GBS pipeline error

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Ross Whetten

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Mar 9, 2012, 2:41:10 PM3/9/12
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi Jeff,
I downloaded and installed the Mar 8 build of Tassel 3.0 standalone,
and I am trying to analyze a fastq file with headers in Casava 1.8
format (for example: @HISEQ:83:C0J7DACXX:8:1101:1274:1979 1:N:0:).

The file is named C0J7DACXX_8_fastq.gz, and is in a directory called
fastq/, with an appropriately-structured barcode file giving the same
flowcell name and lane number. The pipeline script builds the Java
command path and starts reading the fastq file, then returns the
following error:

Using the following FASTQ files:
/data/HiSeq_Feb2012/GBSM/fastq/C0J7DACXX_8_fastq.gz
Reading FASTQ file: /data/HiSeq_Feb2012/GBSM/fastq/
C0J7DACXX_8_fastq.gz
Enzyme: PstI
Error with setupBarcodeFiles:
java.lang.ArrayIndexOutOfBoundsException: 11
Exception in thread "Thread-0" java.lang.NullPointerException
at
net.maizegenetics.gbs.homology.ParseBarcodeRead.setupBarcodeFiles(ParseBarcodeRead.java:
165)
at
net.maizegenetics.gbs.homology.ParseBarcodeRead.<init>(ParseBarcodeRead.java:
41)
at
net.maizegenetics.gbs.pipeline.FastqToTagCountPlugin.countTags(FastqToTagCountPlugin.java:
156)
at
net.maizegenetics.gbs.pipeline.FastqToTagCountPlugin.performFunction(FastqToTagCountPlugin.java:
68)
at
net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:
201)
at
net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:
29)

Have you seen this before?

Thanks,
Ross

Jeff Glaubitz

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Mar 9, 2012, 2:55:13 PM3/9/12
to tas...@googlegroups.com
Hi Ross,

A bug was introduced in the last build (an undocumented change to the expected content of the key file). I am fixing it now, and we will hopefully get a new build posted today.

In the meantime, if you still have the previous version of the standalone, it should work.

Apologies,

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

Thanks,
Ross

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Jeff Glaubitz

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Mar 9, 2012, 4:58:31 PM3/9/12
to tas...@googlegroups.com
Hi Ross,

Okay, this should be fixed in the new standalone just posted.

Best,

Jeff

Hi Ross,

Apologies,

Jeff

Thanks,
Ross

--

Ross Whetten

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Mar 13, 2012, 9:23:12 PM3/13/12
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi Jeff,
The new version gets past the barcode part, but stops just after that,
with the message:
Total barcodes found in lane:96
Total barcodes found in lane:96
Catch testBasicPipeline c=2
e=java.lang.StringIndexOutOfBoundsException: String index out of
range: 64
java.lang.StringIndexOutOfBoundsException: String index out of range:
64
at java.lang.String.substring(String.java:1946)
at
net.maizegenetics.gbs.homology.ParseBarcodeRead.removeSeqAfterSecondCutSite(ParseBarcodeRead.java:
273)

Any suggestions?

Thanks,
Ross


On Mar 9, 5:58 pm, Jeff Glaubitz <jcg...@cornell.edu> wrote:
> Hi Ross,
>
> Okay, this should be fixed in the new standalone just posted.
>
> Best,
>
> Jeff
>
>
>
>
>
>
>
> -----Original Message-----
> From: Jeff Glaubitz
> Sent: Friday, March 09, 2012 2:55 PM
> To: 'tas...@googlegroups.com'
> Subject: RE: [TASSEL-Group] GBS pipeline error
>
> Hi Ross,
>
> A bug was introduced in the last build (an undocumented change to the expected content of the key file).  I am fixing it now, and we will hopefully get a new build posted today.
>
> In the meantime, if you still have the previous version of the standalone, it should work.
>
> Apologies,
>
> Jeff
>
> --
> Jeff Glaubitz
> Project Manager
> Genetic Architecture of Maize and Teosinte
> National Science Foundation award 0820619http://www.panzea.org

