Hello,
sorry if i missed the same problem in other threads in the forum... but we are having trouble running BaseRecalibrator in a sample and i couldn't find the solution.
I tried many steps and here is what i've found until now:
1 - Other samples work fine
2 - Running picard ValidateSamFile in realigned.bam (after IndelRealigner) gives many erros :
2a - Mate negative strand flag does not match read negative strand flag of mate
2b - Mate alignment does not match alignment start of mate
3c - Value was put into PairInfoMap more than once. (fatal)
3 - Running BaseRecalibrator with option -L 1:428-249250621 works fine!
After the fact that -L works fine i discarded the problem in vcf files and reference file. I don't know how to go further in this investigation since GATK 1 realined.bam also gives me the errors in (2) and those error are peanuts comparing the total number of reads.
The big difference here is that we're are using bwa7.
Any ideas? Thanks!
(i'm filtering out "secondary hits" given by bwa7 and will update this thread, if it works it may be helpful in the future)
GATK output:
INFO 14:11:47,441 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:11:47,443 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36
INFO 14:11:47,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:11:47,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 14:11:47,447 HelpFormatter - Program Args: -nct 8 -T BaseRecalibrator -I /mnt/work/rlb/pac661825//OUT_661825.realigned.bam -R ../data/databases//1KGP/GRCh37_female_exome_mt1kg.fasta --knownSites ../data/databases//dbSNP/dbSNP_137/00-All.vcf -o /mnt/work/rlb/pac661825//OUT_661825.grp
INFO 14:11:47,447 HelpFormatter - Date/Time: 2013/03/26 14:11:47
INFO 14:11:47,447 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:11:47,447 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:11:47,458 ArgumentTypeDescriptor - Dynamically determined type of ../data/databases/dbSNP/dbSNP_137/00-All.vcf to be VCF
INFO 14:11:47,500 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:11:47,558 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 14:11:47,565 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 14:11:47,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 14:11:47,587 RMDTrackBuilder - Loading Tribble index from disk for file ../data/databases/dbSNP/dbSNP_137/00-All.vcf
INFO 14:11:47,704 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 8 processors available on this machine
INFO 14:11:47,745 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files
INFO 14:11:47,750 GenomeAnalysisEngine - Done creating shard strategy
INFO 14:11:47,750 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 14:11:47,750 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 14:11:47,773 BaseRecalibrator - The covariates being used here:
INFO 14:11:47,773 BaseRecalibrator - ReadGroupCovariate
INFO 14:11:47,773 BaseRecalibrator - QualityScoreCovariate
INFO 14:11:47,773 BaseRecalibrator - ContextCovariate
INFO 14:11:47,774 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 14:11:47,774 BaseRecalibrator - CycleCovariate
INFO 14:11:47,776 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO 14:11:47,777 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO 14:12:18,626 ProgressMeter - 1:15956928 1.10e+06 30.0 s 28.0 s 0.5% 95.1 m 94.6 m
INFO 14:12:48,655 ProgressMeter - 1:34102053 2.70e+06 60.0 s 22.0 s 1.1% 89.0 m 88.0 m
INFO 14:13:18,685 ProgressMeter - 1:59096606 4.50e+06 90.0 s 20.0 s 1.9% 77.1 m 75.6 m
INFO 14:13:48,714 ProgressMeter - 1:103467532 5.90e+06 120.0 s 20.0 s 3.4% 58.7 m 56.7 m
INFO 14:14:18,745 ProgressMeter - 1:153234111 7.50e+06 2.5 m 20.0 s 5.0% 49.5 m 47.0 m
INFO 14:14:48,774 ProgressMeter - 1:172414433 9.30e+06 3.0 m 19.0 s 5.7% 53.1 m 50.1 m
INFO 14:15:19,054 ProgressMeter - 1:208266349 1.10e+07 3.5 m 19.0 s 6.9% 51.3 m 47.8 m
INFO 14:15:49,095 ProgressMeter - 1:247611815 1.27e+07 4.0 m 19.0 s 8.2% 49.3 m 45.2 m
INFO 14:15:56,507 GATKRunReport - Uploaded run statistics report to AWS S3
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (0) > (-1) STOP -- this should never happen -- call Mauricio! at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:537) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(ReadClipper.java:176) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:389) at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:392) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:244) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:679)
Dear expert,
When I run gatk with fellow command,
java -Xmx10g -Xms10g -jar ~/bin/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -R Homo_sapiens.GRCh37.63/bak/Homo_sapiens.GRCh37.63.dna.chromosome.fa \ -knownSites ~/bin/GenomeAnalysisTK-2.3-4-g57ea19f/dbsnp_137.hg19.vcf \ -I input_4.bam \ -o mySample_CovarTable_Recal.grp
I got this error:
INFO 22:25:22,825 RMDTrackBuilder - Creating Tribble index in memory for file ~/bin/GenomeAnalysisTK-2.3-4-g57ea19f/dbsnp_137.hg19.vcf
java.lang.NoClassDefFoundError: com/sun/javadoc/ProgramElementDoc ... ... ...
