[Useq-users] VCFAnnotator error

[Jesse R. <jes...@u2...>]

Hello,

I am trying to locally run VCFAnnotator, and get the error below. Even though I have specified an annovar directory, it looks like it is a pointing to a directory on the Tomato server. How can I correct?

USeq_8.8.1 Arguments: -v 10764X1_RG.recal.vcf -o 10764X1_RG.recal.ann.vcf -p /Applications/annovar -t /Applications/RSeQC-2.3.3/lib/tabix

Using ALL 1K samples for annotation
Working on file chunk: 1


***************************************
* Starting: Ensembl Annotations
***************************************


IO error during annovar command execution: Cannot run program "/home/u0855942/annovar_version/annotate_variation.pl": error=2, No such file or directory
java.io.IOException: Cannot run program "/home/u0855942/annovar_version/annotate_variation.pl": error=2, No such file or directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041)
	at edu.utah.seq.vcf.VCFAnnotator$AnnovarCommand.runCommand(VCFAnnotator.java:698)
	at edu.utah.seq.vcf.VCFAnnotator.<init>(VCFAnnotator.java:125)
	at edu.utah.seq.vcf.VCFAnnotator.main(VCFAnnotator.java:497)
Caused by: java.io.IOException: error=2, No such file or directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)
	at java.lang.ProcessImpl.start(ProcessImpl.java:130)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022)
	... 3 more

thanks,

Jesse Rowley
Division of Pulmonary Medicine
University of Utah School of Medicine