GATK unified SNP caller error

dakl · 03-26-2010, 09:03 AM

Hi,

Thanks for nice piece of software. I have been trying out the UnifiedGenotyper but am having some issues with it. It crashes if I specify a region larger than a few Mbs, like so:

$ java -Xms32g -Xmx64g -jar /projects/Crisp/bin/GenomeAnalysisTK-1.0.3056/GenomeAnalysisTK.jar -l INFO -R hg18.fasta -T UnifiedGenotyper -I SRR017931.bwa_mapped.sorted.bam -varout bwa_all_test.geli -vf GELI -confidence 50.0 --platform SOLEXA -L chr20:1-5000000
INFO 16:53:06,596 HelpFormatter - ---------------------------------------------------------------------------
INFO 16:53:06,598 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.3056, Compiled 2010/03/22 12:02:00
INFO 16:53:06,598 HelpFormatter - Copyright (c) 2009 The Broad Institute
INFO 16:53:06,599 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 16:53:06,599 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 16:53:06,599 HelpFormatter - Program Args: -l INFO -R hg18.fasta -T UnifiedGenotyper -I SRR017931.bwa_mapped.sorted.bam -varout bwa_all_test.geli -vf GELI -confidence 50.0 --platform SOLEXA -L chr20:1-5000000
INFO 16:53:06,599 HelpFormatter - Date/Time: 2010/03/26 16:53:06
INFO 16:53:06,600 HelpFormatter - ---------------------------------------------------------------------------
INFO 16:53:06,607 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:53:06,674 ReferenceOrderedData - * Adding rod class GFF
INFO 16:53:06,675 ReferenceOrderedData - * Adding rod class dbSNP
INFO 16:53:06,676 ReferenceOrderedData - * Adding rod class HapMapAlleleFrequencies
INFO 16:53:06,676 ReferenceOrderedData - * Adding rod class SAMPileup
INFO 16:53:06,677 ReferenceOrderedData - * Adding rod class GELI
INFO 16:53:06,677 ReferenceOrderedData - * Adding rod class RefSeq
INFO 16:53:06,678 ReferenceOrderedData - * Adding rod class Table
INFO 16:53:06,679 ReferenceOrderedData - * Adding rod class PooledEM
INFO 16:53:06,680 ReferenceOrderedData - * Adding rod class CleanedOutSNP
INFO 16:53:06,680 ReferenceOrderedData - * Adding rod class Sequenom
INFO 16:53:06,681 ReferenceOrderedData - * Adding rod class SangerSNP
INFO 16:53:06,682 ReferenceOrderedData - * Adding rod class SimpleIndel
INFO 16:53:06,682 ReferenceOrderedData - * Adding rod class PointIndel
INFO 16:53:06,683 ReferenceOrderedData - * Adding rod class HapMapGenotype
INFO 16:53:06,683 ReferenceOrderedData - * Adding rod class Intervals
INFO 16:53:06,684 ReferenceOrderedData - * Adding rod class Variants
INFO 16:53:06,685 ReferenceOrderedData - * Adding rod class GLF
INFO 16:53:06,686 ReferenceOrderedData - * Adding rod class VCF
INFO 16:53:06,686 ReferenceOrderedData - * Adding rod class PicardDbSNP
INFO 16:53:06,687 ReferenceOrderedData - * Adding rod class HapmapVCF
INFO 16:53:06,688 ReferenceOrderedData - * Adding rod class Beagle
INFO 16:53:06,689 ReferenceOrderedData - * Adding rod class Plink
INFO 16:53:06,690 ReferenceOrderedData - Processing ROD bindings: 1 -> interval : Intervals : chr20:1-5000000
INFO 16:53:06,690 ReferenceOrderedData - Created binding from interval to chr20:1-5000000 of type class org.broadinstitute.sting.gatk.refdata.IntervalRod
INFO 16:53:06,695 MicroScheduler - Creating linear microscheduler
INFO 16:53:06,702 GenomeAnalysisEngine - Processing 5000000 bases in intervals
INFO 16:53:07,459 TraversalEngine - [PROGRESS] Traversed to chr20:1, processing 1 sites in 0.76 secs (760000.00 secs per 1M sites)
#
# An unexpected error has been detected by Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00002b8dbc15c821, pid=11809, tid=1085090112
#
# Java VM: OpenJDK 64-Bit Server VM (1.6.0-b09 mixed mode linux-amd64)
# Problematic frame:
# V [libjvm.so+0x20a821]
#
# An error report file with more information is saved as:
# /projects/Crisp/bwa_vs_bfast/hs_err_pid11809.log
#
# If you would like to submit a bug report, please visit:
# http://icedtea.classpath.org/bugzilla
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted

Any ideas on this? It occurs if I use -L and specify a region > a few Mbs or if I specify no size at all. I works fine if U use -L chr1:1-500,000 for example. Any ideas on this?

