undescribed snpEff error after command execution

[MGCBrown]

Hello,

I'm trying to use snpEff to annotate variants in a .vcf file that I called with SAMtools.

Here is my command:

java -Xmx4g -jar snpEff.jar -v spetri2.86 glaucomysvarfiltered.vcf > glaucomysvarfiltered.annotated.vcf

After it loads the database and prints "building interval forest", it starts rapidly outputting a bunch of symbols in my terminal window, and when I check to see if I have any process running via $ top, there is no snpEff processes running, and it discontinues printing to my output file.

I tried it a few times now, and the random symbols have continued to be printed on the screen for over an hour.

I've attached a screen shot of the last processes before it goes haywire, and a screen shot of the symbols.

[MGCBrown]

I've noticed that what I thought was a .vcf file created with the SAMtools variant calling pipeline is actually a vCalendar file.

Any explanations as to why I have a vCalendar file? I'm guessing it is not the same as a variant call format (VCF) file.