Hi! I am trying to run unpaired, single sequences in DADA2. I got these sequences from NCBI SRA database that starts like <@SRR12326003.1.1 1 length=250>.
Below is my code and --verbose results. Can someone please tell me what is wrong!!!
qiime dada2 denoise-single --i-demultiplexed-seqs /media/sf_Ubuntu_share_folder/567.qza --p-trunc-len 0 --o-table /media/sf_Ubuntu_share_folder/table.qza --o-representative-sequences /media/sf_Ubuntu_share_folder/repseq.qza --o-denoising-stats /media/sf_Ubuntu_share_folder/stat.qza --p-n-threads 10 --verbose
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-4dn3tfbp/77763192-1489-471d-bb90-415e569f5dae/data /tmp/tmp8dyn2rj_/output.tsv.biom /tmp/tmp8dyn2rj_/track.tsv /tmp/tmp8dyn2rj_ 0 0 2.0 2 Inf independent consensus 1.0 10 1000000 NULL 16
R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.0.2
- Filtering Error in names(answer) <- dots[[1L]] :
'names' attribute [30] must be the same length as the vector [3]
Execution halted
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/denoise.py", line 181, in denoise_single
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-4dn3tfbp/77763192-1489-471d-bb90-415e569f5dae/data', '/tmp/tmp8dyn2rj/output.tsv.biom', '/tmp/tmp8dyn2rj/track.tsv', '/tmp/tmp8dyn2rj', '0', '0', '2.0', '2', 'Inf', 'independent', 'consensus', '1.0', '10', '1000000', 'NULL', '16']' 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/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "<decorator-gen-520>", line 2, in denoise_single
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 218, in denoise_single
band_size='16')
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 192, in _denoise_single
" 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.