I am trying to analyze bacterial 16S rRNA data (SRA accession no. SRP095022) obtained by amplicon sequencing with Bakt_341-F and Bakt_805-R,using an Illumina MiSeq platform (2x300 reads). I have merged the paired end reads with Pandaseq and obtained reads around 450 bp (this merging step was validated since I obtained the same result reported in the related paper). I imported these merged reads into QIIME2 (v.2019.4) with the code below:
qiime tools import
--input-path manifest-Nunez2017.csv
--output-path ../OUTPUTS/demux-joined.qza
--type 'SampleData[JoinedSequencesWithQuality]'
--input-format SingleEndFastqManifestPhred33
I am also attaching manifest file: manifest-Nunez2017.csv (668 Bytes)
Later I used deblur for denoising process. The code is:
qiime deblur denoise-16S
--i-demultiplexed-seqs demux-joined.qza
--p-trim-length 400
--o-representative-sequences rep-seqs-deblur.qza
--p-sample-stats \
--o-stats deblur-stats.qza
However I get this error: Plugin error from deblur: list index out of range
Here is the log file:
Traceback (most recent call last):
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
File "</home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-441>", line 2, in denoise_16S
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_deblur/_denoise.py", line 99, in denoise_16S
hashed_feature_ids=hashed_feature_ids)
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_deblur/_denoise.py", line 196, in _denoise_helper
stats = _gather_stats(demultiplexed_seqs, tmp)
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_deblur/_denoise.py", line 227, in _gather_stats
'trim.derep')
File "/home/ugg/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_deblur/_denoise.py", line 296, in _fasta_counts
counts += int(size.split('=')[1])
IndexError: list index out of range
I have tried couple of things and seacrhed a lot, but could not understand the problem, if the problem arises because of the importing process etc.
I will be really happy if anyone helps me solve this issue..
Thanks..