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.
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.
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