Question: Error uploading VCF file onto Tassel v5
0
gravatar for csjlee08
16 months ago by
csjlee0810
csjlee0810 wrote:

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
gbs tassel • 583 views
ADD COMMENTlink modified 16 months ago by RamRS22k • written 16 months ago by csjlee0810

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

ADD REPLYlink written 16 months ago by RamRS22k
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