Hi, Thankyou so much for the patience for yet another silly question.
I am tired of running the below command:
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trunc-len-f 0
--p-trunc-len-r 0
-- max_ee 2
--p-n-threads 20
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--verbose
and the other command
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trim-left-f 0
--p-trunc-len-f 0
--p-trim-left-r 0
--p-trunc-len-r 0
--p-n-threads 10
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--verbose
My primers are already removed so i am not truncating or trimming my rreads. I guess Dada2 is unable to find the merge? The error is below:
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 "/root/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 350, in denoise_paired
run_commands ([cmd]) File "/root/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 "/root/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' , '/tmp/tmpk5vh83yt/forward', '--input_directory_reverse'
'/tmp/tmpk5vh83yt/reverse', '--output_path'
'--output_track', '/tmp/tmpk5vh83yt/track.tsv'
iltered_directory', '/tmp/tmpk5vh83yt/filt_f'
'--truncation_length_reverse'
'0', '--max_expected_errors', '2.0'
errors_reverse'
'—-max_expected_
' ,--chimera_metho
d', 'consensus'' , '--min_parental_fold', '1.0', '--allow_one_off', 'False',
turned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/root/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/root/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
**results = action (arguments)
File "‹decorator-gen-49>", line 2, in denoise_paired
File "/ root/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 "/root/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in _callable_execut
or_
**output_views = self._callable(view_args) File "/root/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 363, in denoise_paired
raise Exception("An error was encountered while running DADA".....
Exception: An error was encountered while running
DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Can you please tell me what I am doing wrong? Also this is paired end data with CASAVA1.8 format. The symbolic links are all fine and alright and i was able to run the import an ddemux step.
I do not know how to add a picture to this question but I have the demux-paired-end.qzv output that shows the length of my forward and reverse reads
