Automatic File Extension Appended in q2cli

I am having the same type of problem on my mac. I was able to run

qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path /Users/Paige/qiime2-waf-test1/wafseq \
  --source-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path /Users/Paige/qiime2-waf-test1/demux.gza

and it made the file but called it demux.gza.gza for some reason. I can see it when I use ls but no matter what (including renaming) when I try and run

qiime demux summarize \
  --i-data /Users/Paige/qiime2-waf-test1/demux.gza.gza
  --o-visualization /Users/Paige/qiime2-waf-test1/demux.qzv

I get the same error - raise ValueError("%s does not exist." % filepath)

Please help. I already had to go through a huge problem with qiime2 not using the newer version of python that I had installed before I ever installed qiime2.

Hi @Paige_M_Miller!

The QIIME 2 CLI automatically appends .qza to a filename, if it doesn’t see that already specified in an output. In your import example above, you named your file demux.gza — QIIME 2 saw .gza (note, that is a “G”, not a “Q”), and appended .qza to the file. So then you wound up with demux.gza.qza (first there is a “G”, then a “Q”). From here, it looks like you accidentally specified demux.gza.gza (a “G” followed by a “G”) in your summarize command. QIIME 2 is upset because it cant find a file named demux.gza.gza, which makes sense, because the file is actually demux.gza.qza. Wow, my brain feels fuzzy after running through that. Long story short, “g” and “q” look pretty similar!

I would recommend double checking all of your filenames and trying again. Alternatively, update your summarize command to:

qiime demux summarize \
  --i-data /Users/Paige/qiime2-waf-test1/demux.gza.qza
  --o-visualization /Users/Paige/qiime2-waf-test1/demux.qzv

Hmm, something sounds very strange there — we don’t require Python as a native installation prereq, only miniconda, which comes with its own Python installation. Maybe you installed the Python 2.7 edition of Miniconda on accident? When you install QIIME 2 natively, it installs it’s own Python distribution at the same time, so it should be pretty seamless (and that has generally been our experience working with folks here on the forum and at our QIIME 2 workshops). If you still are having issues installing QIIME 2 please open a new thread here and the forum and we can help work through the problems with you!

Keep us posted! :t_rex:


Just wanted to note that both Miniconda2 and Miniconda3 should work for installing QIIME 2 (Miniconda3 is only necessary for devs building QIIME 2 conda packages).


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