Hello,
Ihave an error (return code 1) running DADA2 (qiime2 2019.1) with this:
qiime dada2 denoise-single \
--i-demultiplexed-seqs demux.qza
--p-n-threads 0
--p-trim-left 15
--p-trunc-len 291
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /media/sf_qiime2/temp/qiime2-q2cli-err-5y3wmcox.log
As can you see I changed the tmp folder to other (/media/sf_qiime2/temp/) as is suggested in the discussion An error was encountered while running DADA2 in R (return code 1), but the error still persists.
The log file contains the following information:
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_single.R /media/sf_qiime2/temp/qiime2-archive-hl8vluwv/9526611e-608a-4425-9e9f-99e212ab7669/data /media/sf_qiime2/temp/tmpjuhdtqix/output.tsv.biom /media/sf_qiime2/temp/tmpjuhdtqix/track.tsv /media/sf_qiime2/temp/tmpjuhdtqix 291 15 2.0 2 Inf consensus 1.0 0 1000000 NULL 16
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering Error in filterAndTrim(unfilts, filts, truncLen = truncLen, trimLeft = trimLeft, :
These are the errors (up to 5) encountered in individual cores...
Error in add(bin) : internal: buf !=
Error in add(raw()) : internal: buf !=
Error in add(bin) : internal: buf !=
Error in add(raw()) : internal: buf !=
Error in add(bin) : internal: buf !=
Execution halted
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 152, in _denoise_single
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/media/sf_qiime2/temp/qiime2-archive-hl8vluwv/9526611e-608a-4425-9e9f-99e212ab7669/data', '/media/sf_qiime2/temp/tmpjuhdtqix/output.tsv.biom', '/media/sf_qiime2/temp/tmpjuhdtqix/track.tsv', '/media/sf_qiime2/temp/tmpjuhdtqix', '291', '15', '2.0', '2', 'Inf', 'consensus', '1.0', '0', '1000000', 'NULL', '16']' 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/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-440>", line 2, in denoise_single
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 187, in denoise_single
band_size='16')
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 163, in _denoise_single
" 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.
Aditional informaction: My data are single end PGM/Ion torrent and are imported with:
--type 'SampleData[SequencesWithQuality]'
--input-path se-33-manifest
--output-path demux.qza
--input-format SingleEndFastqManifestPhred33
The se-33-manifest was:
single-end PHRED 33 fastq manifest file for forward reads
sample-id,absolute-filepath,direction
F01,$PWD/se-33/F01.fastq,forward
F02,$PWD/se-33/F02.fastq,forward
F05,$PWD/se-33/F05.fastq,forward
F06,$PWD/se-33/F06.fastq,forward
F07,$PWD/se-33/F07.fastq,forward
F08,$PWD/se-33/F08.fastq,forward
F09,$PWD/se-33/F09.fastq,forward
F10,$PWD/se-33/F10.fastq,forward
F11,$PWD/se-33/F11.fastq,forward
F12,$PWD/se-33/F12.fastq,forward
F13,$PWD/se-33/F13.fastq,forward
F14,$PWD/se-33/F14.fastq,forward
F15,$PWD/se-33/F15.fastq,forward
F16,$PWD/se-33/F16.fastq,forward
I would appreciate any help,
Omar