INFO 17:40:38,765 ProgressMeter - chrX:147886444 3.21e+07 5.5 h 10.3 m 97.9% 5.6 h 7.1 m INFO 17:41:08,775 ProgressMeter - chrX:151653849 3.21e+07 5.5 h 10.3 m 98.0% 5.6 h 6.7 m INFO 17:41:38,785 ProgressMeter - chrX:153812787 3.22e+07 5.5 h 10.3 m 98.1% 5.6 h 6.5 m
java.lang.NoClassDefFoundError: net/sf/samtools/util/CloserUtil
at net.sf.picard.util.PeekableIterator.close(PeekableIterator.java:46)
at net.sf.picard.sam.MergingSamRecordIterator.addIfNotEmpty(MergingSamRecordIterator.java:169)
at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:125)
at net.sf.picard.sam.MergingSamRecordIterator.next(MergingSamRecordIterator.java:39)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1091)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReleasingIterator.next(SAMDataSource.java:1057)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:105)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:81)
at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:41)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:24)
at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:12)
at org.broadinstitute.sting.utils.baq.ReadTransformingIterator.next(ReadTransformingIterator.java:36)
at org.broadinstitute.sting.utils.baq.ReadTransformingIterator.next(ReadTransformingIterator.java:15)
at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShard.fill(ReadShard.java:135)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.advance(ReadShardBalancer.java:153)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.next(ReadShardBalancer.java:116)
at org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer$1.next(ReadShardBalancer.java:75)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:65)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
Caused by: java.lang.ClassNotFoundException: net.sf.samtools.util.CloserUtil
at java.net.URLClassLoader$1.run(URLClassLoader.java:199)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
... 29 more
Caused by: java.util.zip.ZipException: error reading zip file
at java.util.zip.ZipFile.read(Native Method)
at java.util.zip.ZipFile.access$1200(ZipFile.java:29)
at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:447)
at java.util.zip.ZipFile$1.fill(ZipFile.java:230)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:141)
at java.util.jar.Manifest$FastInputStream.fill(Manifest.java:422)
at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:358)
at java.util.jar.Manifest$FastInputStream.readLine(Manifest.java:390)
at java.util.jar.Attributes.read(Attributes.java:359)
at java.util.jar.Manifest.read(Manifest.java:182)
at java.util.jar.Manifest.
Any Idea what is the solution??
Hi all,
I've been analyzing some illumina whole exome sequencing data these days. Yesterday I used GATK(version 2.0) UnifiedGenotyper to call snps and indels with the following commands:
run_gatk.sh -T UnifiedGenotyper -R GRCh37/human_g1k_v37.fasta -I GATK_recal_result.bam -glm BOTH --dbsnp reference/dbsnp_134.b37.vcf -stand_call_conf 50 -stand_emit_conf 10 -o raw2.vcf -dcov 200 --num_threads 10
After running theses commands, I got a vcf file which is very small(when I checked the vcf file, I found these called snps and indels are all from Chromosome1) The error message is as follows:
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:269)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
Caused by: org.broad.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files), for input source: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp
at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:104)
at org.broad.tribble.TribbleIndexedFeatureReader.
Would you please help me solve it ? Thanks a lot
Hello dear GATK Team,
when trying to run Haplotypecaller on my exome files prepared with ReduceReads i get the error stated below. As you can see the newest GATK Version is used. Also UnifiedGenotyper does not produce any errors on te exact same data (90 SOLiD exomes creatted according to Best Practice v4).
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Too many deletions?
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:447)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:396)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:392)
at org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage.annotate(DepthOfCoverage.java:56)
at org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation.annotate(InfoFieldAnnotation.java:24)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:223)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:429)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:104)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:249)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:204)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:179)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:136)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:29)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-3-gde33222):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?
