Error uploading VCF file onto Tassel v5

Question

[csjlee08]

Hello, I am trying to upload my VCF file from my GBS data onto Tasselv5. I am unable to upload it because I get the following error:

[AWT-EventQueue-0] DEBUG net.maizegenetics.tassel.TASSELMainFrame - Problem loading file: /media/greg/Overflow/fastgbs/fastgbsfile/Platypus_0.8.1/AllVariants.sorted.vcf.
  ***Error: java.lang.IllegalStateException: Error Processing VCF Block: Missing FORM**strong text**AT tag.***
java.lang.IllegalStateException: Problem loading file: /media/greg/Overflow/fastgbs/fastgbsfile/Platypus_0.8.1/AllVariants.sorted.vcf.
  Error: java.lang.IllegalStateException: Error Processing VCF Block: Missing FORMAT tag.
    at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:591)
    at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:320)
    at net.maizegenetics.tassel.TASSELMainFrame$2.actionPerformed(TASSELMainFrame.java:516)
    at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
    at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
    at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
    at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
    at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:369)
    at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:980)
    at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1024)
    at java.desktop/java.awt.Component.processMouseEvent(Component.java:6578)
    at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3343)
    at java.desktop/java.awt.Component.processEvent(Component.java:6343)
    at java.desktop/java.awt.Container.processEvent(Container.java:2259)
    at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4961)
    at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2317)
    at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
    at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
    at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4539)
    at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4480)
    at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2303)
    at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2758)
    at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
    at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:766)
    at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
    at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
    at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:736)
    at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90

 

##FORMAT=<ID=GT,Number=1,Type=String,Description="Unphased genotypes">
##FORMAT=<ID=GQ,Number=.,Type=Integer,Description="Genotype quality as phred score">
##FORMAT=<ID=GOF,Number=.,Type=Float,Description="Goodness of fit value">
##FORMAT=<ID=NR,Number=.,Type=Integer,Description="Number of reads covering variant location in this sample">
##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype log10-likelihoods for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites">
##FORMAT=<ID=NV,Number=.,Type=Integer,Description="Number of reads containing variant in this sample">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  aln-pe.sorted
NC_030637.1 597444  .   C   CT  2281    badReads    BRF=0.97;FR=0.5000;HP=2;HapScore=1;MGOF=3662;MMLQ=34;MQ=59.26;NF=2;NR=0;PP=2281;QD=1162.0;SC=GTTGAACCAACTGCAGGTAGT;SbPval=1.0;Source=Platypus;TC=2;TCF=2;TCR=0;TR=2;WE=597452;WS=597434 GT:GL:GOF:GQ:NR:NV  0/1:-233.02,0.0,-35.72:3662:99:2:2
NC_030637.1 738101  .   C   CT  164 badReads;alleleBias BRF=0.96;FR=0.5000;HP=2;HapScore=1;MGOF=1758;MMLQ=34;MQ=59.95;NF=4;NR=1;PP=164;QD=41.4;SC=TTCAGGAGAACTGCAGAAGGA;SbPval=0.01;Source=Platypus;TC=70;TCF=13;TCR=57;TR=5;WE=738109;WS=738091    GT:GL:GOF:GQ:NR:NV  0/1:-21.31,0.0,-300.0:1758:99:70:5

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.