Hello there!
I have run into an issue with denoising after merging reads and quality filter. The issue seems to be some issue with SortMeRNA, though I'm not sure what. Here is the code I ran for the denoising:
nohup qiime deblur denoise-16S
--i-demultiplexed-seqs Bacteria-merged-filtered.qza
--p-trim-length 372
--p-sample-stats
--p-jobs-to-start 161
--o-stats deblur-stats.qza
--o-representative-sequences rep-seqs-deblur.qza
--o-table table-deblur.qza
Interestingly, deblur went through all of the files before finishing. Here is the major deblur log deblur_broken.txt (483.6 KB) and the brief nohup output nohup_broken.txt (496 Bytes).
One of the samples failed for deblurring, but this was to be expected. The last sample, "M-PS-R1", also appears to have issues, but I'm not sure that would tank the program. Here is full the code I have used, ricky_deblur_asv_pipeline.txt (3.9 KB).
Just in case people had questions about the data, I will include the initial quality of the imported reads, 16s_deblur_demux.qzv (325.1 KB), the reads after cutadapt trimming (both primers in regular orientation and reverse complement) 16s_Bacteria_trimmed-seqs.qzv (337.1 KB), the files after merging reads (since deblur only takes single reads) merged_sequences.qzv (327.7 KB), and the merged reads after quality filtering,Bacteria-merged-filtered.qzv (333.5KB)
Has anyone run into this error or something similar? Testing SortMeRNA reveals nothing out of the ordinary, only that it has been installed.
conda list sortmerna
$ Name Version Build Channel
sortmerna 2.0 he860b03_4 bioconda
$sortmerna --version
SortMeRNA version 2.0, 29/11/2014
$ indexdb_rna -h | head
Program: SortMeRNA version 2.0, 29/11/2014
Copyright: 2012-2015 Bonsai Bioinformatics Research Group:
LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe
OTU-picking extensions and continuing support developed in the Knight Lab,
BioFrontiers Institute, University of Colorado at Boulder
Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU Lesser General Public License for more details.
Contact: Evguenia Kopylova, jenya.kopylov@gmail.com
Thank you in advance for any help!