Hi all,
I am denoising 16s PacBio data and running dada2 last night has given me a unexpected error when I run this code:
qiime dada2 denoise-ccs
--i-demultiplexed-seqs Raw_data_archival/archived_reads.qza
--p-min-len 1000
--p-max-len 1800
--p-max-ee 4
--p-front AGRGTTYGATYMTGGCTCAG
--p-adapter RGYTACCTTGTTACGACTT
--p-max-mismatch 3
--p-n-threads 0
--output-dir dada2_output02
--verbose
The error is as follows:
- Report read numbers through the pipeline
Error in cbind(prim, out[, 2], matrix(0, nrow = nrow(out), ncol = 2)) :
number of rows of matrices must match (see arg 3)
1: cbind(prim, out[, 2], matrix(0, nrow = nrow(out), ncol = 2))
Traceback (most recent call last):
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 467, in denoise_ccs
run_commands([cmd])
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 37, in run_commands
subprocess.run(cmd, check=True)
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/var/folders/_3/v5c3hf4j2g34qxfwkqc95rq00000gn/T/qiime2/s.d./data/6c89b129-41b2-4d04-9597-a48fc3cce54f/data', '--output_path', '/var/folders/_3/v5c3hf4j2g34qxfwkqc95rq00000gn/T/tmpw408at7a/output.tsv.biom', '--output_track', '/var/folders/_3/v5c3hf4j2g34qxfwkqc95rq00000gn/T/tmpw408at7a/track.tsv', '--removed_primer_directory', '/var/folders/_3/v5c3hf4j2g34qxfwkqc95rq00000gn/T/tmpw408at7a/nop', '--filtered_directory', '/var/folders/_3/v5c3hf4j2g34qxfwkqc95rq00000gn/T/tmpw408at7a/filt', '--forward_primer', 'AGRGTTYGATYMTGGCTCAG', '--reverse_primer', 'RGYTACCTTGTTACGACTT', '--max_mismatch', '3', '--indels', 'False', '--truncation_length', '0', '--trim_left', '0', '--max_expected_errors', '4', '--truncation_quality_score', '2', '--min_length', '1000', '--max_length', '1800', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '3.5', '--allow_one_off', 'False', '--num_threads', '0', '--learn_min_reads', '1000000', '--homopolymer_gap_penalty', 'NULL', '--band_size', '32']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in denoise_ccs
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "/Users/s.d./miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 476, in denoise_ccs
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.
As it is filtering verbose tells me that the filtering percent is around 98 which seems correct to me. Is the error telling me there is an issue compiling the data into a table? Thanks for the help with this one.
