Hapmap from FILLIN to VCF Error writing VCF file

[Ginnie M]

Hi,
I used FILLIN to impute a file and got a nice hmp file out. There were no errors during the imputation process. However, I then wanted to convert the file to vcf  for some downstream things. I just did a git pull and ran through the process again to make sure everything was up to date (v. 5.2.18  Date: December 10, 2015)

Tassel Pipeline Arguments: -Xmx64g -debug -h /path/to/ImputedFile.hmp.txt -export /path/to/ImputedFile -exportType VCF

The standard out error is: ERROR net.maizegenetics.analysis.data.ExportPlugin - Error writing VCF file (standard error output to follow)

I've looked at the marker that the file quits on--in chromosome 2, stops after the 200 somthing-th marker, and can't see anything wrong in the hmp file (whitespace looks normal, correct symbol present for heterozygote, etc.). Any thoughts?
Thank you,
Ginnie


The standard error file:
java.lang.ArrayIndexOutOfBoundsException: 0
        at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:274)
        at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:357)
        at net.maizegenetics.analysis.data.ExportPlugin.performFunction(ExportPlugin.java:89)
        at net.maizegenetics.analysis.data.ExportMultiplePlugin.performFunction(ExportMultiplePlugin.java:88)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1538)
        at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:257)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
java.lang.IllegalArgumentException: Error writing VCF file: /home/gmorriso/data/Imputation/ZeaSyn046_default_selfimpute.vcf: 0
        at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:547)
        at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:357)
        at net.maizegenetics.analysis.data.ExportPlugin.performFunction(ExportPlugin.java:89)
        at net.maizegenetics.analysis.data.ExportMultiplePlugin.performFunction(ExportMultiplePlugin.java:88)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1538)
        at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:257)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
        at net.maizegenetics.analysis.data.ExportMultiplePlugin.performFunction(ExportMultiplePlugin.java:89)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1538)
        at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:257)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

[Ginnie M]

I did some more exploration of the file, still found nothing wrong. Then, I tried changing the FILLIN output (hapmap)  to h5. That worked. I then converted that h5 file to vcf. That vcf file appears to be correct and ok.

In summary: FILLIN output will not be written to vcf, but by converting to h5 first, one can get that data in vcf.

[Zack Miller]

Hi Ginnie,

This is interesting, would you be able to privately send me your hmp and h5 files.  You can even subset your data to have just the positions which cause issues.  This will help me debug what is going on with the conversion.

We are aware of some issues when converting hmp to vcf, and would like to make sure we have covered every problem.  

Thanks,

Zack