I have been trying to run DADA2 without chimera checking but I get an error everytime. I’m using QIIME2-2017-12 on an HPC cluster and using the following code:
> qiime dada2 denoise-paired \ > --i-demultiplexed-seqs Demux/demuxPE-AT.qza \ > --o-table Dada2/tablePE-AT \ > --o-representative-sequences Dada2/rep-seqsPE-AT \ > --p-trim-left-f 13 \ > --p-trim-left-r 13 \ > --p-trunc-len-f 150 \ > --p-trunc-len-r 150 \ > --p-n-threads 0 \ > --p-chimera-method none \ > --verbose
The error file contains the following:
> Loading required package: Rcpp > The sequences being tabled vary in length. > Error in is.data.frame(x) : object 'seqtab.nochim' not found > Calls: rowSums -> is.data.frame > Execution halted > Traceback (most recent call last): > File "/software/software/QIIME2/2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired > run_commands([cmd]) > File "/software/software/QIIME2/2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands > subprocess.run(cmd, check=True) > File "/software/software/QIIME2/2017.12/lib/python3.5/subprocess.py", line 398, in run > output=stdout, stderr=stderr) > subprocess.CalledProcessError: Command '['run_dada_paired.R', '/local/501194/tmph7hrhop3/forward', '/local/501194/tmph7hrhop3/reverse', '/local/501194/tmph7hrhop3/output.tsv.biom', '/local/501194/tmph7hrhop3/filt_f', '/local/501194/tmph7hrhop3/filt_r', '150', '150', '13', '13', '2.0', '2', 'none', '1.0', '0', '1000000']' returned non-zero exit status 1 > > During handling of the above exception, another exception occurred: > > Traceback (most recent call last): > File "/software/software/QIIME2/2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in __call__ > results = action(**arguments) > File "<decorator-gen-354>", line 2, in denoise_paired > File "/software/software/QIIME2/2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable > output_types, provenance) > File "/software/software/QIIME2/2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_executor_ > output_views = self._callable(**view_args) > File "/software/software/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.
The problem seems to be at the chimera checking stage, from the output file:
- Denoise remaining samples …
- Remove chimeras (method = none)
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 /local/501194/tmph7hrhop3/forward /local/501194/tmph7hrhop3/reverse /local/501194/tmph7hrhop3/output.tsv.biom /local/501194/tmph7hrhop3/filt_f /local/501194/tmph7hrhop3/filt_r 150 150 13 13 2.0 2 none 1.0 0 1000000
When I run the same command, but without the “–p-chimera-method none”, it all works fine and I get table and rep-seqs files.
Any help on this would be much appreciated,