Dear Colleagues
I used QIIME2 2019.4 and perform an analysis. The same analysis I had to do on the same data using latest available 2019.7, 2019.10 for some reason but here DADA2 is giving some errors.
I found that 2019.10 has a different manifest file format. I made new manifest accordingly but I am still getting this error message.
(qiime2-2019.10) qiime2@qiime2core2019-10:/media/sf_qiime2.data/ABM_data/hmy-corrected$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 10
--p-trim-left-r 10
--p-trunc-len-f 250
--p-trunc-len-r 250
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--p-n-threads 0
--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_paired.R /tmp/tmpd4zi4e1l/forward /tmp/tmpd4zi4e1l/reverse /tmp/tmpd4zi4e1l/output.tsv.biom /tmp/tmpd4zi4e1l/track.tsv /tmp/tmpd4zi4e1l/filt_f /tmp/tmpd4zi4e1l/filt_r 250 250 10 10 2.0 2.0 2 consensus 1.0 0 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4
- Filtering Error in names(answer) <- names1 :
'names' attribute [47] must be the same length as the vector [24]
Execution halted
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpd4zi4e1l/forward', '/tmp/tmpd4zi4e1l/reverse', '/tmp/tmpd4zi4e1l/output.tsv.biom', '/tmp/tmpd4zi4e1l/track.tsv', '/tmp/tmpd4zi4e1l/filt_f', '/tmp/tmpd4zi4e1l/filt_r', '250', '250', '10', '10', '2.0', '2.0', '2', 'consensus', '1.0', '0', '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/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, 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.
Please advise. I am attaching here my demux and manifest files pe-64-manifest.txt (7.3 KB) demux