Hi,
I am a little confused as I have exactely the same issue then the last solved one previously (please see this link (No Space Left on Device for qiime feature-classifier ) with the feature classifier. i changed the tmp directory with TEMPDIR=/some/directory but I still have have the same problème.
Any suggestion on how you solved this problème will be appreciated
Thanks
Hi @biotama - what command are you running to change your temporary directory? The snippet you provided above has a minor typo, the environment variable name is TMPDIR, not TEMPDIR, so that is probably what is going on here. If tweaking the variable name like I suggest here doesn’t help, please provide all of the commands you are running, including your feature classifier command, and the command for setting the environment variable. Thanks! 
Hi, oh sorry for the mistake in the command, here is the commands i run:
ls /data
skynet@skynet-HP-Z640-Workstation:~$ export TMPDIR=/data
skynet@skynet-HP-Z640-Workstation:~$ echo $TMPDIR
/data
skynet@skynet-HP-Z640-Workstation:~$ source activate qiime2-2017.12
(qiime2-2017.12) skynet@skynet-HP-Z640-Workstation:~$ cd qiime2-final
(qiime2-2017.12) skynet@skynet-HP-Z640-Workstation:~/qiime2-final$ qiime feature-classifier classify-sklearn --i-classifier silva-119-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
I just wanted to add that in my case this issue happened only on linux machine, I tried to run the command on Mac OS and it seems Work but it take all the memory (I have just 4go) leading to a big bug, so I can’t do anything…
Thanks
Is this environment activation resetting your TMPDIR variable? What does echo $TMPDIR return after you activate your conda env?
It returns the same place /data after or before activating conda env
Thx
Well, it sounds like you are running out of disk space 
What does df -h have to tell you about the /data path? If that isn’t a separate mount it will be listed under the “mounted on” entry for /.
Can you also please provide the exact error you are receiving? Copy and paste please. Thanks!
I don’t know if this correct… I run the df -h and it returns this list below
skynet@skynet-HP-Z640-Workstation:/data$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 32G 0 32G 0% /dev
tmpfs 6.3G 658M 5.7G 11% /run
/dev/sdc3 19G 14G 3.5G 80% /
tmpfs 32G 4.3M 32G 1% /dev/shm
tmpfs 5.0M 4.0K 5.0M 1% /run/lock
tmpfs 32G 0 32G 0% /sys/fs/cgroup
/dev/sda2 96M 63M 34M 66% /boot/efi
/dev/sdc5 2.2T 2.0T 155G 93% /home
tmpfs 6.3G 96K 6.3G 1% /run/user/1000
/dev/sda4 918G 640G 279G 70% /media/skynet/Nouveau nom
/dev/sdc2 451G 291G 160G 65% /media/skynet/Nouveau nom1
/dev/sde2 932G 158G 774G 17% /media/skynet/PhilLebel
And here is the complete error
(qiime2-2017.12) skynet@skynet-HP-Z640-Workstation:~/qiime2-final$ qiime feature-classifier classify-sklearn --i-classifier silva-119-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza --p-n-jobs 1
Traceback (most recent call last):
File "/home/skynet/miniconda3/envs/qiime2-2017.12/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 191, in __call__
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 263, in handle_in_params
kwargs, fallback=cmd_fallback
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/handlers.py", line 375, in get_value
return qiime2.Artifact.load(path)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/result.py", line 64, in load
archiver = archive.Archiver.load(filepath)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 297, in load
rec = archive.mount(path)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 198, in mount
root = self.extract(filepath)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 209, in extract
zf.extract(name, path=str(filepath))
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/zipfile.py", line 1335, in extract
return self._extract_member(member, path, pwd)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/zipfile.py", line 1399, in _extract_member
shutil.copyfileobj(source, target)
File "/home/skynet/miniconda3/envs/qiime2-2017.12/lib/python3.5/shutil.py", line 82, in copyfileobj
fdst.write(buf)
OSError: [Errno 28] No space left on device
(qiime2-2017.12) skynet@skynet-HP-Z640-Workstation:~/qiime2-final$
My apologies for taking you busy with this…
No worries @biotama!
Thanks for all the extra info, that was super useful! So, looking at your df results, you only have 3.5G of space available for /data, it is entirely possible that you are fully exhausting that tiny bit of space when running feature-classifier.
It does look like your home directory has plenty of space (155G free), how about setting TMPDIR to /home/skynet/tmp? You would need to make that directory first, and of course you could stash that somewhere else more appropriate to your home directory layout. Please give that a shot and let us know how it goes!
Hi, now it works!!! thanks thermokarst! it takes one CPU, is there any option to add more than one?
Thanks
There is a parameter (n-jobs) that controls this, check out the docs to learn more!
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