I have downloaded dbSNP data and trying to sort the .vcf file with the command line:

java -Xms10g -Xmx20g -Djava.io.tmpdir=tmp -jar picard.jar SortVcf INPUT=00-All_chr.vcf OUTPUT=00-All_chr_sorted.vcf SEQUENCE_DICTIONARY=hg38.dict

I did add "chr" to the chromosome information in the dbSNP data.

The following is part of the log in the end of the log file after running the command line. I did not get any error message, and it ran for more than an hour, but the result file is empty.

Can anyone please help me with this?

INFO    2015-09-17 19:10:44     SortVcf read   143,025,000 records.  Elapsed time: 04:21:07s.  Time for last 25,000:    3s.  Last read position: chrY:2,405,259
INFO    2015-09-17 19:10:44     SortVcf read   143,050,000 records.  Elapsed time: 04:21:07s.  Time for last 25,000:    0s.  Last read position: chrY:3,851,348
INFO    2015-09-17 19:10:44     SortVcf read   143,075,000 records.  Elapsed time: 04:21:07s.  Time for last 25,000:    0s.  Last read position: chrY:7,480,875
INFO    2015-09-17 19:10:44     SortVcf read   143,100,000 records.  Elapsed time: 04:21:07s.  Time for last 25,000:    0s.  Last read position: chrY:10,151,437
INFO    2015-09-17 19:10:45     SortVcf read   143,125,000 records.  Elapsed time: 04:21:08s.  Time for last 25,000:    0s.  Last read position: chrY:11,324,243
INFO    2015-09-17 19:10:45     SortVcf read   143,150,000 records.  Elapsed time: 04:21:08s.  Time for last 25,000:    0s.  Last read position: chrY:12,617,451
INFO    2015-09-17 19:10:45     SortVcf read   143,175,000 records.  Elapsed time: 04:21:08s.  Time for last 25,000:    0s.  Last read position: chrY:15,351,020
INFO    2015-09-17 19:10:45     SortVcf read   143,200,000 records.  Elapsed time: 04:21:08s.  Time for last 25,000:    0s.  Last read position: chrY:19,370,690
INFO    2015-09-17 19:10:45     SortVcf read   143,225,000 records.  Elapsed time: 04:21:08s.  Time for last 25,000:    0s.  Last read position: chrY:21,843,643
INFO    2015-09-17 19:10:46     SortVcf read   143,250,000 records.  Elapsed time: 04:21:09s.  Time for last 25,000:    0s.  Last read position: chrY:57,084,728
[Thu Sep 17 19:10:59 CEST 2015] picard.vcf.SortVcf done. Elapsed time: 261.39 minutes.
Runtime.totalMemory()=12853444608
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
        at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:84)
        at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:21)
        at java.util.TimSort.countRunAndMakeAscending(TimSort.java:360)
        at java.util.TimSort.sort(TimSort.java:234)
        at java.util.Arrays.sort(Arrays.java:1512)
        at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:218)
        at htsjdk.samtools.util.SortingCollection.doneAdding(SortingCollection.java:190)
        at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:265)
        at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:58)
        at picard.vcf.SortVcf.writeSortedOutput(SortVcf.java:171)
        at picard.vcf.SortVcf.doWork(SortVcf.java:90)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)