I have an artifact that I would like to summarize using
demux summarize. It is of the following type:
> qiime tools peek qiime2/fastq.qza
Data format: SingleLanePerSamplePairedEndFastqDirFmt
I try to summarize it as follows, but get an error:
> qiime demux summarize --i-data qiime2/fastq.qza --o-visualization qiime2/fastq-summary.qzv --verbose
Plugin error from demux:
[Errno 2] No such file or directory: '/var/folders/3s/cq8_0h3j2bd3fmc73f9yh6fh0000gn/T/qiime2-archive-khh1lljw/9035bc99-9a6f-4b24-8aba-ccf90d7ac882/data/SRR5080238_1_L001_R1_001.fastq.gz'
I’m using Qiime2 2018.2.0 (demux 2018.2.0) on Mac OS X 10.13.3.
Sorry for the delayed response, and thank you so much for that info, that is exactly what I would have asked for!
As for what’s going on, I’m not really certain. If you were to run:
qiime tools extract qiime2/fastq.qza --output-dir check-fastq-qza-internals/
and then run:
# the -R flag will make it recursive
ls -R check-fastq-qza-internals/
what output do you see?
I’m wondering if the data is really missing, or if perhaps something cleared out your temporary directory.
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