However when I use it directly in feature-classifier, I got this error:
(1/2) Invalid value for “–i-classifier”: ‘silva-132-99-515-806-nb-classifier.qza’ is not a QIIME 2 Artifact (.qza)
(2/2) Invalid value for “–i-reads”: ‘rep-seqs.qza’ is not a QIIME 2 Artifact (.qza)
Here is the command:
qiime feature-classifier classify-sklearn --i-classifier silva-132-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
The rep-seqs.qza file was obtained from dada2 and I was able to obtain taxonomy.qza file when I used Greengenes classifier (downloaded from the same link above) with the same rep-seq.qza file.
I could not figure out what the problem is. Is it memory problem? I used the laptop (Intel core i5, Dell) with ubuntu. I have also checked the scikit-learn version as 0.20.2 since I am using qiime2-2019.04 version.
Based on the command, I have a suspicion that you’ve got a path problem. I’ve been noticing recently that if I pass a path that doesn’t exist, I’ll get a “not an Artifact” error. So, I would check where you have your files and where you’re running your command. (pwd and ls are two of my favorite bash commands.)
Thanks for your reply. I have checked the place of files. I think that the problem was not induced by this, because I put ‘silva-132-99-515-806-nb-classifier.qza’ ,‘rep-seqs.qza’ and ‘gg-13-8-99-515-806-nb-classifier.qza (greengene database download as silva database)’ in the same place. When I run “qiime feature-classifier classify-sklearn \ --i-classifier gg-13-8-99-515-806-nb-classifier.qza \ --i-reads rep-seqs.qza \ --o-classification taxonomy.qza”, it was successfully worked. However, when I run “qiime feature-classifier classify-sklearn \ --i-classifier silva-132-99-515-806-nb-classifier.qza \ --i-reads rep-seqs.qza \ --o-classification taxonomy.qza”, I got an error with
“(1/2) Invalid value for “–i-classifier”: ‘silva-132-99-515-806-nb-classifier.qza’ is not a QIIME 2 Artifact (.qza)
(2/2) Invalid value for “–i-reads”: ‘rep-seqs.qza’ is not a QIIME 2 Artifact (.qza)”
Yes, I took 4 pictures. You can see that I put ‘silva-132-99-515-806-nb-classifier.qza’ ,‘rep-seqs.qza’ and ‘gg-13-8-99-515-806-nb-classifier.qza’ in the same place. When I run “qiime feature-classifier classify-sklearn \ --i-classifier silva-132-99-515-806-nb-classifier.qza \ --i-reads rep-seqs.qza \ --o-classification taxonomy.qza”, I got an error with
“(1/2) Invalid value for “–i-classifier”: ‘silva-132-99-515-806-nb-classifier.qza’ is not a QIIME 2 Artifact (.qza)
(2/2) Invalid value for “–i-reads”: ‘rep-seqs.qza’ is not a QIIME 2 Artifact (.qza)”
But when I run “qiime feature-classifier classify-sklearn \ --i-classifier gg-13-8-99-515-806-nb-classifier.qza \ --i-reads rep-seqs.qza \ --o-classification taxonomy.qza”, it was successfully worked
It looks like you don’t have very much space available on your hard drive, your root partition has only 4G left (and I don’t see a /tmp partition, so it is limited to that as well). This is not really enough room for QIIME 2 to extract the SILVA classifier (greengenes is a bit smaller so it’s able to squeeze in, but barely).
Unfortunately the CLI should be telling us you ran out of room instead of complaining about the .qza being wrong, but this will be fixed in the next release. Nonetheless, you’ll need much more room I think.
You may be able to use a external drive and combining that with:
export TMPDIR=/your/external/drive
(you can search TMPDIR for more details)
you will probably be able to get things moving again.
Thanks for posting your partition usage! Base on this, it appears you do not have a dedicated TMP partition, which is pretty normal, and so we look at the root partition to determine the size:
Based on this, it is relatively full. But not so full I would expect it to fail. Just to make sure this is actually what we think it is, are you certain that the filepaths you are using are completely correct? Right now the error that we see is mangling these three cases internally:
Artifact.load fails due to lack of space
Artifact.load fails because the file does not exist
Artifact.load fails because the file isn't a qza
We can't differentiate them at the moment, but the next release will fix that.
Are you able to increase the disk size for VirtualBox? That may help, otherwise you could add a mounted volume and set TMPDIR to that location. If that doesn't work let me know, there may be a fourth case we are unaware of.
Thanks a lot! I will follow your suggestions. the paths, I think they are right, generally, I execute the commands at the current directory including all the files, just in case of any errors.
Hi, I am experiencing the same error, as mentioned above. I have checked the space, filepath and the artifact but nothing seems to work. I started that with 2019.10 version and then with 2020 version, changed classifier to silva from gg and then tried to download then again from the website. Also tried to directly gave the command and not submit a job at uni cluster. But nothing seems to work. Is there any way to get rid of this problem?
