Hello,
I have received an error while running dada2. I run with --verbose and received these below:
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/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/forward /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/reverse /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/output.tsv.biom /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt_f /var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt_r 295 246 0 0 2.0 2 consensus 1.0 1 1000000
During startup - 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: 312, 313.
Execution halted
Traceback (most recent call last):
File "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/Users/Jewelna/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 "/Users/Jewelna/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', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/forward', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/reverse', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/output.tsv.biom', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt_f', '/var/folders/2d/w4vr4wg11k31xmms2slc85rc0000gn/T/tmp7u1a9pa1/filt_r', '295', '246', '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 "/Users/Jewelna/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 "/Users/Jewelna/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/Users/Jewelna/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 "/Users/Jewelna/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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
What could be the problem?