Hi Team,
I have been trying to do the denoising of my data using the deblur. Following the tutorial ‘‘https://docs.qiime2.org/2019.1/tutorials/read-joining/’’, i have joined and filtered the paired end reads, but deblur denoise plugin is giving me the error below:
Plugin error from deblur:
Command ‘[‘deblur’, ‘workflow’, ‘–seqs-fp’, ‘/tmp/qiime2-archive-ppi4z3cm/01ce9654-3f1b-4288-a0cb-ec86f3b857ba/data’, ‘–output-dir’, ‘/tmp/tmpp0x7_2p2’, ‘–mean-error’, ‘0.005’, ‘–indel-prob’, ‘0.01’, ‘–indel-max’, ‘3’, ‘–trim-length’, ‘435’, ‘–left-trim-length’, ‘0’, ‘–min-reads’, ‘10’, ‘–min-size’, ‘2’, ‘–jobs-to-start’, ‘1’, ‘-w’, ‘–keep-tmp-files’]’ returned non-zero exit status 1.
Command used:
qiime deblur denoise-16S --i-demultiplexed-seqs home/qiime2/Desktop/demux-joined-filtered.qza --p-trim-length 435 --p-sample-stats --o-representative-sequences home/qiime2/Desktop/rep-seqs.qza --o-table home/qiime2/Desktop/table.qza --o-stats home/qiime2/Desktop/deblur-stats.qza
The below information is for your reference:
For trim length : No matter what length I give, it throws similar error.
This is the interactive plot information and overview of the demultiplexed filtered count:
| Minimum: | 266 |
|---|---|
| Median: | 58303.5 |
| Mean: | 59164.08 |
| Maximum: | 83565 |
| Total: | 2958204 |
These are the steps that I have done:
raw reads to demux input file with manifest file (prepared)
used input format PairedEndFastqManifestPhred33V2(as Phread64V2 gives error,)
Joining Reads using vsearch
visualizing the summary of demux data
Sequence quality control
visualizing summary of filtered demux data
Doubts:
Could this be possible as I have used raw data assuming that the primers and adaptors have already been removed from the reads? The files reads with extention: *L001_R001.fastq.gz. (as I don’t have access to the indices used for the sequencing)
Best
Ojasvi