Hi,
I’m new in qiime2. When I run dada2 command I have the following error:
Command: run_dada_paired.R /tmp/tmp75twh9df/forward /tmp/tmp75twh9df/reverse /tmp/tmp75twh9df/output.tsv.biom /tmp/tmp75twh9df/track.tsv /tmp/tmp75twh9df/filt_f /tmp/tmp75twh9df/filt_r 300 300 0 0 2.0 2 consensus 1.0 8 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering The filter removed all reads: /tmp/tmp75twh9df/filt_f/W7_S7_L001_R1_001.fastq.gz and /tmp/tmp75twh9df/filt_r/W7_S7_L001_R2_001.fastq.gz not written.
The filter removed all reads: /tmp/tmp75twh9df/filt_f/W6_S6_L001_R1_001.fastq.gz and /tmp/tmp75twh9df/filt_r/W6_S6_L001_R2_001.fastq.gz not written.
The filter removed all reads: /tmp/tmp75twh9df/filt_f/W5_S5_L001_R1_001.fastq.gz and /tmp/tmp75twh9df/filt_r/W5_S5_L001_R2_001.fastq.gz not written.
The filter removed all reads: /tmp/tmp75twh9df/filt_f/W4_S4_L001_R1_001.fastq.gz and /tmp/tmp75twh9df/filt_r/W4_S4_L001_R2_001.fastq.gz not written.
Error in names(answer) <- names1 :
‘names’ attribute [9] must be the same length as the vector [7]
Execution halted
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmp75twh9df/forward’, ‘/tmp/tmp75twh9df/reverse’, ‘/tmp/tmp75twh9df/output.tsv.biom’, ‘/tmp/tmp75twh9df/track.tsv’, ‘/tmp/tmp75twh9df/filt_f’, ‘/tmp/tmp75twh9df/filt_r’, ‘300’, ‘300’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘8’, ‘1000000’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 366, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/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.
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.
But if I run the same command in a Mac it works. Both in Windows and Mac qiime2 is installed with virtualbox. Please any helps will be very appreciated.
Marco