##### ERROR ------------------------------------------------------------------------------------------
The Command line used (abbreviated):
java -Xmx30g -jar /home/common/GenomeAnalysisTK-2.2-3/GenomeAnalysisTK.jar \
-R /home/common/hg19/ucschg19/ucsc.hg19.fasta \
-T HaplotypeCaller \
-I ReduceReads/XXXXX.ontarget.MarkDups.nRG.reor.Real.Recal.reduced.bam [x90]\
--dbsnp /home/common/hg19/dbsnp_135.hg19.vcf \
-o 93Ind_ped_reduced_HC_snps.raw.vcf \
-ped familys.ped \
--pedigreeValidationType SILENT \
-stand_call_conf 20.0 \
-stand_emit_conf 10.0
I had annotated raw indel file (given by UnifiedGenotyper), 1000G_omni2.5.b37.sites.vcf and hapmap_3.3.b37.sites.vcf with all possible annotations including QD (QualByDepth) using VariantAnnotator. However, i got an error when i tried to run VariantRecalibrator. It was complaing that QD has not been found in training variant. Is QD important annotation for indel filtering. Can it be ignored ?
P.S. - i did not use sample bam file while annotating training data set.
.
.
.
INFO 15:11:55,999 RMDTrackBuilder - Loading Tribble index from disk for file NCBI_dbsnp_for_GATK.vcf
INFO 15:12:21,650 TraversalEngine - chr1:128346793 1.98e+07 30.0 s 1.5 s 4.1% 12.1 m 11.6 m
INFO 15:12:51,650 TraversalEngine - chr9:130658800 5.26e+07 60.0 s 1.1 s 53.9% 111.2 s 51.2 s
INFO 15:13:13,618 VariantDataManager - QD: mean = NaN standard deviation = NaN
INFO 15:13:16,417 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator
##### ERROR ------------------------------------------------------------------------------------------
Hi all, I'm running VariantRecalibrator on a SNP set (47 exomes) and I get this error:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-3-gde33222):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)
##### ERROR ------------------------------------------------------------------------------------------
this is the command line:
java -Djava.io.tmpdir=/lustre2/scratch/ -Xmx32g -jar /lustre1/tools/bin/GenomeAnalysisTK-2.2-3.jar \
-T VariantRecalibrator \
-R /lustre1/genomes/hg19/fa/hg19.fa \
-input /lustre1/workspace/Ferrari/Carrera/Analysis/UG/bpd_ug.SNP.vcf \
-resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /lustre1/genomes/hg19/annotation/hapmap_3.3.hg19.sites.vcf.gz \
-resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 /lustre1/genomes/hg19/annotation/1000G_omni2.5.hg19.sites.vcf.gz \
-resource:dbsnp,VCF,known=true,training=false,truth=false,prior=6.0 /lustre1/genomes/hg19/annotation/dbSNP-137.chr.vcf -an QD \
-an HaplotypeScore \
-an MQRankSum \
-an ReadPosRankSum \
-an FS \
-an MQ \
-an DP \
-an QD \
-an InbreedingCoeff \
-mode SNP \
-recalFile /lustre2/scratch/Carrera/Analysis2/snp.ug.recal.csv \
-tranchesFile /lustre2/scratch/Carrera/Analysis2/snp.ug.tranches \
-rscriptFile /lustre2/scratch/Carrera/Analysis2/snp.ug.plot.R \
-U ALLOW_SEQ_DICT_INCOMPATIBILITY \
--maxGaussians 6
I've already tried to decrease the --maxGaussians option to 4, I've also added --percentBad option (setting it up to 0.12, as for INDEL) but I still get the error.
I've added the option -debug to see what's happening, but apparently this has been removed from GATK-2.2.
