I used qiime2-2019.7 to analysis 16S seqs in Linux server. I encountered error when running dada2 denoise-paired step.
Here is my command:
qiime dada2 denoise-paired
–i-demultiplexed-seqs 01demux/demux.qza
–o-table 06dada2/table.qza
–o-representative-sequences 06dada2/rep_seqs.qza
–o-denoising-stats 06dada2/dada2_stats.qza
–p-hashed-feature-ids
–p-trunc-len-f 290 \
–p-trunc-len-r 230
–p-trim-left-f 23
–p-trim-left-r 26
–p-n-threads 8
–verbose
This returns the following 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/tmpj1_0n5aa/forward /tmp/tmpj1_0n5aa/reverse /tmp/tmpj1_0n5aa/output.tsv.biom /tmp/tmpj1_0n5aa/track.tsv /tmp/tmpj1_0n5aa/filt_f /tmp/tmpj1_0n5aa/filt_r 0 0 23 26 2.0 2.0 2 consensus 1.0 16 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3
-
*Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, : *
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These are the errors (up to 5) encountered in individual cores...*
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4861, 4152.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4861, 4152.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4861, 4152.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4861, 4152.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4861, 4152.
Execution halted
Traceback (most recent call last):
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 234, in denoise_paired
run_commands([cmd])
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpj1_0n5aa/forward’, ‘/tmp/tmpj1_0n5aa/reverse’, ‘/tmp/tmpj1_0n5aa/output.tsv.biom’, ‘/tmp/tmpj1_0n5aa/track.tsv’, ‘/tmp/tmpj1_0n5aa/filt_f’, ‘/tmp/tmpj1_0n5aa/filt_r’, ‘0’, ‘0’, ‘23’, ‘26’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘16’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 249, 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.
I have searched the problem in qiime2 forum, there are some similar topics. But I go through the error detail, there are not exactly the same. So anyone can figure out what’s the problem and how can I correct it . Many thanks.