Hi,
I have been getting an error while trying to run DADA2. I went through the similar topics (Exit code -11 and the workaround creating .Rprofile file with .libPaths(.libPaths()[2]) inside)
I do not want to keep bringing new, similar topics, but I had no luck with the solutions mentioned before. Any thoughts?
(If you think completely getting rid of Rstudio would do the trick, I can do that, run my paired end DADA2, then install Rstudio again. Just want to make a informed guess)
Thank you very much.
I am pasting the code, the error, and what I found inside the error log below.
(qiime2-2017.9) dhcp-morris-2127:FISH ErikaGanda$ ls
paired-end-demux.qza paired-end-demux.qzv pe-64 pe-64-manifest
(qiime2-2017.9) dhcp-morris-2127:FISH ErikaGanda$ qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --o-table table --o-representative-sequences rep-seqs --p-trim-left-f 20 --p-trim-left-r 1 --p-trunc-len-f 265 --p-trunc-len-r 219
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -5),
please inspect stdout and stderr to learn more.
Debug info has been saved to /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-q2cli-err-1_4i94ut.log
dhcp-morris-2127:T ErikaGanda$ cat qiime2-q2cli-err-1_4i94ut.log
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 /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/forward /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/reverse /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/output.tsv.biom /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_f /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_r 265 219 20 1 2.0 2 consensus 1.0 1 1000000
dyld: Library not loaded: @rpath/libncurses.5.dylib
Referenced from: /Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/libreadline.6.2.dylib
Reason: image not found
Traceback (most recent call last):
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/forward', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/reverse', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/output.tsv.biom', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_f', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_r', '265', '219', '20', '1', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status -5
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__
results = action(**arguments)
File "<decorator-gen-320>", line 2, in denoise_paired
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/qiime2/sdk/action.py", line 201, in callable_wrapper
output_types, provenance)
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/qiime2/sdk/action.py", line 334, in _callable_executor_
output_views = callable(**view_args)
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/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 -5), please inspect stdout and stderr to learn more.