Hi,
Recently we had a problem in running the dada2 pipeline on our new sequence data within the qiime2-201712 environment.
The command blocks used:
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux.qza
--o-table table
--o-representative-sequences rep-seqs
--p-trim-left-f 20
--p-trim-left-r 21
--p-trunc-len-f 280
--p-trunc-len-r 190
--p-n-threads 16
--verbose
We ran the command blocks on another demux.qza file that has been denoised by the dada2 successfully but encountered the same error again, which says:
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.4.0
- Filtering Error in
colnames<-(*tmp*, value = c("AqFl1-100_S25_L001_R1_001.fastq.gz", :
attempt to set 'colnames' on an object with less than two dimensions
Execution halted
Traceback (most recent call last):
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpl0chlnrm/forward', '/tmp/tmpl0chlnrm/reverse', '/tmp/tmpl0chlnrm/output.tsv.biom', '/tmp/tmpl0chlnrm/filt_f', '/tmp/tmpl0chlnrm/filt_r', '280', '190', '20', '21', '2.0', '2', 'consensus', '1.0', '16', '1000000']' returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in callable_executor
output_views = self._callable(**view_args)
File "/home/nutrition_group/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 194, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
We tried to figure out the problem and found that this error may be caused by an older version of the ShortRead package, which however has been updated in our R studio.