wasade
commented
6 years ago Hi @rderelle, this issue was fixed in the recent Deblur v1.1.0 release
Closed rderelle closed 6 years ago
wasade
commented
6 years ago Hi @rderelle, this issue was fixed in the recent Deblur v1.1.0 release
Hi,
I'm getting an error message when trying to use Deblur to denoise multiple fasta files on a Mac laptop.
My command line is: deblur workflow --seqs-fp all_fasta.fas --output-dir aaa -t 150
The file all_fasta.fas contains all fasta sequences in qiime2 format. Delblur successfully splits the file into samples, denoise each sample but fails at the end to generate the biom file.
The error message in my terminal is: Traceback (most recent call last): File "/Users/xxx/miniconda3/bin/deblur", line 684, in
deblur_cmds()
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(args, kwargs)
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(args, **kwargs)
File "/Users/xxx/miniconda3/bin/deblur", line 655, in workflow
outputfasta_fp=outputfasta_fp, minreads=min_reads)
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/deblur/workflow.py", line 705, in create_otu_table
obs = scipy.sparse.dok_matrix((1E9, len(deblurred_list)), dtype=np.double)
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/scipy/sparse/dok.py", line 88, in init
self._shape = check_shape((M, N))
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/scipy/sparse/sputils.py", line 281, in check_shape
new_shape = tuple(operator.index(arg) for arg in args)
File "/Users/xxx/miniconda3/lib/python3.5/site-packages/scipy/sparse/sputils.py", line 281, in
new_shape = tuple(operator.index(arg) for arg in args)
TypeError: 'float' object cannot be interpreted as an integer
Do you know what could be wrong (with my data or my Deblur installation) ?
many thanks Romain