Hi, I'm trying to run Dada2 with denoise-paired, but I'm getting an error. My data comes from an Illumina 16S V3-V4. I've tried changing several parameters, as I saw on the forum that this might be the solution, but I haven't had any luck. Here's what I'm trying to run and the error I'm getting:
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired_end_demux_16S.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 220
--p-trunc-len-r 220
--p-max-ee-f 2
--p-max-ee-r 2
--p-trunc-q 2
--p-n-threads 1
--p-n-reads-learn 100000
--o-table table_paired_end_16S.qza
--o-representative-sequences rep-seqs_paired_end_16S.qza
--o-denoising-stats denoising-stats_paired_end_16S.qza
--verbose
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/tmp_7hsf77d/forward --input_directory_reverse /tmp/tmp_7hsf77d/reverse --output_path /tmp/tmp_7hsf77d/output.tsv.biom --output_track /tmp/tmp_7hsf77d/track.tsv --filtered_directory /tmp/tmp_7hsf77d/filt_f --filtered_directory_reverse /tmp/tmp_7hsf77d/filt_r --truncation_length 220 --truncation_length_reverse 220 --trim_left 0 --trim_left_reverse 0 --max_expected_errors 2 --max_expected_errors_reverse 2 --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 100000
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
55306460 total bases in 251393 reads from 1 samples will be used for learning the error rates.
55306460 total bases in 251393 reads from 1 samples will be used for learning the error rates.
3) Denoise samples ....................................................................................................................................
..............................................
*** caught segfault ***
address 0x10, cause 'memory not mapped'
Traceback:
1: asMethod(object)
2: as(quality(srt), "matrix")
3: qtables2(fq)
4: derepFastq(filts[[j]])
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
File "/home/qiime/.miniconda/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/home/qiime/.miniconda/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime/.miniconda/envs/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/tmp_7hsf77d/forward', '--input_directory_reverse', '/tmp/tmp_7hsf77d/reverse', '--output_path', '/tmp/tmp_7hsf77d/output.tsv.biom', '--output_track', '/tmp/tmp_7hsf77d/track.tsv', '--filtered_directory', '/tmp/tmp_7hsf77d/filt_f', '--filtered_directory_reverse', '/tmp/tmp_7hsf77d/filt_r', '--truncation_length', '220', '--truncation_length_reverse', '220', '--trim_left', '0', '--trim_left_reverse', '0', '--max_expected_errors', '2', '--max_expected_errors_reverse', '2', '--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', '100000']' died with <Signals.SIGSEGV: 11>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/qiime/.miniconda/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/home/qiime/.miniconda/envs/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 "/home/qiime/.miniconda/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/qiime/.miniconda/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime/.miniconda/envs/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 -11), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.
Some people on the forum suggest it's a memory problem but I don't think that's my case because i have 125gb and 24 CPUs.
I would appreciate it if someone could help me!