I’m trying to run the DADA2 step on my demux.qzv file containing 53 forward and 53 reverse demultiplexed, paired end sequences. Like previous forum posts i’ve read, takes a very long time and finally thought I got through a run… until I opened up QIIME again and got the message below in the terminal. I’m not sure what the error exactly was (something with the memory availability, possibly?) I would greatly appreciate any suggested next steps to take given the below message. Many thanks in advance.
"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/tmplc5xeep2/forward /tmp/tmplc5xeep2/reverse /tmp/tmplc5xeep2/output.tsv.biom /tmp/tmplc5xeep2/filt_f /tmp/tmplc5xeep2/filt_r 200 200 0 0 2.0 2 consensus 1.0 0 1000000 R version 3.3.2 (2016-10-31) Loading required package: Rcpp There were 50 or more warnings (use warnings() to see the first 50) DADA2 R package version: 1.4.0 1) Filtering ............................Error: cannot allocate vector of size 550.2 Mb Execution halted Warning message: system call failed: Cannot allocate memory Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired run_commands([cmd]) File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands subprocess.run(cmd, check=True) File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/subprocess.py", line 398, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmplc5xeep2/forward', '/tmp/tmplc5xeep2/reverse', '/tmp/tmplc5xeep2/output.tsv.biom', '/tmp/tmplc5xeep2/filt_f', '/tmp/tmplc5xeep2/filt_r', '200', '200', '0', '0', '2.0', '2', 'consensus', '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 "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__ results = action(**arguments) File "<decorator-gen-338>", line 2, in denoise_paired File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 220, in bound_callable output_types, provenance) File "/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 355, in _callable_executor_ output_views = self._callable(**view_args) File "/home/qiime2/miniconda/envs/qiime2-2017.10/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."