error message from deblur

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

Hi @SciCatalyst,
Could you please run this command with the --verbose flag to view the complete error message?

Thanks.

Dear Bokulich,
Greetings.
I would like to inform that the problem has been resolved.
Actually I am running QIIME on Ubuntu in Oracle Virtual Box and was suggested that allocation of memory may be a problem, so just changed it and it worked. EUREKAAA!!!

Thank you.

Best,

Ojasvi

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