Nguyen duc anh

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Feb 21, 2014, 3:42:06 AM2/21/14
to tas...@googlegroups.com
Hi Jeff and Ross
I have a problem when read raw data, matched-name between raw data file and key file but i get follow error. Please tell me how to fix it? thanks you
 
trananh@trananh-All-Series:~/
tassel$ ./run_pipeline.pl -fork1 -FastqToTagCountPlugin -i fastq -k mungbean.txt -e ApeKI -o taqCounts -endPlugin -runfork1
Tassel Pipeline Arguments: -fork1 -FastqToTagCountPlugin -i fastq -k mungbean.txt -e ApeKI -o taqCounts -endPlugin -runfork1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.165  Date: January 16, 2014
net.maizegenetics.gbs.pipeline.FastqToTagCountPlugin

Using the following FASTQ files:
/home/trananh/tassel/fastq/ABC12AAXX_1_fastq.gz
Reading FASTQ file: /home/trananh/tassel/fastq/ABC12AAXX_1_fastq.gz
Enzyme: ApeKI
AGGC MB245:ABC12AAXX:1:Myplate1:A01
GATT MB40:ABC12AAXX:1:Myplate1:A02
ACCGT MB62:ABC12AAXX:1:Myplate1:A03
CGTCA MB189:ABC12AAXX:1:Myplate1:A04
TCGCA MB178:ABC12AAXX:1:Myplate1:A05
CGCAT MB104:ABC12AAXX:1:Myplate1:A06
TCATAGT MB2:ABC12AAXX:1:Myplate1:A07
TTACGAT MB79:ABC12AAXX:1:Myplate1:A08
GGCTAGA MB36:ABC12AAXX:1:Myplate1:A09
ACAATGGA MB223:ABC12AAXX:1:Myplate1:A10
ACAAGAGT MN94:ABC12AAXX:1:Myplate1:A11
GAACATGA MB226:ABC12AAXX:1:Myplate1:A12
AGCATT MB92:ABC12AAXX:1:Myplate1:B01
CTCCGA MB83:ABC12AAXX:1:Myplate1:B02
TTGGCA MB134:ABC12AAXX:1:Myplate1:B03
CCACGT MB86:ABC12AAXX:1:Myplate1:B04
GATGTC MB89:ABC12AAXX:1:Myplate1:B05
TGTTAC MB219:ABC12AAXX:1:Myplate1:B06
CAGTTA MB16:ABC12AAXX:1:Myplate1:B07
GCCTAT MB49:ABC12AAXX:1:Myplate1:B08
AGTGGC MB123:ABC12AAXX:1:Myplate1:B09
TGACCT MB142:ABC12AAXX:1:Myplate1:B10
TTGCAC MB192:ABC12AAXX:1:Myplate1:B11
CTAGCT MB140:ABC12AAXX:1:Myplate1:B12
AATCGTT MB125:ABC12AAXX:1:Myplate1:C01
CTATGGA MB151:ABC12AAXX:1:Myplate1:C02
TACGGTA MB6:ABC12AAXX:1:Myplate1:C03
ACTATGT MB81:ABC12AAXX:1:Myplate1:C04
CGTGAAT MB43:ABC12AAXX:1:Myplate1:C05
TTGCAGA MB61:ABC12AAXX:1:Myplate1:C06
AACTTGT MB126:ABC12AAXX:1:Myplate1:C07
TGACGTA MB91:ABC12AAXX:1:Myplate1:C08
GCTATAA MB105:ABC12AAXX:1:Myplate1:C09
ATCGTAT MB182:ABC12AAXX:1:Myplate1:C10
TACTGAT MB37:ABC12AAXX:1:Myplate1:C11
CTTGAGA MB74:ABC12AAXX:1:Myplate1:C12
TCAAGTT MB87:ABC12AAXX:1:Myplate1:D01
GATCATA MB174:ABC12AAXX:1:Myplate1:D02
GCATTGA MB188:ABC12AAXX:1:Myplate1:D03
CAGGTAT MB12:ABC12AAXX:1:Myplate1:D04
TGCAATA MB14:ABC12AAXX:1:Myplate1:D05
ATATCGT MB44:ABC12AAXX:1:Myplate1:D06
AGTCTAT MB66:ABC12AAXX:1:Myplate1:D07
GTCTGAA MB69:ABC12AAXX:1:Myplate1:D08
ATCAGTT MB94:ABC12AAXX:1:Myplate1:D09
CAGTTGA MB141:ABC12AAXX:1:Myplate1:D10
