I am facing a technical issue and really appreciate an advice.
I have trimmed primers from my raw data using cutadapt paired end to produce qza file.
Please follow the link for qza folder (Sign in to your account)
Please see attached for qzv filetrimmed-seqs.qzv (291.3 KB) .
Then I used following commands to run command for dada2 analysis.
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 0 --p-trunc-len-r 248 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza
After running command I am getting error "Plugin error from dada2" and a error log was saved.
I am pasting the error below.
(qiime2-2020.2) [email protected]:/media/sf_Shared_Folder/Final$ cat /tmp/qiime2-q2cli-err-bhy2omnu.log 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/tmp2x49fpuj/forward /tmp/tmp2x49fpuj/reverse /tmp/tmp2x49fpuj/output.tsv.biom /tmp/tmp2x49fpuj/track.tsv /tmp/tmp2x49fpuj/filt_f /tmp/tmp2x49fpuj/filt_r 0 248 0 0 2.0 2.0 2 consensus 1.0 1 1000000 R version 3.5.1 (2018-07-02) Loading required package: Rcpp DADA2: 1.10.0 / Rcpp: 1.0.3 / RcppParallel: 4.4.4 1) Filtering ................ 2) Learning Error Rates 167947 total bases in 724 reads from 16 samples will be used for learning the error rates. 179552 total bases in 724 reads from 16 samples will be used for learning the error rates. Error in err[c(1, 6, 11, 16), ] <- 1 : incorrect number of subscripts on matrix Execution halted Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired run_commands([cmd]) File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands subprocess.run(cmd, check=True) File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp2x49fpuj/forward', '/tmp/tmp2x49fpuj/reverse', '/tmp/tmp2x49fpuj/output.tsv.biom', '/tmp/tmp2x49fpuj/track.tsv', '/tmp/tmp2x49fpuj/filt_f', '/tmp/tmp2x49fpuj/filt_r', '0', '248', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__ results = action(**arguments) File "</home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-455>", line 2, in denoise_paired File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable output_types, provenance) File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_ output_views = self._callable(**view_args) File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, in denoise_paired " and stderr to learn more." % e.returncode) Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I was going through the forum and found this post with similar kind of problem (Doing taxonomy analysis and getting abundancies with manifests - #9 by ebolyen)
But I am not able to understand the problem since my sequencing facility provided me with fastq file with quality score. I can see lot of F, : and , symbols below nucleotide sequence in my fastq files. Are they quality score. If I am not able to use dada2 for this data then what should do next? any suggestion will be appreciated.
Thank you for the help.