To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Using hs37d5 genome to call SVs on data aligned with hg19

Steph_UCSteph_UC Member
edited February 2016 in GenomeSTRiP

Hi, I need help please.

SO my question here is does the message below has to do with the fact that I happened to call SVs on hg19 aligned data with the HS37D5 genome? If so how can I fix it without having to realign all my bam files; or run the whole SVPreprocess again (takes a while with my resources).
SVPreprocess worked without trouble, and SVDiscovery ran all the way to this point (almost the end).

Please help, Here is the trace error message.

INFO 22:09:02,218 31-Jan-2016 SVDiscovery - Processing locus: hs37d5:1-35477943:100-1000000
INFO 22:09:02,218 31-Jan-2016 SVDiscovery - Locus search window: hs37d5:1-35477943
WARNING: BAM index file /projects/Families/mybams/person7.bam.bai is older than BAM /projects/Families/mybams/person7.bam
INFO 22:09:03,388 31-Jan-2016 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: Invalid reference index -1
at htsjdk.samtools.QueryInterval.(
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryContained(
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: Invalid reference index -1
ERROR ------------------------------------------------------------------------------------------

INFO 22:09:26,161 QGraph - Writing incremental jobs reports...
INFO 22:09:26,162 QGraph - 2 Pend, 0 Run, 1 Fail, 85 Done
INFO 22:09:26,166 QCommandLine - Writing final jobs report...
INFO 22:09:26,166 QCommandLine - Done with errors

Post edited by Steph_UC on


Sign In or Register to comment.