Index: 0, Size: 0 error when loading vcf file in Tassel 5

[Hans van Leeuwen]

Hello,

I am trying to load a vcf file in Tassel 5 (http://tassel.bitbucket.org/installer/TASSEL_5_windows-x64.exe)

The file is attached to this post.

This file can be loaded without problems in Tassel 4.

However, in Tassel 5 it will not load and give an error message.

The error that I see in the Tassel 5 logging window is:

Err Site Number:0

Err:MyRefGenome_EIAKD15208 29378 . C C,T . PASS NS=93;DP=10567;AF=0.9150,0.0850 GT:DP 0/0:64 0/1:134 0/0:97 0/0:240 0/0:55 0/0:47 0/0:92 0/0:136 0/0:217 0/0:51 0/0:28 0/0:201 0/0:94 0/0:257 0/0:300 0/0:121 0/0:67 0/0:14 0/0:106 0/0:282 0/0:6 0/0:28 0/0:152 0/0:133 0/0:61 0/0:83 0/0:307 ./.:7 ./.:1 0/0:57 0/0:12 1/1:130 0/0:291 0/0:74 0/0:239 0/0:107 0/1:29 0/0:25 0/0:153 0/0:207 0/0:87 1/1:108 0/0:22 0/0:98 0/0:170 0/0:258 0/0:66 0/0:69 0/0:407 0/0:25 0/0:192 0/0:20 1/1:12 0/1:10 1/1:25 0/0:64 0/0:344 0/0:95 0/0:280 0/0:52 1/1:144 0/0:118 0/0:42 0/0:39 0/0:147 0/1:229 1/1:56 0/0:66 0/0:76 0/0:79 0/0:100 0/1:31 0/0:258 0/0:35 0/1:69 0/0:263 0/0:202 0/0:186 0/0:24 0/1:302 0/0:65 0/1:13 0/0:22 0/0:163 0/0:27 0/0:123 0/0:36 0/0:229 0/0:39 1/1:10 0/0:97 0/0:20 ./.:322 0/0:130 0/0:13 1/1:13

java.lang.ArrayIndexOutOfBoundsException: -1

at net.maizegenetics.dna.snp.io.ProcessVCFBlock.run(BuilderFromVCF.java:396)

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)

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

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

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

at net.maizegenetics.dna.map.PositionListBuilder.validateOrdering(PositionListBuilder.java:132)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.completeInMemoryBuilding(BuilderFromVCF.java:220)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:161)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:95)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:62)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:68)

at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:327)

at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:164)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)

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

Any help or tips are appreciated,

Thank you,

Hans

[Terry Casstevens]

Dear Hans,

I'm not all specifications of VCF. But our code is expecting the
header information (i.e. INFO, FILTER, FORMAT) to begin with ##. And
your headers only have #. Do you know if that's a problem with your
format? Or a problem with our code?

Best,

Terry

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[Hans van Leeuwen]

Dear Terry,

That is correct. I checked the vcf 4.1 standard and those lines should indeed start with ##. I will contact the provider who delivered these files to us.

Looks like the checks in Tassel 5 are more stringent than in Tassel 4.

Thank you so much.

Best regards,

Hans

[Stripe Rust]

same for me. 

in tassel 4 i had no problem, but now when I try to analyse I get the error message: 

Index: 0, Sive: 0

how can I find the problem with the file?

[Terry Casstevens]

Please follow these instructions to get more information.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Best,

Terry

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