Production pipeline Error with setupBarcodeFiles: java.lang.ArrayIndexOutOfBoundsException: 6

[ananta]

Hi, 

I am trying to run production pipeline with 

run_pipeline.pl -Xmx16g -fork1 -ProductionSNPCallerPlugin -i tasselGBS/fastq -k /tasselGBS/keyfile/barcodeproduction.txt -e ApeKI -m /tasselGBS/topm/AllZeaGBSv2.7_ProdTOPM_20130605.topm.h5 -o /tasselGBS/hapmap/production -endPlugin -runfork1  

I got the following error, 

 

Working on GBS raw sequence file: /tasselGBS/fastq/AH7PJ9ADXX_1_fastq.txt

This file is assumed to be in fastq format

Enzyme: ApeKI

Error with setupBarcodeFiles: java.lang.ArrayIndexOutOfBoundsException: 6

In fastqtotbt, however, there was no problem

It also seems like the barcode setup is different. For production pipeline my barcode set up is as 

Flowcell Lane Barcode Sample LibraryPrepID Enzyme

AH8HVYADXX 1 CTCC ab-066 1 ApeKI

AH8HVYADXX 1 TGCA ac-13 2 ApeKI

AH8HVYADXX 1 ACTG ad-111 3 ApeKI

AH8HVYADXX 1 GTCT ann 4 ApeKI

AH8HVYADXX 1 GAAT axt-02 5 ApeKI

................................................................................

Thanks,

Ananta

[Terry Casstevens]

It doesn't seem like your keyfile has all the columns needed? See
attached sample keyfile.

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[Jeff Glaubitz]

In Tassel 3 & 4, only the first 7 columns of the sample key file that Terry sent are needed (up to and including "col"). The order of the columns matters.

In Tassel 5, the libraryPrepID (column 8) is also needed. In Tassel 3 & 4, the libraryPrepID is utilized if it is present in column 8 and is an integer.

Best,

Jeff

--
Jeff Glaubitz
Project Manager
Biology of Rare Alleles in Maize and its Wild Relatives
National Science Foundation award IOS-1238014
http://www.panzea.org
Institute for Genomic Diversity
Cornell University
175 Biotechnology Bldg
Ithaca, NY 14853
Phone: 607-255-1386
jcg...@cornell.edu

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CACHsrTs27OyHjKSuRweCHgLEt%2BfzbNi%2BjmCx06b8U9bkZO5WaA%40mail.gmail.com.

[ananta acharya]

Thanks Terry and Jeff, I referred to the key file and prepared it. Even with Tassel 4 (v 4.2.3), it expected LibraryPrepID and Enzyme. and It seems working. 

One question, How is the LibraryPrepID supposed to work? My understanding is if you run the same plate in multiple lanes, you give the same ID for each well positions. Does this also work if I have same sample in different well position. Lets say, I have sample a in A01 well in one plate and H12 in another plate, can I give the same LibraryPrepID?

Thanks

------------------------------------------------------------
Ananta Raj Acharya
Research Assistant
Center for Applied Genetic Technologies
The University of Georgia

------------------------------------------------------------
"We have not found the best way to do anything, we are only searching and searching and hopefully improving"---Anonymous

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/b4e8afc0c6644fdfa869bd10b8815081%40BY2PR04MB615.namprd04.prod.outlook.com.

[Jeff Glaubitz]

The LibraryPrepID is a unique identifier for each well on a library prep plate.  It is NOT a DNA sample ID.  Rather it refers to a particular DNA sample & barcode adapter combination in a well on a particular library prep plate.  If you run the same libraryPrepPlate on multiple lanes, then samples will be merged based on this ID.

 

>Even with Tassel 4 (v 4.2.3), it expected LibraryPrepID and Enzyme

Sorry, I confused Tassel3 & 4.  The ProductionSNPCallerPlugin of Tassel4 needs a LibraryPrepID, and checks for an “Enzyme” column too.  It doesn’t really use the Enzyme column, however, so I will remove this check (change will appear in the next release of Tassel4).

 

Best,

 

Jeff

 

--

Jeff Glaubitz

Project Manager

Biology of Rare Alleles in Maize and its Wild Relatives

National Science Foundation award IOS-1238014

http://www.panzea.org

Institute for Genomic Diversity

Cornell University

175 Biotechnology Bldg

Ithaca, NY 14853

Phone: 607-255-1386

jcg...@cornell.edu

 

From: tas...@googlegroups.com [mailto:tas...@googlegroups.com] On Behalf Of ananta acharya
Sent: Thursday, June 12, 2014 9:11 AM
To: tas...@googlegroups.com
Subject: Re: [TASSEL-Group] Production pipeline Error with setupBarcodeFiles: java.lang.ArrayIndexOutOfBoundsException: 6

 

Thanks Terry and Jeff, I referred to the key file and prepared it. Even with Tassel 4 (v 4.2.3), it expected LibraryPrepID and Enzyme. and It seems working. 

 

One question, How is the LibraryPrepID supposed to work? My understanding is if you run the same plate in multiple lanes, you give the same ID for each well positions. Does this also work if I have same sample in different well position. Lets say, I have sample a in A01 well in one plate and H12 in another plate, can I give the same LibraryPrepID?

 

Thanks

 

------------------------------------------------------------
Ananta Raj Acharya
Research Assistant
Center for Applied Genetic Technologies
The University of Georgia

------------------------------------------------------------
"We have not found the best way to do anything, we are only searching and searching and hopefully improving"---Anonymous

 

On Wed, Jun 11, 2014 at 4:37 PM, Jeff Glaubitz <jcg...@cornell.edu> wrote:

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[ananta acharya]

Thanks for update Jeff

Ananta

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