Hi,
I am experiencing an error with a new dataset I just received and I don’t understand how to fix it. I can import and run the demultiplexing steps, but when I try to summarize the demultiplexing I get an error.
Debug info has been saved to /var/folders/kk/ppfc6f0x2v36xxkd7lpln88w0000gn/T/qiime2-q2cli-err-qu75omdf.log
Is there a standard reason for this error to occur? I can seem to figure out how to file where the debug info has been saved so if there is any guidance on that I’d be happy to provide it.
I re-ran with the --verbose and here are the details:
(qiime2-2018.6) eduroam121-33:16s_july26_Run Molly-Mac$ qiime demux summarize --i-data /Users/Molly-Mac/My_FILES/16s_july26_Run/Demulti_SmPro_PlasmidTrial_sequences.qza --o-visualization Dmultivis_SmPr_PlasmidTrial.qzv --verbose
Traceback (most recent call last):
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in summarize
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 429, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_demux/_summarize/_visualizer.py”, line 121, in summarize
lambda x: os.path.join(str(data), x))
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/pandas/core/series.py”, line 3194, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File “pandas/_libs/src/inference.pyx”, line 1472, in pandas._libs.lib.map_infer
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_demux/_summarize/_visualizer.py”, line 121, in
lambda x: os.path.join(str(data), x))
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/posixpath.py”, line 89, in join
genericpath._check_arg_types(‘join’, a, *p)
File “/Users/Molly-Mac/miniconda2/envs/qiime2-2018.6/lib/python3.5/genericpath.py”, line 143, in _check_arg_types
(funcname, s.class.name)) from None
TypeError: join() argument must be str or bytes, not ‘float’
Hmm, this sounds like something funky is happening with your Sample IDs in this viz. Can you give us a sampling of a few Sample IDs in your metadata file? I suspect you just found a bug in this viz, this info will help confirm. Thanks!
Thanks @Molly_Bletz - all looks good there - can you share Demulti_SmPro_PlasmidTrial_sequences3.qza? If not, can you run qiime tools export on it, run ls -lah on the output dir and provide those results here? Also, there will be a file in the dir called ‘MANIFEST’, please attach here, too (again, only if you can’t share the qza)/ Feel free to DM a link to me if you don’t want to post publicly. Thanks!
Thanks for sharing @Molly_Bletz! You found a bug! I opened up an issue here. This was caused by a # in a Sample ID (SmProDNA.Va#2Control). If you update your sample metadata to remove that # and re-run demux emp-single again, that will strip the # from the ID, then you should be good to go. Sorry, that is a bummer because it looks like it took about 80 min to demux the first time, but, this should get you moving. Keep us posted!
Thanks @thermokarst Worked like a charm after removing that #. I usually remove those kinds of characters from the SampleIDs, but must have missed that one. Thanks again!
I opened up an 
Thanks again!