Plugin error from demux: requres 12nt instead 8nt

Hello,

I run into wierd error, appriciate any help I can get! I search for the similar error but didn’T find anything…
I’m running Atacama soil tutorial, but with my data. I successfully made emp-paired-end-sequences.qza file, but when I went with demux command I got this error.

1.Running version qiime2-2019.4, installed on ASW EC2 Linux AMI.
2. ERROR C/P:

Plugin error from demux:

** Golay decoding requires 12nt barcodes. The barcode attempting to be decoded (CTTAGGGA) is of length 8nt.**

Debug info has been saved to /tmp/qiime2-q2cli-err-khf_sou2.log

  1. This whole error message:
    cat /tmp/qiime2-q2cli-err-khf_sou2.log
    Traceback (most recent call last):
    ** File “/home/ec2-user/miniconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call**
    ** results = action(arguments)
    ** File “</home/ec2-user/miniconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-431>”, line 2, in emp_paired**
    ** File “/home/ec2-user/miniconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable**
    ** output_types, provenance)**
    ** File “/home/ec2-user/miniconda2/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/ec2-user/miniconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_demux/_demux.py”, line 393, in emp_paired**
    ** barcode_read, ecc_errors = decoder.decode(raw_barcode_read)**
    ** File “/home/ec2-user/miniconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_demux/_ecc.py”, line 141, in decode**
    ** “length %dnt.” % (seq, len(seq)))**
    ValueError: Golay decoding requires 12nt barcodes. The barcode attempting to be decoded (CTTAGGGA) is of length 8nt.

Thanks for the help!
Anamarija

Hi @anamarija,
Welcome aboard!
I think the error message says it all. By default demux is expecting 12nt Golay barcodes, however your barcodes are only 8nt long and I’m actually not sure if there is even any 8nt Golays (someone else can confirm this) out there. Regardless, you just change this default by adding the following parameter.

--p-no-golay-error-correction 
2 Likes

Hi @Mehrbod_Estaki,

Thanks for replying, I’ll try this parameter…

I agree that error is self-explanatory, but it is impossible that I’m the only person that has 8nt barcodes, so there must be a way around this. Especially since In Qiime1 this wasn’t an issue…

1 Like

no worries! the option to use golay barcode error correction was just added to that action. So you are not the only person with 8nt barcodes, just the first to have issues with the tutorial hot off the press.

There is a way around this: adding the parameter that @Mehrbod_Estaki described.

It was an issue in QIIME 1 if you used the default settings in split_libraries_fastq.py (default barcode_type == golay_12). It was not an issue if you set that parameter to a different value.

Good luck!

1 Like

Hi guys, thanks for the help (Nikolas & Mehrbod)!
I tried with this paramater and I can report that it worked!!! :slight_smile:
I appriciate it so much.

Have a nice day!

1 Like

Hi @anamarija,
Glad you got it working!

Just for clarification, 8nt barcodes are of course quite common, I just meant I wasn’t personally sure if there were any common error-correcting types at 8 nt, though a quick look at the original paper revealed that they were indeed 8nt long initially (Hamming in qiime1). I learnt something new too!

2 Likes

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