Thanks
Daniel

pfsulliv · 03-28-2010, 10:27 AM

I had a similar problem. The GATK people advised me to update the version of java, and this fixed the issue. pfs

dakl · 03-29-2010, 05:25 AM

Hi,

I updated the java version to jre1.6.0_18 and it did the trick.

Thanks a lot for the info.
Daniel

loveseq · 11-23-2010, 10:14 PM

loveseq · 11-23-2010, 10:27 PM

Hi,

the image i posted doesn't appear. so i have to write my question!
my code is as follows:
[renml@microcystis ~]$ java -jar GenomeAnalysisTK.jar -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci
INFO 14:03:05,468 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:03:05,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.4705, Compiled 2010/11/18 14:06:00
INFO 14:03:05,470 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:03:05,470 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:03:05,471 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:03:05,471 HelpFormatter - Program Args: -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci
INFO 14:03:05,471 HelpFormatter - Date/Time: 2010/11/24 14:03:05
INFO 14:03:05,471 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:03:05,471 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:03:05,472 AbstractGenomeAnalysisEngine - Strictness is SILENT
INFO 14:03:05,588 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
2026
INFO 14:03:05,718 TraversalEngine - [PROGRESS] Traversed 2,026 sites in 0.16 secs (79.47 secs per 1M sites)
INFO 14:03:05,719 TraversalEngine - Total runtime 0.16 secs, 0.00 min, 0.00 hours
INFO 14:03:05,720 TraversalEngine - 0 reads were filtered out during traversal out of 33 total (0.00%)
INFO 14:03:05,722 GATKRunReport - Aggregating data for run report

java version "1.6.0_21"
Java(TM) SE Runtime Environment (build 1.6.0_21-b06)
Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode

could anyone help me?

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03-26-2010, 09:03 AM	#1
dakl Member Location: sweden Join Date: May 2009 Posts: 15	GATK unified SNP caller error Hi, Thanks for nice piece of software. I have been trying out the UnifiedGenotyper but am having some issues with it. It crashes if I specify a region larger than a few Mbs, like so: $ java -Xms32g -Xmx64g -jar /projects/Crisp/bin/GenomeAnalysisTK-1.0.3056/GenomeAnalysisTK.jar -l INFO -R hg18.fasta -T UnifiedGenotyper -I SRR017931.bwa_mapped.sorted.bam -varout bwa_all_test.geli -vf GELI -confidence 50.0 --platform SOLEXA -L chr20:1-5000000 INFO 16:53:06,596 HelpFormatter - --------------------------------------------------------------------------- INFO 16:53:06,598 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.3056, Compiled 2010/03/22 12:02:00 INFO 16:53:06,598 HelpFormatter - Copyright (c) 2009 The Broad Institute INFO 16:53:06,599 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 16:53:06,599 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 16:53:06,599 HelpFormatter - Program Args: -l INFO -R hg18.fasta -T UnifiedGenotyper -I SRR017931.bwa_mapped.sorted.bam -varout bwa_all_test.geli -vf GELI -confidence 50.0 --platform SOLEXA -L chr20:1-5000000 INFO 16:53:06,599 HelpFormatter - Date/Time: 2010/03/26 16:53:06 INFO 16:53:06,600 HelpFormatter - --------------------------------------------------------------------------- INFO 16:53:06,607 GenomeAnalysisEngine - Strictness is SILENT INFO 16:53:06,674 ReferenceOrderedData - * Adding rod class GFF INFO 16:53:06,675 ReferenceOrderedData - * Adding rod class dbSNP INFO 16:53:06,676 ReferenceOrderedData - * Adding rod class HapMapAlleleFrequencies INFO 16:53:06,676 ReferenceOrderedData - * Adding rod class SAMPileup INFO 16:53:06,677 ReferenceOrderedData - * Adding rod class GELI INFO 16:53:06,677 ReferenceOrderedData - * Adding rod class RefSeq INFO 16:53:06,678 ReferenceOrderedData - * Adding rod class Table INFO 16:53:06,679 ReferenceOrderedData - * Adding rod class PooledEM INFO 16:53:06,680 ReferenceOrderedData - * Adding rod class CleanedOutSNP INFO 16:53:06,680 ReferenceOrderedData - * Adding rod class Sequenom INFO 16:53:06,681 ReferenceOrderedData - * Adding rod class SangerSNP INFO 16:53:06,682 ReferenceOrderedData - * Adding rod class SimpleIndel INFO 16:53:06,682 ReferenceOrderedData - * Adding rod class PointIndel INFO 16:53:06,683 ReferenceOrderedData - * Adding rod class HapMapGenotype INFO 16:53:06,683 ReferenceOrderedData - * Adding rod class Intervals INFO 16:53:06,684 ReferenceOrderedData - * Adding rod class Variants INFO 16:53:06,685 ReferenceOrderedData - * Adding rod class GLF INFO 16:53:06,686 ReferenceOrderedData - * Adding rod class VCF INFO 16:53:06,686 ReferenceOrderedData - * Adding rod class PicardDbSNP INFO 16:53:06,687 ReferenceOrderedData - * Adding rod class HapmapVCF INFO 16:53:06,688 ReferenceOrderedData - * Adding rod class Beagle INFO 16:53:06,689 ReferenceOrderedData - * Adding rod class Plink INFO 16:53:06,690 ReferenceOrderedData - Processing ROD bindings: 1 -> interval : Intervals : chr20:1-5000000 INFO 16:53:06,690 ReferenceOrderedData - Created binding from interval to chr20:1-5000000 of type class org.broadinstitute.sting.gatk.refdata.IntervalRod INFO 16:53:06,695 MicroScheduler - Creating linear microscheduler INFO 16:53:06,702 GenomeAnalysisEngine - Processing 5000000 bases in intervals INFO 16:53:07,459 TraversalEngine - [PROGRESS] Traversed to chr20:1, processing 1 sites in 0.76 secs (760000.00 secs per 1M sites) # # An unexpected error has been detected by Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00002b8dbc15c821, pid=11809, tid=1085090112 # # Java VM: OpenJDK 64-Bit Server VM (1.6.0-b09 mixed mode linux-amd64) # Problematic frame: # V [libjvm.so+0x20a821] # # An error report file with more information is saved as: # /projects/Crisp/bwa_vs_bfast/hs_err_pid11809.log # # If you would like to submit a bug report, please visit: # http://icedtea.classpath.org/bugzilla # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug. # Aborted Any ideas on this? It occurs if I use -L and specify a region > a few Mbs or if I specify no size at all. I works fine if U use -L chr1:1-500,000 for example. Any ideas on this? Thanks Daniel

