Qiime tools view stopped working

[Maxim_Rubin]

Hi,

qiime tools view command stopped working on my computer. I get the following output:

qiime tools view demux.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/bioinf/miniconda3/envs/qiime2-2019.1/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/tools.py”, line 326, in view
char = click.getchar()
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/termui.py”, line 572, in getchar
return f(echo)
File “/home/bioinf/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/click/_termui_impl.py”, line 616, in getchar
ch = os.read(fd, 32)
BlockingIOError: [Errno 11] Resource temporarily unavailable
[12777:12799:0220/142905.786387:ERROR:browser_process_sub_thread.cc(209)] Waited 3 ms for network service
Opening in existing browser session.

I will appreciate your help!

[timanix (Timur Yergaliyev)]

Hi!
I don’t know what causing this problem, but you are not the first one here with similar issues.
You can use this page to view your qzv files
https://view.qiime2.org/

[ebolyen (Evan Bolyen)]

Hi @Maxim_Rubin,

Does this happen consistently whenever you run the command?

It looks like you are on linux, so I don’t really have an explanation for this:

 BlockingIOError: [Errno 11] Resource temporarily unavailable

I suspect /tmp/ is a network file system with some unusually high latency?

If that’s the case, then changing your temporary directory might alleviate the issue, does the following help?

mkdir -p trash/
TMPDIR=trash qiime tools view demux.qzv

[Maxim_Rubin]

Hi @ebolyen,

Many thanks for the reply!
The problem does occur consistently. Changing the temporary directory didn’t help though.

I guess I just will view the files via studio/web page.
Thanks again!

[thermokarst]

Hey @Maxim_Rubin - did you change your TMP dir before, or after activating your conda env? If you did it before, can you try again after? If it still doesn’t work, can you activate, change TMP, then, run the env command and paste the results here? Thanks!