I have downloaded QIIME2 2022.2Version from conda environment using the commands given in the qiime docs. I have downloaded the data from NCBI SRA and imported in QIIME2 with the help of following commands Use the manifest file to import the sequences into QIIME 2:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path SRA/fastq/manifest/manifest.tsv \
--output-path demux.qza \
--input-format PairedEndFastqManifestPhred33V2
I visualized the demux.qza file using- qiime demux summarize --i-data demux.qza --o-visualization demux.qzv
The sequences are already demultiplexed and no apadpters were present but when i tried to create ASVs using DADA2 . I got the following error
-qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 220
--p-trunc-len-r 190
--p-n-threads 0
--output-dir work/DADA2_denoising_output
--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_paired.R /tmp/tmpennq2f9g/forward /tmp/tmpennq2f9g/reverse /tmp/tmpennq2f9g/output.tsv.biom /tmp/tmpennq2f9g/track.tsv /tmp/tmpennq2f9g/filt_f /tmp/tmpennq2f9g/filt_r 220 190 0 0 2.0 2.0 2 12 independent consensus 1.0 0 1000000
R version 4.1.2 (2021-11-01) Loading required package: Rcpp DADA2: 1.22.0 / Rcpp: 1.0.8 / RcppParallel: 5.1.5
Filtering Error in x$yield(...) :
_DNAencode(): invalid DNAString input character: '' (byte value 4)
Execution halted
Traceback (most recent call last):
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired
run_commands([cmd])
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpennq2f9g/forward', '/tmp/tmpennq2f9g/reverse', '/tmp/tmpennq2f9g/output.tsv.biom', '/tmp/tmpennq2f9g/track.tsv', '/tmp/tmpennq2f9g/filt_f', '/tmp/tmpennq2f9g/filt_r', '220', '190', '0', '0', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call results = action(**arguments) File "", line 2, in denoise_paired File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable outputs = self.callable_executor(scope, callable_args, File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor output_views = self._callable(**view_args) File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 292, 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.
I have looked for all the possible options but nothing worked .Can somebody help me with this. Thanks in advanceenter image description here