Any help is appreciated...
thanks
Hi all,
Has anyone else gotten the following:
java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:242) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:306) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:35) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:149) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
My command line was: java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -V w01.sorted.vcf -o w01.phased.vcf -f "mom+dad=child" -R hg19.fa
Cheers,
Paul
Hi to all I have a problem in understanding an error output produced by PrintReads tool. This is my command line(the recal.grp file is correctly produced by BaseRecalibrator tool):
java -jar /Archive/Software/GATK2.1-8/GenomeAnalysisTK.jar -T PrintReads -I /Path-to-BAMfile -BQSR /Path-to-recal.grp -o /Path-to-output
The error output is:
As apparently no further information are available I cannot understand what is the issue. Thank for the help! Giuliano
Hi,
I got this error today running BaseRecalibrator:
java.lang.NullPointerException at java.util.concurrent.locks.AbstractQueuedSynchronizer.hasQueuedPredecessors(AbstractQueuedSynchronizer.java:1453) at java.util.concurrent.locks.ReentrantLock$FairSync.tryAcquire(ReentrantLock.java:240) at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireInterruptibly(AbstractQueuedSynchronizer.java:1158) at java.util.concurrent.locks.ReentrantLock.lockInterruptibly(ReentrantLock.java:340) at java.util.concurrent.PriorityBlockingQueue.take(PriorityBlockingQueue.java:244) at org.broadinstitute.sting.utils.nanoScheduler.Reducer.reduceAsMuchAsPossible(Reducer.java:121) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:510) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:636)
The command arguments I used are: -nct 4 -T BaseRecalibrator --intermediate_csv_file inter.csv -I realigned.bam -R Homo_sapiens.GRCh37.68.dna.chromosome.all.fasta -o recal_data.grp --plot_pdf_file recal.pdf -knownSites dbsnp_137.b37.vcf -knownSites Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites 1000G_phase1.indels.b37.vcf --disable_indel_quals
This command has previously worked with other data using the same version of GATK.
on the forum page
http://gatkforums.broadinstitute.org/discussion/1209/how-to-run-the-gatk-for-the-first-time#latest
there are two examples. The first runs fine. The second generates this error
MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'
but the input files are the same. I only changed "Reads" to "Loci" in the command. I am running Unix so I do not need to retype the entire command. This command works fine
java -jar GenomeAnalysisTK.jar -T CountReads -R exampleFASTA.fasta -I exampleBAM.bam
This command produces the error
java -jar GenomeAnalysisTK.jar -T CountLoci -R exampleFASTA.fasta -I exampleBAM.bam -o output.txt
Any suggestions?
ERROR MESSAGE: SAM/BAM file genome_110616_SN365_A_s_7_seq_GQJ-1.pe.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
i am very new to GATK and i was trying to invoke the readcount command and i got the error above what is read groups.
thank you
Hi all, I'm trying to perform BQRS on a bam file I have. Unfortunately I get this error:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (0) > (-1) STOP -- this should never happen, please check read: HWI-ST1296:110:C1P16ACXX:8:2116:15747:68300 2/2 101b aligned read. (CIGAR: 5D74M27S)
The culprit appears to be this read pair:
HWI-ST1296:110:C1P16ACXX:8:2116:15747:68300 147 chr2 230419662 24 5D74M27S = 230419667 -74 GAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGTGAAAGGAAGGGAAAAGAAAAAGGAAAGGAAGGCAATCCCTGCCCAGGTTCTTAATTTTC #####A>:3CC>;=>DC@;>66;.3@DAA>CA@77.)((./))@FBB.<<??/9*0*******00*?1***1*1)1)<)B3++2+2+22++2222+4++B= PG:Z:MarkDuplicates RG:Z:GB_L008.1 NM:i:9 AS:i:43 XS:i:45
HWI-ST1296:110:C1P16ACXX:8:2116:15747:68300 99 chr2 230419667 53 83M18S = 230419662 74 GAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAGAAAGGAAGGAAAAAGAGAAAGGGAAGGAAGGAAATTCATGCTCAGTATCTAATTTTTA ??;ADDDDHBF3DA=GBGB@D;EFC<3CDHBHICDEGEGIE=@@A@D@;C;;2?@7;=7>>;5>;;@B1<@CB<?>>::4++>@@>CC44>>@DC(:CA## PG:Z:MarkDuplicates RG:Z:GB_L008.1 NM:i:0 AS:i:83 XS:i:50
Program arguments were:
-R /lustre1/genomes/hg19/fa/hg19.fa -knownSites /lustre1/genomes/hg19/annotation/dbSNP-137.chr.vcf -I GB_dedup.realign.bam -T BaseRecalibrator --covariate QualityScoreCovariate --covariate CycleCovariate --covariate ContextCovariate --covariate ReadGroupCovariate --unsafe ALLOW_SEQ_DICT_INCOMPATIBILITY -nct 64 -o jobdir/GB.grp
I'm running the latest nightbuild of GATK. Any hint is very much appreciated
d