GBSSeqToTagDBPlugin: Error in Reading Annotated Taxon File:sample_key.txt

[xyl]

when I run first step in GBSv2 pipeline, I encountered this error.

The command I used:

run_pipeline.pl -fork1 -GBSSeqToTagDBPlugin -e ApeKI -i data -k sample_key.txt -o gbsV2db -mxTagL 64 -mnTagL 20 -mnQS 20 -endPlugin -runfork1

exerpt from error:

Error in Reading Annotated Taxon File:sample_key.txt

java.lang.IndexOutOfBoundsException: Index: 1, Size: 0

at java.util.ArrayList.rangeCheck(ArrayList.java:653)

at java.util.ArrayList.get(ArrayList.java:429)

at net.maizegenetics.taxa.TaxaListIOUtils.readTaxaAnnotationFile(TaxaListIOUtils.java:277)

at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processData(GBSSeqToTagDBPlugin.java:93)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:94)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1444)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

a paired end sequences in the data folder:

TomatoBC2F6_NoIndex_L001_R1_001.fastq.gz  
TomatoBC2F6_NoIndex_L001_R2_001.fastq.gz

and here are first few lines in the sample_key.txt file, which worked fine with tassel3 GBS pipeline:

Flowcell Lane Barcode Sample PlateName Row Column LibraryPrepID

BC5YCLACXX 1 CTCC 8_S_1001 TomatoBC2F6 A 1 1100

BC5YCLACXX 1 TGCA 12_S_1798 TomatoBC2F6 A 2 1101

BC5YCLACXX 1 ACTA BC2F6_9057 TomatoBC2F6 A 3 1102

BC5YCLACXX 1 CAGA BC2F6_9058 TomatoBC2F6 A 4 1103

BC5YCLACXX 1 AACT BC2F6_9060 TomatoBC2F6 A 5 1104

BC5YCLACXX 1 GCGT BC2F6_9061 TomatoBC2F6 A 6 1105

BC5YCLACXX 1 TGCGA BC2F6_9062 TomatoBC2F6 A 7 1106

BC5YCLACXX 1 CGAT BC2F6_9064 TomatoBC2F6 A 8 1107

BC5YCLACXX 1 CGCTT BC2F6_9065 TomatoBC2F6 A 9 1108

Any help would be appreciated!

Thanks!

[Jurgens de Bruin]

Hi,

I am having the same problem and would also appreciate any help on this.

[Lynn Carol Johnson]

Will you try adding a “FullSampleName” column to your key file and re-running the test?  

From: Jurgens de Bruin <debr...@gmail.com>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Monday, March 2, 2015 at 4:30 AM
To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Subject: [TASSEL-Group] Re: GBSSeqToTagDBPlugin: Error in Reading Annotated Taxon File:sample_key.txt

Hi,

I am having the same problem and would also appreciate any help on this.

On Saturday, 28 February 2015 01:49:09 UTC+2, xyl wrote:

when I run first step in GBSv2 pipeline, I encountered this error.

The command I used:

run_pipeline.pl -fork1 -GBSSeqToTagDBPlugin-e ApeKI-i data -k sample_key.txt -o gbsV2db -mxTagL 64-mnTagL 20-mnQS 20-endPlugin -runfork1

exerpt from error:

BC5YCLACXX 1CGCTT BC2F6_9065TomatoBC2F6 A9 1108

Any help would be appreciated!

Thanks!

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[xyl]

Does position of column important?

and, does FullSampleName look like this: BC2F6_9058:BC5YCLACXX:1:1103 ?

Thanks!

[Lynn Carol Johnson]

Position of the column isn’t important.  The FullSampleName should be in the form of <SampleName>:<LibraryPrepID>.

I will update the wiki to include this information.  

Lynn

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[Jeff Glaubitz]

For example,

BC2F6_9058:1103

 

The angle brackets <> are meant to indicate that the value is up to the user to supply.

 

Best,

 

Jeff

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/D119EFC8.6FDC%25lcj34%40cornell.edu.

[Lynn Carol Johnson]

Also, this is not a required form.  You can have other data included as per the examples below (taken from the tassel-5-test Pipeline_testing_key.txt example).  What you showed would be fine.

B73C05F2ACXX:5:250020986

Mo17:C05F2ACXX:5:250020994

From: Jeff Glaubitz <jcg...@cornell.edu>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>

Date: Monday, March 2, 2015 at 11:09 AM
To: "tas...@googlegroups.com" <tas...@googlegroups.com>

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CY1PR0401MB0985CA8232697FEB5F6BC86489100%40CY1PR0401MB0985.namprd04.prod.outlook.com.

[Elhan Ersoz]

Hi all,

I was just working on setting up the TASSEL5-GBS pipeline. I found a typo in the documentation at the wiki

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline/GBSSeqToTagDBPlugin 

flag option read 

-db <Output Database File> : Output Database File (REQUIRED) 

However this generates

[main] ERROR net.maizegenetics.plugindef.AbstractPlugin - Unrecognized argument: -db

the flag based on the Plugin description should be

-o <Output Database File> : Output Database File (required)

Posting here incase anyone else encounters the same issue following the wiki pages.

-Elhan

[Terry Casstevens]

Sorry Elhan, documentation is right. New build of Tassel 5 coming
today that will match.

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[Elhan Ersoz]

OK. I will wait until and install the new build then.

Thanks Terry!

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[chri...@yahoo.com.br]

Hi,
Just check if your key file has an empty last line. If yes, remove it. Also, add the FullSampleName column as mentioned.
It worked for me...

Cheers
Chris.