Hi! I'm trying to import my data, but I'm not sure where I've gone wrong. I have this error after 5 hours of running the command:
Plugin error from deblur:
Duplicate sample IDs!
Debug info has been saved to /var/folders/yg/wtspl3kd78z1mymc99k3zkl00000gp/T/qiime2-q2cli-err-pi766zjc.log
Here are the commands I have used that have run OK until the last command:
qiime tools import
qiime demux summarize
qiime quality-filter q-score
qiime demux summarize
qiime deblur denoise-16S
I've opened the demux files (both filtered and unfiltered) and downloaded the .csv for the sample names and double checked for duplicates and there weren't any. Here are the relevant files:
fastq_manifest_16S_sarah.txt (23.3 KB)
per-sample-fastq-counts.csv (1.6 KB)
16S-demux.qzv (289.4 KB)
demux-filtered-16S.qzv (292.2 KB)
what version of QIIME 2 are you using?
could you please post the full error message? (re-run with the
--verbose flag, or open the log file where debug info has been saved)
It sounds like you are possibly running an outdated version of deblur that could not handle sample IDs with underscores in the names, as described here:
Thank you for report. What I believe is going on is that Deblur is treating _ as a special denotation character, as was done in QIIME1 for demultiplexed output, which Deblur was originally designed to process. In brief, the demultiplexed output in QIIME1 required that sequence identifiers conform to <SAMPLEID>_<INTEGER>, and the sample ID associated with the sequence was determined by splitting the sequence identifier into its sample ID and a unique integer components. My guess ri…
If that is the case, just install the latest version of QIIME 2 and your problems should dissolve away!
I hope that helps.
I'm definitely using the 2019.4 version of QIIME2. Deblur version is definitely 2019.4.
Python version: 3.6.7
QIIME 2 release: 2019.4
QIIME 2 version: 2019.4.0
q2cli version: 2019.4.0
I'm currently re-running with --verbose as you've said, but here is the file with all the debug info copied and pasted into a text document (as I can't upload .log files):
deblur_log.txt (199.2 KB)
Is the worst case scenario just me changing all the underscores to dashes?
Thanks for all your help!
Update: I've tried denoising my data with DADA2, and it's worked. I think it did take a bit less time than deblur. I still came back with the same error for the deblur run though.
Yes, it looks like that is the solution here if you want to use deblur.
I was mistaken about that bug having been fixed in more recent releases; I did a little more digging, and it looks like underscores in sample ids are still
not supported in q2-deblur. This is specific to q2-deblur; you can use q2-dada2 and other plugins in QIIME 2 without an issue (as you found) if your sample ids contain underscores.