Thank you very much sir. I have successfully imported my raw data into qiime2 artifact!
However, I facing a problem on denoising the data using dada plug in.
My demux file can be obtained from Dropbox - File Deleted - Simplify your life.
I ran the commands as follows:
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux.qza
--p-trim-left-f 5
--p-trim-left-r 5
--p-trunc-len-f 284
--p-trunc-len-r 255
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats stats.qza
After almost 2 hours of running, it resulted in Plug in error:
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 /tmp/tmpc10jnsao/forward /tmp/tmpc10jnsao/reverse /tmp/tmpc10jnsao/output.tsv.biom /tmp/tmpc10jnsao/track.tsv /tmp/tmpc10jnsao/filt_f /tmp/tmpc10jnsao/filt_r 284 255 5 5 2.0 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 ..........
- Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 208306 reads in 16532 unique sequences.
Sample 2 - 266625 reads in 50971 unique sequences.
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 229, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2018.6/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpc10jnsao/forward', '/tmp/tmpc10jnsao/reverse', '/tmp/tmpc10jnsao/output.tsv.biom', '/tmp/tmpc10jnsao/track.tsv', '/tmp/tmpc10jnsao/filt_f', '/tmp/tmpc10jnsao/filt_r', '284', '255', '5', '5', '2.0', '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/qiime2-2018.6/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/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/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 "/home/qiime2/miniconda/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 -9), please inspect stdout and stderr to learn more.
May I know what's exactly happening? I wonder if the trunc-len for forward and reverse should be identical? Looking for constructive advice.
Thanks.