So I imported Illumina miseq reads using the manifest function. I read several prior posts suggesting that I did not need to perform demultiplexing on this type of input so I proceeded to try demux summarize and am getting the error message pasted below. I am currently using qiime2-2021.4, any help in resolving this would be greatly appreciated.
(qiime2-2021.4) $ qiime demux summarize --i-data paired-end-demux.qza --o-visualization demux.qzv
Plugin error from demux:
type object 'object' has no attribute 'dtype'
Debug info has been saved to /tmp/qiime2-q2cli-err-ec1sbort.log
Whether you need to demultiplex or not depends on the data provided to you by your sequencing center. What are your files from them called/look like? Can you paste the command that you used to import here? Did you receive any errors when running your qiime tools import command?
The files are fastq files straight off the miseq, though it was set to automatically trim the illumina adapters, files are named in the S1_L001_R1_001.fastq.gz, S1_L001_R2.fastq.gz format. My import command is pasted below, and the sequences read in with no errors.
Full error log is pasted below, any assistance is greatly appreciated:
Traceback (most recent call last):
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in summarize
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 452, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_demux/_summarize/_visualizer.py", line 105, in summarize
'result_data': pd.DataFrame(, columns=summary_columns),
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/core/frame.py", line 466, in init
mgr = init_dict({}, index, columns, dtype=dtype)
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 242, in init_dict
val = construct_1d_arraylike_from_scalar(np.nan, len(index), nan_dtype)
File "/home/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pandas/core/dtypes/cast.py", line 1221, in construct_1d_arraylike_from_scalar
dtype = dtype.dtype
AttributeError: type object 'object' has no attribute 'dtype'
After looking into this more, it looks like this is due to a bug in the version of Pandas used in this version of QIIME 2. I think the fastest and easiest way to handle this would be to update to a newer release of QIIME 2 using the instructions found on this page.
I created a separate environment with the newer version of QIIME 2 and there was no error for this function. I'll get rid of the old version and use the new one going forward, thank you very much for the help.