Hey everyone, I am new to Qiime2 and am having problems with converting a qza to qzv file.
Here are the commands and errors in ubuntu:
qiime feature-table summarize \
--i-table skin_table.qza \
(1/1) Invalid value for '--o-visualization': '' is not a writable directory,
cannot write output to it.
I am not too sure on how to go forward with this.
Welcome to the forum!
Everything looks correct with your command and the formatting for your output file - what this tells me is that this may be a permissions issue in your current working directory. How are you running QIIME 2? On your personal computer? Through a virtual machine?
Additionally, can you please run the following command in your terminal and copy/paste the entire output in your response?
This will list out all of the permissions in your current working directory. Thanks!
Hi @lizgehret, I'm running QIIME 2 on my personal computer.
The entire output is :
dr-xr-xr-x 1 rubinij rubinij 512 Aug 3 18:05 .
dr-xr-xr-x 1 rubinij rubinij 512 Aug 5 16:35 ..
-r-xr-xr-x 1 rubinij rubinij 6148 Aug 3 18:05 .DS_Store
-r-xr-xr-x 1 rubinij rubinij 452277 Aug 3 18:05 85_otu_taxonomy.txt
-r-xr-xr-x 1 rubinij rubinij 7324324 Aug 3 18:05 85_otus.fasta
-r-xr-xr-x 1 rubinij rubinij 1742321 Aug 3 18:05 85_otus.qza
-r-xr-xr-x 1 rubinij rubinij 8280844 Aug 3 18:05 'Lab_skin 1.docx'
-r-xr-xr-x 1 rubinij rubinij 2331650 Aug 3 18:05 classifier.qza
-r-xr-xr-x 1 rubinij rubinij 1599346 Aug 3 18:05 representative_sequences.qza
-r-xr-xr-x 1 rubinij rubinij 4898 Aug 3 18:05 skin_metadata.txt
-r-xr-xr-x 1 rubinij rubinij 464121 Aug 3 18:05 skin_table.qza
Thanks for helping me out!!
Thanks for sharing that output! It looks like you don't have write permissions in any of these listed directories - which is why you received the
not a writable directory error. Since this is your personal machine, you should be able to modify your user permissions on your own.
You'll want to grant yourself write access to the directory you are working in, which will be by entering this command into your terminal:
chmod u+w .
Here is a great article that discusses Linux user permissions and how to modify your read/write/execute access:
After modifying your directory permissions, you should be able to re-run your original command without any issues. Hope this helps!
Thank you ! I am able to grant myself access and the error is gone. The article was really helpful as well.