I had an error appear while running dada2
I ran the command
qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --verbose --p-trunc-len-f 220 --p-trunc-len-r 200 --output-dir dada2_denoised
and got the following results
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/tmpwb5osl7g/forward /tmp/tmpwb5osl7g/reverse /tmp/tmpwb5osl7g/output.tsv.biom /tmp/tmpwb5osl7g/track.tsv /tmp/tmpwb5osl7g/filt_f /tmp/tmpwb5osl7g/filt_r 220 200 0 0 2.0 2 consensus 1.0 1 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering Error in add(bin) : record does not start with ‘@’
Execution halted
Traceback (most recent call last):
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpwb5osl7g/forward’, ‘/tmp/tmpwb5osl7g/reverse’, ‘/tmp/tmpwb5osl7g/output.tsv.biom’, ‘/tmp/tmpwb5osl7g/track.tsv’, ‘/tmp/tmpwb5osl7g/filt_f’, ‘/tmp/tmpwb5osl7g/filt_r’, ‘220’, ‘200’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 366, in callable_executor
output_views = self._callable(**view_args)
File “/fslhome/nathanri/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 244, 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.
So it says the " record does not start with ‘@’"
I’m assuming this is because my fastq.gz files do not have the ‘@’ in them. However, when I look at several of my samples within the file, they do. Is there anyway to know which sample its talking about? Because it’s clearly not every single sample. Is this even problem?