TGTGCAA MB148:ABC12AAXX:1:Myplate1:D11
CGACAGT MB53:ABC12AAXX:1:Myplate1:D12
ACGTGTA MB131:ABC12AAXX:1:Myplate1:E01
GATGCAT MB82:ABC12AAXX:1:Myplate1:E02
CTAATGT MB191:ABC12AAXX:1:Myplate1:E03
GTCGATA MB72:ABC12AAXX:1:Myplate1:E04
TATACGT MB54:ABC12AAXX:1:Myplate1:E05
GCGTAAT MB64:ABC12AAXX:1:Myplate1:E06
AGCGTTA MB114:ABC12AAXX:1:Myplate1:E07
ATCCGGA MB193:ABC12AAXX:1:Myplate1:E08
TCAGTAT MB59:ABC12AAXX:1:Myplate1:E09
CAATGTT MB171:ABC12AAXX:1:Myplate1:E10
GTTACGA MB138:ABC12AAXX:1:Myplate1:E11
TGCATAT MB46:ABC12AAXX:1:Myplate1:E12
CAAGAAGT MB97:ABC12AAXX:1:Myplate1:F01
GTCATGGT MB163:ABC12AAXX:1:Myplate1:F02
AACAGTGA MB181:ABC12AAXX:1:Myplate1:F03
GTGCAAGA MB122:ABC12AAXX:1:Myplate1:F04
CAATAGGA MB26:ABC12AAXX:1:Myplate1:F05
TGCAGTGT MB34:ABC12AAXX:1:Myplate1:F06
AGGCTAGA MB152:ABC12AAXX:1:Myplate1:F07
CTAGTGGT MB4:ABC12AAXX:1:Myplate1:F08
GCTAGTGT MB57:ABC12AAXX:1:Myplate1:F09
AGTTGGCA MB63:ABC12AAXX:1:Myplate1:F10
TCGCAAGT MB124:ABC12AAXX:1:Myplate1:F11
CGATGTGT MB133:ABC12AAXX:1:Myplate1:F12
AACGTAGA MB157:ABC12AAXX:1:Myplate1:G01
CTCACGGA MB103:ABC12AAXX:1:Myplate1:G02
TAGCGTGT MB185:ABC12AAXX:1:Myplate1:G03
ACGTAAGA MB28:ABC12AAXX:1:Myplate1:G04
CGTATGGT MB8:ABC12AAXX:1:Myplate1:G05
GTACGTGT MB239:ABC12AAXX:1:Myplate1:G06
TTCGAAGA MB121:ABC12AAXX:1:Myplate1:G07
AATACGGA MB173:ABC12AAXX:1:Myplate1:G08
TGACTGGT MB128:ABC12AAXX:1:Myplate1:G09
GCGGATGT MB208:ABC12AAXX:1:Myplate1:G10
CATTGAGA MB41:ABC12AAXX:1:Myplate1:G11
GTAACAGA MB243:ABC12AAXX:1:Myplate1:G12
AGCTTGGT MB241:ABC12AAXX:1:Myplate1:H01
ACAGATGA MB68:ABC12AAXX:1:Myplate1:H02
CAGTTGGT MB20:ABC12AAXX:1:Myplate1:H03
TGCAAGAA MB162:ABC12AAXX:1:Myplate1:H04
ACTCGAGA MB172:ABC12AAXX:1:Myplate1:H05
GGAGCTGT KPS2:ABC12AAXX:1:Myplate1:H06
CTGAGTGT MB21:ABC12AAXX:1:Myplate1:H07
GATCAGAA MB175:ABC12AAXX:1:Myplate1:H08
TGCATAGA MB247:ABC12AAXX:1:Myplate1:H09
GAACGAAT MB180:ABC12AAXX:1:Myplate1:H10
TTGGCGGA MB160:ABC12AAXX:1:Myplate1:H11
CGCCGCAT MB42:ABC12AAXX:1:Myplate1:H12
Error with setupBarcodeFiles: java.lang.ArrayIndexOutOfBoundsException: 0

Exception in thread "Thread-0" java.lang.NullPointerException
    at net.maizegenetics.gbs.homology.ParseBarcodeRead.setupBarcodeFiles(ParseBarcodeRead.java:343)

    at net.maizegenetics.gbs.homology.ParseBarcodeRead.<init>(ParseBarcodeRead.java:41)
    at net.maizegenetics.gbs.pipeline.FastqToTagCountPlugin.countTags(FastqToTagCountPlugin.java:156)
    at net.maizegenetics.gbs.pipeline.FastqToTagCountPlugin.performFunction(FastqToTagCountPlugin.java:68)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
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