Attention:
The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

Error stack trace Indexoutofboundsexception

max_shpakmax_shpak Austin TXMember

I have been trying to run IndelRealigner with the following commands ($tumorPfx etc are file names)

java -d64 -jar $gatkJar -R $hgReference -T IndelRealigner -rf BadCigar -I $tumorPfx.bam -known $G1000_Mills -known $G100\
0_Phase1_Indels -targetIntervals $tumorSample.intervals -o $tumorPfx.realn.bam

and have been getting the following output and error:

ERROR stack trace

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:635)

On this website, I found a similar error with somebody trying to run HaplotypeCaller, albeit with Index and Size = 3, where it was remarked that it may be due to a bug or a java version issue. Is the same thing going on here?

Thank you, Max

Tagged:

Best Answer

Answers

Sign In or Register to comment.