Barcode key file GBS pipeline

[ananta]

I am new to the forum and TASSEL in general.

I am trying to setup barcode key file as documented in tutorial. But I
get the error saying

Error with SetupBarcodeFiles:
java.lang.ArrayIndexOutOfBoundsException: 0
Total Barcodes found in lane: 0
Total Barcodes found in lane: 0
No Barcodes found. Skipping this flowcell lane.

My key file is in the format of..


Flowcell Lane Barcode Sample PlateName Row Column
a_sequence 1 AACT Altet4_AACT MyPlate1 A 1
a_sequence 1 ACAAA CF15_ACAAA MyPlate1 A 2
a_sequence 1 ACCGT CC78_ACCGT MyPlate1 A 3
a_sequence 1 ACCTAA MS186_ACCTAA MyPlate1 A 4
a_sequence 1 ACTA CC78_ACTA MyPlate1 A 5
a_sequence 1 AGCCC NECS141_AGCCC MyPlate1 A 6
a_sequence 1 AGGAT NECS141_AGGAT MyPlate1 B 1
a_sequence 1 AGGC CC78_AGGC MyPlate1 B 2
a_sequence 1 AGTGGA MS13_AGTGGA MyPlate1 B 3
a_sequence 1 ATATGT CC78_ATATGT MyPlate1 B 4
a_sequence 1 ATCGTA CF15_ATCGTA MyPlate1 B 5
a_sequence 1 ATGCCT NECS141_ATGCCT MyPlate1 B 6
a_sequence 1 ATTGA MS13_ATTGA MyPlate1 C 1
a_sequence 1 CAGA CF15_CAGA MyPlate1 C 2

and I am working with fastq file in a windows system using
runpipeline.bat -fork1 -
FastqToTagCountPlugin...............................

Thank you

[coolgenes]

this is the same error message I received when flowcell name and lane
in the key file and the naming of the gzip'd file need to match
exactly. Reference "TASSLE 3.0 Genotyping by Sequencing (GBS)
pipeline documentation" page 3, under the section "Gory Details:"
Once I renamed my data file and flowcell name and lane in the key file
to match the examples give (ie. FLOWCELL_LANE_qseq.txt.gz) it
worked.
Hope it works for you also.
Brad

[Jeff Glaubitz]

Thanks Brad! Note that if you are using fastq sequence files (as most folks are nowadays), then the naming convention
FLOWCELL_LANE_fastq.gz
should work.

Jeff

--
Jeff Glaubitz
Project Manager
Genetic Architecture of Maize and Teosinte
National Science Foundation award 0820619
http://www.panzea.org
Institute for Genomic Diversity
Cornell University
175 Biotechnology Bldg
Ithaca, NY 14853
Phone: 607-255-1386
jcg...@cornell.edu

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[ananta]

Thanks Brad and Jeff,

It worked....

On Feb 1, 2:54 pm, Jeff Glaubitz <jcg...@cornell.edu> wrote:
> Thanks Brad! Note that if you are using fastq sequence files (as most folks are nowadays), then the naming convention
> FLOWCELL_LANE_fastq.gz
> should work.
>
> Jeff
>
> --
> Jeff Glaubitz
> Project Manager
> Genetic Architecture of Maize and Teosinte

> National Science Foundation award 0820619http://www.panzea.org

[Jack Boyle]

Just to help future people out:

I also had this problem and also had great difficulty finding any help in the documentation.

The error message I got was slightly different:

GBSSeqToTagDBPlugin:processData - found NO files represented in key file.

Please verify your file names are formatted correctly and that your key file contains the required headers.

But Jeff's suggestion above seemed to fix it.

[Nannuru Vinay]

Hello everyone,

How do we do the barcode key file, can it be done by any plugin or normally in an excel file.

Thanks.