Hi, I got the following error when trying to perform quality control with DADA2:
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/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/forward /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/reverse /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/output.tsv.biom /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/track.tsv /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_f /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_r 260 190 19 42 2.0 2 consensus 1.0 1 1000000
cannot find system Renviron
Error: package or namespace load failed for ‘utils’:
.onLoad a ?chou? dans loadNamespace() pour 'utils', d?tails :
appel : options(op.utils[toset])
erreur : valeur incorrecte pour 'editor'
Error: package or namespace load failed for ‘stats’:
.onLoad a ?chou? dans loadNamespace() pour 'utils', d?tails :
appel : options(op.utils[toset])
erreur : valeur incorrecte pour 'editor'
Pendant le d?marrage - Warnmeldungen:
1: package ‘utils’ in options("defaultPackages") was not found
2: package ‘stats’ in options("defaultPackages") was not found
3: Setting LC_COLLATE failed, using "C"
4: Setting LC_TIME failed, using "C"
5: Setting LC_MESSAGES failed, using "C"
6: Setting LC_MONETARY failed, using "C"
R version 3.4.1 (2017-06-30)
Le chargement a n?cessit? le package : Rcpp
Error: package or namespace load failed for ‘Rcpp’:
.onLoad a ?chou? dans loadNamespace() pour 'utils', d?tails :
appel : options(op.utils[toset])
erreur : valeur incorrecte pour 'editor'
Erreur : le package ‘Rcpp’ ne peut ?tre charg?
Ex?cution arr?t?e
Traceback (most recent call last):
File "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 229, in denoise_paired
run_commands([cmd])
File "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/forward', '/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/reverse', '/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/output.tsv.biom', '/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/track.tsv', '/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_f', '/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_r', '260', '190', '19', '42', '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 "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound_callable
output_types, provenance)
File "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 367, in callable_executor
output_views = self._callable(**view_args)
File "/Users/whalenlab/anaconda3/envs/qiime2-2018.6/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
The command I used was
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end3-demux.qza --p-trim-left-f 19 --p-trim-left-r 42 --p-trunc-len-f 260 --p-trunc-len-r 190 --p-n-threads 1 --p-max-ee 2 --verbose --o-representative-sequences rep-seqs-dada3.qza --o-table table-dada3.qza --output-dir dada-two
I deleted the startup files of R in my computer a week ago and I did try to put back things from the trash. Is my error somehow related to the deleted R startup files?
Thank you so much.
*Update: I reinstalled R but this same error message appears.
**Update: I uninstalled RStudio and that does not seem to change things. I was able to perform the quality control on a different set of sequences two weeks ago. The only difference between now and then I can think of is that I attempted to install RStudio last week and tried to solve the problem that RStudio could not start by deleting the R startup files.
