Hello there,
I'm working with ITS sequences from 45 samples in total. They were sequenced through an Illumina Novaseq 6000 instrument. Using the last version of QIIME2 (2023.5), my problem occurs while I perform the denoising analysis through dada2 with the following command:
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-f 155 --p-trunc-len-r 155 --p-trim-left-f 2 --p-trim-left-r 2 --p-n-threads 0 --o-table table_ITS --output-dir stats_dada/ --verbose --o-denoising-stats table_stats_ITS
based on this demultiplexing plot:
QIIME_RawData_QualityPlot_ITS.qzv (312.4 KB)
The error message is the following:
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-f 155 --p-trunc-len-r 155 --p-trim-left-f 2 --p-trim-left-r 2 --p-n-threads 0 --o-table table_ITS --output-dir stats_dada/ --verbose --o-denoising-stats table_stats_ITS
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/tmpcbsngj63/forward --input_directory_reverse /tmp/tmpcbsngj63/reverse --output_path /tmp/tmpcbsngj63/output.tsv.biom --output_track /tmp/tmpcbsngj63/track.tsv --filtered_directory /tmp/tmpcbsngj63/filt_f --filtered_directory_reverse /tmp/tmpcbsngj63/filt_r --truncation_length 155 --truncation_length_reverse 155 --trim_left 2 --trim_left_reverse 2 --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 0 --learn_min_reads 1000000
R version 4.2.3 (2023-03-15)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6
2) Filtering Error in names(answer) <- names1 :
'names' attribute [45] must be the same length as the vector [38]
4: mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE),
mapply(c, filt, filt.rev, SIMPLIFY = FALSE), MoreArgs = list(truncQ = truncQ,
truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight,
maxLen = maxLen, minLen = minLen, maxN = maxN, minQ = minQ,
maxEE = maxEE, rm.phix = rm.phix, rm.lowcomplex = rm.lowcomplex,
orient.fwd = orient.fwd, matchIDs = matchIDs, id.sep = id.sep,
id.field = id.field, n = n, OMP = OMP, qualityType = qualityType,
compress = compress, verbose = verbose), mc.cores = ncores,
mc.silent = TRUE)
3: filterAndTrim(unfilts, filts, unfiltsR, filtsR, truncLen = c(truncLen,
truncLenR), trimLeft = c(trimLeft, trimLeftR), maxEE = c(maxEE,
maxEER), truncQ = truncQ, rm.phix = TRUE, multithread = multithread)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(filterAndTrim(unfilts, filts, unfiltsR, filtsR,
truncLen = c(truncLen, truncLenR), trimLeft = c(trimLeft,
trimLeftR), maxEE = c(maxEE, maxEER), truncQ = truncQ,
rm.phix = TRUE, multithread = multithread))
Traceback (most recent call last):
File "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpcbsngj63/forward', '--input_directory_reverse', '/tmp/tmpcbsngj63/reverse', '--output_path', '/tmp/tmpcbsngj63/output.tsv.biom', '--output_track', '/tmp/tmpcbsngj63/track.tsv', '--filtered_directory', '/tmp/tmpcbsngj63/filt_f', '--filtered_directory_reverse', '/tmp/tmpcbsngj63/filt_r', '--truncation_length', '155', '--truncation_length_reverse', '155', '--trim_left', '2', '--trim_left_reverse', '2', '--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', '0', '--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 "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/lib/python3.8/site-packages/q2cli/commands.py", line 468, in __call__
results = action(**arguments)
File "<decorator-gen-72>", line 2, in denoise_paired
File "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable
outputs = self._callable_executor_(
File "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/alexandrosmoscaphd/miniconda3/envs/qiime2-2023.5_n/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.
I will be happy to provide more information if required.
Cheers