Hello Qiime2 Forum,
I seem to be running into some difficulty when doing sequence quality control using the deblur plugin for my demultiplexed paired-end sequences.
Here is the demultiplexed visualization file to refer to if needed: Paired-end-demux-sequences.qzv (290.7 KB)
Firstly, as referenced by the “Moving Pictures” tutorial, I did the initial quality filtering process based on quality scores which was successful. The command that I did is below:
qiime quality-filter q-score \ > --i-demux Paired-end-demux-sequences.qza \ > --o-filtered-sequences Paired-demux-filtered.qza \ > --o-filter-stats Paired-demux-filter-stats.qza
Paired-demux-filter-stats.qza (10.7 KB)
From there, I went forward in the Deblur workflow with
qiime deblur denoise-16S method. The command I inputted into the terminal is as follows:
qiime deblur denoise-16S --i-demultiplexed-seqs Paired-demux-filtered.qza --p-trim-length 300 --o-representative-sequences Paired-rep-seqs-deblur.qza --o-table Paired-table-deblur.qza --p-sample-stats --o-stats Paired-deblur-stats.qza
Each time that I put this command, even with different --p-trim-length values, I would end up with the following error:
Plugin error from deblur: Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2-archive-9xp_xuqn/88595039-92d4-42f5-90f9-e04d4add2012/data', '--output-dir', '/tmp/tmp8n29ubx7', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '300', '--left-trim-length', '0', '--min-reads', '10', '--min-size', '2', '--jobs-to-start', '1', '-w', '--keep-tmp-files']' returned non-zero exit status 1. Debug info has been saved to /tmp/qiime2-q2cli-err-owfipnwf.log
Here is the deblur.log for reference. I had to share 2 files on this topic through Google Drive since they were too large.
I tried to use the DADA2 plugin instead but I would also end up with the same error. I looked through past forum posts for guidance but still no luck… Any ideas on what I should do next?