but get error message that all.qza is not a qiime2 artifact.
in the folder, all.qza is definitely present. I also checked with -ls that the file can be found. I also had a look at the visualization of all.qzv and it looks fine.
From the previous (closed) post above it seems this is a bug. I am a total newbie to bioinformatics and not sure how to continue now.
I went to GitHub - qiime2/q2cli: Command line interface for QIIME 2 and downloaded the latest version but not sure how to incorporate that?
Thanks for posting your question. As far as I can tell, you are doing everything right. I would also check the path using ls and open up the .qzv file just like you did.
Would you feel comfortable posting the all.qza and all.qzv files? Maybe we can take a look to see what's going on.
Colin
P.S. Were you able to run qiime dada2 denoise-paired using the data from the tutorial? It's also possible that something went wrong during installation, and doing the tutorial is a great way to make sure your setup works.
Hi Colin, thanks for your response.
As I meanwhile managed to magically start running it but ran into more errors, I have another post going (error while running DADA2 in R (return code 1), all reads filtered. - #2 by Mehrbod_Estaki) so I think this thread can be closed? Thanks for your thoughts though! The problem seems to be something with the setup rather than my qza because when I run the tutorial data I get the same error message now than with my data: PermissionError: [Errno 13] Permission denied: '/etc/sysconfig/clock'
(qiime2-2019.4) n9606661@lyra04:~/qiime2-moving-pictures-tutorial> qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 120 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Write output
Traceback (most recent call last):
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
File "</home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-449>", line 2, in denoise_single
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 393, in callable_executor
spec.qiime_type, output_view, spec.view_type, prov)
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 271, in _from_view
provenance_capture=provenance_capture)
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 316, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/format/v5.py", line 21, in write
provenance_capture)
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/format/v1.py", line 26, in write
prov_dir, [root / cls.METADATA_FILE, archive_record.version_fp])
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/provenance.py", line 312, in finalize
self.write_action_yaml()
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/provenance.py", line 289, in write_action_yaml
fh.write(yaml.dump({'execution': self.make_execution_section()},
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/provenance.py", line 255, in make_execution_section
runtime['start'] = start = self._ts_to_date(self.start)
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/archive/provenance.py", line 249, in _ts_to_date
return datetime.fromtimestamp(ts, tzlocal.get_localzone())
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/tzlocal/unix.py", line 131, in get_localzone
_cache_tz = _get_localzone()
File "/home/n9606661/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/tzlocal/unix.py", line 85, in _get_localzone
with open(tzpath, 'rt') as tzfile: PermissionError: [Errno 13] Permission denied: '/etc/sysconfig/clock'
Yikes! Do you have a sysadmin you can check with about this? QIIME 2 is trying to get your local timezone to record the timestamp in provenance, but your system appears to have locked down the timezone setting file, which is a bit atypical --- most linux systems will expose this file as read-only:
ls -lah /etc/sysconfig/clock
-rw-r--r-- 1 root root 30 Jun 10 11:45 /etc/sysconfig/clock
Let us know what your sysadmin says, I suspect this file's permission issue is going to cause problems well outside of QIIME 2, so they would probably appreciate a head's up about this.