Hello,
I am having a hard to trying to figure out what this error message means on dada2. It says dada 2 return code -9, which I don't really know what that means. Would appreciate any feed back on why it may not be working!
Thanks,
Max
(qiime2-2017.12) qiime2@qiime2core2017-12:~ qiime dada2 denoise-single --i-demultiplexed-seqs /home/qiime2/Greenhouse_experiment_2017/16S/Ghexpt2017_SE16S_trimmed.qza --p-trunc-len 276 --p-trim-left-f 0 --p-max-ee 4 --verbose --o-table /home/qiime2/Greenhouse_experiment_2017/16S/table_SE.qza --o-representative-sequences /home/qiime2/Greenhouse_experiment_2017/16S/rep-seqs_SE.qza
Error: no such option: --p-trim-left-f
(qiime2-2017.12) qiime2@qiime2core2017-12:~ qiime dada2 denoise-single --i-demultiplexed-seqs /home/qiime2/Greenhouse_experiment_2017/16S/Ghexpt2017_SE16S_trimmed.qza --p-trunc-len 276 --p-max-ee 4 --verbose --o-table /home/qiime2/Greenhouse_experiment_2017/16S/table_SE.qza --o-representative-sequences /home/qiime2/Greenhouse_experiment_2017/16S/rep-seqs_SE.qza
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_single.R /tmp/qiime2-archive-rxa3lqlm/1609ed3c-d590-4871-992f-67a90a889611/data /tmp/tmppnzx_px3/output.tsv.biom /tmp/tmppnzx_px3 276 0 4.0 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 The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A211_125_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A577_478_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A578_479_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A580_482_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A581_483_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A583_485_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A584_486_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A586_488_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A588_490_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A608_501_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmppnzx_px3/Gh_expt2017_A609_502_L001_R1_001.fastq.gz not written.
Some input samples had no reads pass the filter.
.............................................................................................................................x................................................................................................................................................................................................................................................................................................................................................................xx..xx.xx.x.x..........xx...................................................................... - Learning Error Rates
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 126, in denoise_single
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-rxa3lqlm/1609ed3c-d590-4871-992f-67a90a889611/data', '/tmp/tmppnzx_px3/output.tsv.biom', '/tmp/tmppnzx_px3', '276', '0', '4.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status -9
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in call
results = action(**arguments)
File "", line 2, in denoise_single
File "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/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 "/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 137, in denoise_single
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
See above for debug info.