03-28-2010, 10:27 AM	#2
pfsulliv Junior Member Location: NC, USA Join Date: Mar 2010 Posts: 3	I had a similar problem. The GATK people advised me to update the version of java, and this fixed the issue. pfs

03-29-2010, 05:25 AM	#3
dakl Member Location: sweden Join Date: May 2009 Posts: 15	Hi, I updated the java version to jre1.6.0_18 and it did the trick. Thanks a lot for the info. Daniel

11-23-2010, 10:14 PM	#4
loveseq Junior Member Location: Wuhan China Join Date: May 2010 Posts: 3

11-23-2010, 10:27 PM	#5
loveseq Junior Member Location: Wuhan China Join Date: May 2010 Posts: 3	Hi, the image i posted doesn't appear. so i have to write my question! my code is as follows: [renml@microcystis ~]$ java -jar GenomeAnalysisTK.jar -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci INFO 14:03:05,468 HelpFormatter - --------------------------------------------------------------------------- INFO 14:03:05,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.4705, Compiled 2010/11/18 14:06:00 INFO 14:03:05,470 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:03:05,470 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 14:03:05,471 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 14:03:05,471 HelpFormatter - Program Args: -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci INFO 14:03:05,471 HelpFormatter - Date/Time: 2010/11/24 14:03:05 INFO 14:03:05,471 HelpFormatter - --------------------------------------------------------------------------- INFO 14:03:05,471 HelpFormatter - --------------------------------------------------------------------------- INFO 14:03:05,472 AbstractGenomeAnalysisEngine - Strictness is SILENT INFO 14:03:05,588 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 2026 INFO 14:03:05,718 TraversalEngine - [PROGRESS] Traversed 2,026 sites in 0.16 secs (79.47 secs per 1M sites) INFO 14:03:05,719 TraversalEngine - Total runtime 0.16 secs, 0.00 min, 0.00 hours INFO 14:03:05,720 TraversalEngine - 0 reads were filtered out during traversal out of 33 total (0.00%) INFO 14:03:05,722 GATKRunReport - Aggregating data for run report java version "1.6.0_21" Java(TM) SE Runtime Environment (build 1.6.0_21-b06) Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode could anyone help me?