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'
Plugin error from dada2:
** [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.
Command: run_dada_single.R /tmp/qiime2-archive-prx2uzes/99cf0944-0254-4510-95ae-029351285aa7/data /tmp/tmpevkficge/output.tsv.biom /tmp/tmpevkficge/track.tsv /tmp/tmpevkficge 120 0 2.0 2 Inf consensus 1.0 1 1000000 NULL 16
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.1 / RcppParallel: 4.4.2
- Filtering ..................................
- Learning Error Rates
19539480 total bases in 162829 reads from 34 samples will be used for learning the error rates. - Denoise samples ..................................
- Remove chimeras (method = consensus)
- Report read numbers through the pipeline
- 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'
Plugin error from dada2:
** [Errno 13] Permission denied: '/etc/sysconfig/clock'**