Also...I might as well ask this here given the errors I am encountering trying to make this work. DADA2 is not working either...see code/error below! Again, I am very appreciative of your help and support!
(base) [anthony.frazier@ceres meta_analysis]$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs fondue-output-new/paired_reads.qza
--p-trim-left-f 13
--p-trim-left-r 13
--p-trunc-len-f 300
--p-trunc-len-r 300
--verbose
--o-table fondue-output-new/table.qza
--o-representative-sequences fondue-output-new/rep-seqs.qza
--o-denoising-stats fondue-output-new/denoising-stats.qza
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.R --input_directory /tmp/tmpou4zdjbx/forward --input_directory_reverse /tmp/tmpou4zdjbx/reverse --output_path /tmp/tmpou4zdjbx/output.tsv.biom --output_track /tmp/tmpou4zdjbx/track.tsv --filtered_directory /tmp/tmpou4zdjbx/filt_f --filtered_directory_reverse /tmp/tmpou4zdjbx/filt_r --truncation_length 300 --truncation_length_reverse 300 --trim_left 13 --trim_left_reverse 13 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000
Warning message:
package ‘optparse’ was built under R version 4.2.3
R version 4.2.2 (2022-10-31)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.11 / RcppParallel: 5.1.6
2) Filtering ..................
3) Learning Error Rates
386876 total bases in 1348 reads from 18 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
6: stop("Error matrix is NULL.")
5: getErrors(err, enforce = TRUE)
4: dada(drps, err = NULL, errorEstimationFunction = errorEstimationFunction,
selfConsist = TRUE, multithread = multithread, verbose = verbose,
MAX_CONSIST = MAX_CONSIST, OMEGA_C = OMEGA_C, ...)
3: learnErrors(filts, nreads = nreads.learn, multithread = multithread)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(learnErrors(filts, nreads = nreads.learn, multithread = multithread))
Traceback (most recent call last):
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpou4zdjbx/forward', '--input_directory_reverse', '/tmp/tmpou4zdjbx/reverse', '--output_path', '/tmp/tmpou4zdjbx/output.tsv.biom', '--output_track', '/tmp/tmpou4zdjbx/track.tsv', '--filtered_directory', '/tmp/tmpou4zdjbx/filt_f', '--filtered_directory_reverse', '/tmp/tmpou4zdjbx/filt_r', '--truncation_length', '300', '--truncation_length_reverse', '300', '--trim_left', '13', '--trim_left_reverse', '13', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '1', '--learn_min_reads', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 539, in _execute_action
results = action(**arguments)
File "", line 2, in denoise_paired
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/software/el9/apps/qiime2/2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 339, in denoise_paired
raise Exception("An error was encountered while running DADA2"
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.
(base) [anthony.frazier@ceres meta_analysis]$
