See details below. The advice in similar posts to chnage truncation did not resutls in a succesful output. Additionally, the use of qiime dada2 denoise-single resulted in a similar error message.
(qiime2-2019.4) [ec2-user@ip-172-31-19-212 ~]$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 19
--p-trunc-len-f 151
--p-trim-left-r 20
--p-trunc-len-r 130
--o-table table-v34.qza
--o-representative-sequences rep-seqs-v34.qza
--p-n-threads 4
--p-n-reads-learn 5
--output-dir dada2-v34
--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/tmpc9bz2e9i/forward /tmp/tmpc9bz2e9i/reverse /tmp/tmpc9bz2e9i/output.tsv.biom /tmp/tmpc9bz2e9i/track.tsv /tmp/tmpc9bz2e9i/filt_f /tmp/tmpc9bz2e9i/filt_r 151 130 19 20 2.0 2 consensus 1.0 4 5
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.1 / RcppParallel: 4.4.2
- Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
These are the errors (up to 5) encountered in individual cores...
Error in writeFastq(fqF, fout[[1]], "w", compress = compress) :
failed to write record 419
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 418
Error in writeFastq(fqR, fout[[2]], "a", compress = compress) :
failed to write record 15452
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
failed to write record 26917
Error in writeFastq(fqF, fout[[1]], "w", compress = compress) :
failed to write record 419
Execution halted
Traceback (most recent call last):
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpc9bz2e9i/forward', '/tmp/tmpc9bz2e9i/reverse', '/tmp/tmpc9bz2e9i/output.tsv.biom', '/tmp/tmpc9bz2e9i/track.tsv', '/tmp/tmpc9bz2e9i/filt_f', '/tmp/tmpc9bz2e9i/filt_r', '151', '130', '19', '20', '2.0', '2', 'consensus', '1.0', '4', '5']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
File "</home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-451>", line 2, in denoise_paired
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/home/ec2-user/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 246, 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.
