Hi everyone,
I have some problems running DADA2. I was working with QIIME2-2018.4 and got the following error:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more
I see others got the same so I uninstall QIIME2-2018.4 and install QIIME2-2018.6. However, I got the same error…
I thought it could be something with of my new sequences and I run DADA2 with previous ones that actually worked, but I got the same error, and that’s why I try uninstalling and reinstalling QIIME2
The command I used was:
qiime dada2 denoise-paired --i-demultiplexed-seqs seq-seguimiento-prueba.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 275 --p-trunc-len-r 250 --o-table table-prueba1.qza --o-representative-sequences seq-prueba1.qza --o-denoising-stats denoising-stats-prueba1.qza
And I got this:
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 /var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/forward /var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/reverse /var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/output.tsv.biom /var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/track.tsv /var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/filt_f /var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/filt_r 275 250 0 0 2.0 2 consensus 1.0 1 1000000
Durante la inicializaci?n - Warning messages:
1: Setting LC_COLLATE failed, using “C”
2: Setting LC_TIME failed, using “C”
3: Setting LC_MESSAGES failed, using “C”
4: Setting LC_MONETARY failed, using “C”
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 100000, 11102.
Ejecuci?n interrumpida
Traceback (most recent call last):
File “/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/anaconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/forward’, ‘/var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/reverse’, ‘/var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/output.tsv.biom’, ‘/var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/track.tsv’, ‘/var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/filt_f’, ‘/var/folders/kp/ly6vb8yd3m55sypghf0vmblm0000gp/T/tmp0471habt/filt_r’, ‘275’, ‘250’, ‘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 “/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 367, in callable_executor
output_views = self._callable(**view_args)
File “/anaconda3/envs/qiime2-2018.6/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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Any idea what I am doing wrong?
Thank you so much