExpr
context = getContext(kwargs, frame_depth=1)
File "/homes/aplic/noarch/software/Python/2.7.13-foss-2017a/lib/python2.7/site-packages/numexpr/necompiler.py", line 545, in getContext
raise ValueError("Unknown keyword argument '%s'" % d.popitem()[0])
ValueError: Unknown keyword argument 'copy_args'
Closing remaining open files: /homes/users/msolis/scratch/fam/results/analysis_BQSR_S5.hdf5... done

Has anyone had the same problem? Any solution?

Thank you so much in advance,

Manolo.

[Krithika]

Hi, I too have the same issue. I get the same error when I try to actually call CNVs. The previous steps worked fine. Were you able to find a solution to this issue?

Thanks
Krithika