Hi Matt,
I am still getting this error from DADA2 Denoising step, please help me figure out how to address this one.
cat /tmp/qiime2-q2cli-err-q4l8egu9.log
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering …
- Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 2210368 reads in 2188405 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
Convergence after 5 rounds.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Error rates could not be estimated.
Error in err[c(1, 6, 11, 16), ] <- 1 :
incorrect number of subscripts on matrix
Calls: dada
Execution halted
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_paired.R /tmp/tmpodsqctkg/forward /tmp/tmpodsqctkg/reverse /tmp/tmpodsqctkg/output.tsv.biom /tmp/tmpodsqctkg/track.tsv /tmp/tmpodsqctkg/filt_f /tmp/tmpodsqctkg/filt_r 200 180 10 10 2.0 2 consensus 1.0 40 1000000
Traceback (most recent call last):
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
run_commands([cmd])
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpodsqctkg/forward’, ‘/tmp/tmpodsqctkg/reverse’, ‘/tmp/tmpodsqctkg/output.tsv.biom’, ‘/tmp/tmpodsqctkg/track.tsv’, ‘/tmp/tmpodsqctkg/filt_f’, ‘/tmp/tmpodsqctkg/filt_r’, ‘200’, ‘180’, ‘10’, ‘10’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘40’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>”, line 2, in denoise_paired
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/imelda/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 246, 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.
Thanks,
Imee