Plugin Error from deblur

[mpbaideme (Matt)]

Mac OS X (Terminal)
Miniconda
qiime2-2017.10

I’ve been running into an issue while running the following deblur command:

• qiime deblur denoise-16S --i-demultiplexed-seqs /path/demux-filtered.qza --p-trim-length -1 --o-representative-sequences /path/rep-seqs-deblur.qza --o-table /path/table-deblur.qza --o-stats /path/deblur-stats.qza

Input file was generated using the ‘qiime quality-filter q-score --o-filtered-sequences’ command.

The following error was generated:

• Plugin error from deblur:

• Command ‘[‘deblur’, ‘workflow’, ‘–seqs-fp’, ‘/var/folders/37/l3v4ty9d2jdbssnc7cp2f4gw0000gn/T/qiime2-archive-t1csnrsj/6593ebd0-1520-477b-99dd-a500642381d1/data’, ‘–output-dir’, ‘/var/folders/37/l3v4ty9d2jdbssnc7cp2f4gw0000gn/T/tmpg5bhd6xa’, ‘–mean-error’, ‘0.005’, ‘–indel-prob’, ‘0.01’, ‘–indel-max’, ‘3’, ‘–trim-length’, ‘-1’, ‘–min-reads’, ‘10’, ‘–min-size’, ‘2’, ‘–jobs-to-start’, ‘1’, ‘-w’]’ returned non-zero exit status 1

I’m fairly certain everything is installed and working properly but could be wrong. I removed my original 2017.10 environment, cleaned conda’s cache, and updated conda before re-running my entire set of code and still encountering into the same issue. Any suggestions?

Thanks for your time.
Matt

[wasade (Daniel McDonald)]

Hey @mpbaideme, would it be possible to rerun the deblur plugin call using --verbose? And if possible, would it be feasible to share the demux-filtered.qza artifact with me?

Best,
Daniel

[mpbaideme (Matt)]

@wasade,

I added the '--verbose' into my deblur plugin call line and re-ran. I got different feedback within qiime, however, still ended up with a deblur plugin error (log file attached).

My demux-filtered.qza file is 125+ MB. Is there a preferred method for sharing since I can't attach it?

Thanks.

Terminal Saved Output.txt (10.2 KB)

[wasade (Daniel McDonald)]

Thanks @mpbaideme! It looks like the sequences are not of a common length. Would it be possible to try setting, say, --p-trim-length 150? Deblur requires the reads are the same length; reads below the trim length will be omitted and reads longer than the trim length will be truncated.

Best,
Daniel

[mpbaideme (Matt)]

That worked! Thanks so much. I’m not sure why I had the “-1” in the original command line but I see my mistake now.