Qiime tools view not working with chrome

(Juan Díaz Carrasco) #1

Hi, i’m having problems with qzv visualizations when running qiime tools view command from the terminal (ubuntu).

Things i’ve already tried unsuccesfully:

  • changing TMPDIR before or after activating the conda env
  • using different qiime versions envs (the 2019-01 and older ones)

PS: using https://view.qiime2.org/ works, but it is impractical for me.

Here I paste my results:

(qiime2.11) [email protected]:~/x$ qiime tools view x-taxa-bar-plots-dada2.qzv
Press the ‘q’ key, Control-C, or Control-D to quit. This view may no longer be accessible or work correctly after quitting.Traceback (most recent call last):
File “/home/usuario/anaconda2/envs/qiime2.11/bin/qiime”, line 11, in
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/q2cli/tools.py”, line 320, in view
char = click.getchar()
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/termui.py”, line 572, in getchar
return f(echo)
File “/home/usuario/anaconda2/envs/qiime2.11/lib/python3.5/site-packages/click/_termui_impl.py”, line 616, in getchar
ch = os.read(fd, 32)
BlockingIOError: [Errno 11] Resource temporarily unavailable
Created new window in existing browser session.

Thanks in advance!

(Matthew Ryan Dillon) #2

Hey there @ju4n_dc! We have seen this once or twice before — I think this has to do with a filesystem / file access issue. Can you run df -h and provide the results here?

(Juan Díaz Carrasco) #3

Hi Matthew, thanks!

Here it goes!

(qiime2.11) [email protected]:~/x$ df -h
Filesystem      Size  Used Avail Use% Mounted on
udev            7.8G     0  7.8G   0% /dev
tmpfs           1.6G  9.7M  1.6G   1% /run
/dev/sda5       428G  170G  237G  42% /
tmpfs           7.8G   51M  7.8G   1% /dev/shm
tmpfs           5.0M  4.0K  5.0M   1% /run/lock
tmpfs           7.8G     0  7.8G   0% /sys/fs/cgroup
cgmfs           100K     0  100K   0% /run/cgmanager/fs
tmpfs           1.6G   48K  1.6G   1% /run/user/1000

(Matthew Ryan Dillon) #4

Hmm, nothing too interesting there. I wonder if this machine has run out of available file descriptors? Maybe this is an inode issue? Maybe the kernel driver for the filesystem is buggy? I’m not too sure, but my hunch is that this has nothing to do with QIIME 2 per se, and is rather just some system-related issue. Is there a sysadmin you can contact to look into this for you? :t_rex:

(Juan Díaz Carrasco) #5

I just broke my ubuntu trying to fix this problem :disappointed_relieved:. So i’m moving to virtualbox to install qiime2 on a fresh ubuntu. Thanks anyway!

(Matthew Ryan Dillon) #6

yikes :frowning:

sorry to hear that…