Hello, all
I am using qiime2 to analyze ITS2 amplicon sequencing data, and now saw immediate errors when using the following command,
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux-ITS-paired-end.qza --p-trunc-len-f 265 --p-trim-left-f 19 --p-trunc-len-r 250 --p-trim-left-r 20 --p-n-threads 16 --p-max-ee 4 --o-table ITS-table-both_forward_reverse_max_ee_4 --o-representative-sequences ITS-seqs_both_forward_reverse_max_ee_4 --verbose
Errors are
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/tmpyf29ch6o/forward /tmp/tmpyf29ch6o/reverse /tmp/tmpyf29ch6o/output.tsv.biom /tmp/tmpyf29ch6o/filt_f /tmp/tmpyf29ch6o/filt_r 265 250 19 20 4.0 2 consensus 1.0 16 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
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: 34413, 28920.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 34413, 28920.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 34413, 28920.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 34413, 28920.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 34413, 28920.
Execution halted
Traceback (most recent call last):
File “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 179, in denoise_paired
run_commands([cmd])
File “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 35, in run_commands
subprocess.run(cmd, check=True)
File “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpyf29ch6o/forward’, ‘/tmp/tmpyf29ch6o/reverse’, ‘/tmp/tmpyf29ch6o/output.tsv.biom’, ‘/tmp/tmpyf29ch6o/filt_f’, ‘/tmp/tmpyf29ch6o/filt_r’, ‘265’, ‘250’, ‘19’, ‘20’, ‘4.0’, ‘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 “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/opt/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 194, 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.
And also, for analyzing ITS2 data, what is the recommended overlap length for doing the end merging? Any tutorial on this now?
Cheers