Hi,
I'm getting the following error when I try to run the DADA2 denoising step (qiime 2018.4) with a small 16S dataset (2x150) on ubuntu 16.04.
"Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-89jqjumm.log"
Commands:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path u01-manifest
--output-path u01-demux.qza
--source-format PairedEndFastqManifestPhred33
qiime dada2 denoise-paired
--i-demultiplexed-seqs u01-demux.qza
--p-trunc-len-f 150
--p-trunc-len-r 149
--p-trim-left-f 0
--p-trim-left-r 0
--output-dir u01-denoise-dada2
Debug log:
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/tmpz8rk9v01/forward /tmp/tmpz8rk9v01/reverse /tmp/tmpz8rk9v01/output.tsv.biom /tmp/tmpz8rk9v01/track.tsv /tmp/tmpz8rk9v01/filt_f /tmp/tmpz8rk9v01/filt_r 150 149 0 0 2.0 2 consensus 1.0 1 1000000
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 - 14397 reads in 5342 unique sequences.
Sample 2 - 14438 reads in 4676 unique sequences.
Sample 3 - 14476 reads in 5887 unique sequences.
Sample 4 - 14647 reads in 6065 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
selfConsist step 7
selfConsist step 8
selfConsist step 9
selfConsist step 10
Self-consistency loop terminated before convergence.
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
Traceback (most recent call last):
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 229, in denoise_paired
run_commands([cmd])
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpz8rk9v01/forward', '/tmp/tmpz8rk9v01/reverse', '/tmp/tmpz8rk9v01/output.tsv.biom', '/tmp/tmpz8rk9v01/track.tsv', '/tmp/tmpz8rk9v01/filt_f', '/tmp/tmpz8rk9v01/filt_r', '150', '149', '0', '0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 366, in callable_executor
output_views = self._callable(**view_args)
File "/home/usuario/anaconda2/envs/qiime2.4/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 244, 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.
I've followed the same steps before using other datasets without problems
any help is welcome
thanks in advance
:qiime2: