Hello.
I am new to qiime2 and currently going through moving pictures tutorial. After demultiplexing data and visualizing it with demux summarize I tried to use dada2 command with exactly same parameters as in tutorial (file names are slightly different)
qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 120 --o-representative-sequences repseqsdada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza
The command didn’t work and the error message occured:
Plugin error from dada2:
- No reads passed the filter. trunc_len (120) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.*
All reads in this dataset have lenght of 152 and it was confirmed during previous step. Similar error occured even with value of --p-trunc-len 1, but with --p-trunc-len 0 program worked fine.
I am using qiime 2019.4 installed with conda.
I reran the command with --verbose flag. The error mesage looked like this:
*Command: run_dada_single.R /tmp/qiime2-archive-me0kc2x5/eb6e8af2-d500-4e5e-a7db-226c28d05d35/data /tmp/tmpo2i1yiy8/output.tsv.biom /tmp/tmpo2i1yiy8/track.tsv /tmp/tmpo2i1yiy8 120 0 2.0 2 Inf consensus 1.0 1 1000000 NULL 16
/home/igor/miniconda3/envs/qiime2-2019.4/lib/R/bin/R: 238: .: Can’t open /home/igor/miniconda3/envs/qiime2-2019.4/lib/R/etc/ldpaths
Traceback (most recent call last):
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 152, in _denoise_single
run_commands([cmd])
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-me0kc2x5/eb6e8af2-d500-4e5e-a7db-226c28d05d35/data’, ‘/tmp/tmpo2i1yiy8/output.tsv.biom’, ‘/tmp/tmpo2i1yiy8/track.tsv’, ‘/tmp/tmpo2i1yiy8’, ‘120’, ‘0’, ‘2.0’, ‘2’, ‘Inf’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’, ‘NULL’, ‘16’]’ returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-449>”, line 2, in denoise_single
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(*view_args)
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 187, in denoise_single
band_size=‘16’)
File “/home/igor/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 159, in _denoise_single
" filter." % trunc_len)
ValueError: No reads passed the filter. trunc_len (120) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.