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HaplotypeCaller - Code exception

mpmachadompmachado LisboaMember

Dear GATK Team,
I'm trying to run HaplotypeCaller, on a Bowtie2 bam file, but I'm having a Code exception.
Any idea how to fix it?
Best regards,
Miguel Machado

Command:
/scratch/mpmachado/NGStools/java_oracle/jre1.8.0_45/bin/java -jar /scratch/mpmachado/NGStools/gatk/GenomeAnalysisTK.jar -T HaplotypeCaller -R /scratch/mpmachado/trabalho1diversidade/genomaReferencia/dadosGenoma/NC_004368.fna -I /scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam --out output.raw.snps.indels.vcf --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES --sample_ploidy 1

INFO 16:21:59,507 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:21:59,511 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
INFO 16:21:59,511 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:21:59,511 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:21:59,516 HelpFormatter - Program Args: -T HaplotypeCaller -R /scratch/mpmachado/trabalho1diversidade/genomaReferencia/dadosGenoma/NC_004368.fna -I /scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam --out output.raw.snps.indels.vcf --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES --sample_ploidy 1
INFO 16:21:59,521 HelpFormatter - Executing as [email protected] on Linux 2.6.32-5-amd64 i386; Java HotSpot(TM) Server VM 1.8.0_45-b14.
INFO 16:21:59,521 HelpFormatter - Date/Time: 2015/07/07 16:21:59
INFO 16:21:59,521 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:21:59,521 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:22:00,257 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:22:00,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 16:22:00,370 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:22:00,401 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 16:22:00,410 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
INFO 16:22:01,869 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.NullPointerException
at java.util.TreeMap.compare(TreeMap.java:1290)
at java.util.TreeMap.put(TreeMap.java:538)
at java.util.TreeSet.add(TreeSet.java:255)
at org.broadinstitute.gatk.utils.sam.ReadUtils.getSAMFileSamples(ReadUtils.java:70)
at org.broadinstitute.gatk.engine.samples.SampleDBBuilder.addSamplesFromSAMHeader(SampleDBBuilder.java:66)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeSampleDB(GenomeAnalysisEngine.java:846)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:296)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
ERROR
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm, that's odd. Have you validated your input file with Picard ValidateSamFile?

    I see also that you're using Java 1.8. Technically we only support Java 1.7 at the moment, so consider switching your java version and see if it makes a difference.

  • mpmachadompmachado LisboaMember

    I ran Picard ValidateSamFile as followed and got some errors. I googled those errors, but I didn't find any tip on how to fix them!
    However, I ran again GATK using Java 1.7 but I still got the same code exception (you can find it bellow).
    Thank you for your help.
    Miguel Machado

    Command:
    java -jar /scratch/mpmachado/NGStools/picard/picard/dist/picard.jar ValidateSamFile INPUT=/scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam MODE=SUMMARY

    [Wed Jul 08 10:26:03 WEST 2015] picard.sam.ValidateSamFile INPUT=/scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam MODE=SUMMARY MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
    [Wed Jul 08 10:26:03 WEST 2015] Executing as [email protected] on Linux 2.6.32-5-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_26-b03; Picard version: 1.135(83ec44e03ec8d07ef180ef86b7a62d59a80dedd3_1435607037) JdkDeflater

    HISTOGRAM java.lang.String

    Error Type Count
    ERROR:HEADER_RECORD_MISSING_REQUIRED_TAG 1
    ERROR:MISMATCH_FLAG_MATE_NEG_STRAND 5294
    ERROR:MISSING_PLATFORM_VALUE 1

    [Wed Jul 08 10:26:26 WEST 2015] picard.sam.ValidateSamFile done. Elapsed time: 0.39 minutes.
    Runtime.totalMemory()=396099584
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

    Command:
    /scratch/mpmachado/NGStools/java_oracle/jre1.7.0_79/bin/java -jar /scratch/mpmachado/NGStools/gatk/GenomeAnalysisTK.jar -T HaplotypeCaller -R /scratch/mpmachado/trabalho1diversidade/genomaReferencia/dadosGenoma/NC_004368.fna -I /scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam --out output.raw.snps.indels.vcf --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES --sample_ploidy 1

    INFO 10:25:23,397 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:25:23,400 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
    INFO 10:25:23,400 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 10:25:23,400 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 10:25:23,405 HelpFormatter - Program Args: -T HaplotypeCaller -R /scratch/mpmachado/trabalho1diversidade/genomaReferencia/dadosGenoma/NC_004368.fna -I /scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam --out output.raw.snps.indels.vcf --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES --sample_ploidy 1
    INFO 10:25:23,409 HelpFormatter - Executing as [email protected] on Linux 2.6.32-5-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15.
    INFO 10:25:23,409 HelpFormatter - Date/Time: 2015/07/08 10:25:23
    INFO 10:25:23,409 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:25:23,409 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:25:24,113 GenomeAnalysisEngine - Strictness is SILENT
    INFO 10:25:24,239 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
    INFO 10:25:24,250 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 10:25:24,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
    INFO 10:25:24,312 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
    INFO 10:25:25,892 GATKRunReport - Uploaded run statistics report to AWS S3

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

    java.lang.NullPointerException
    at java.util.TreeMap.compare(Unknown Source)
    at java.util.TreeMap.put(Unknown Source)
    at java.util.TreeSet.add(Unknown Source)
    at org.broadinstitute.gatk.utils.sam.ReadUtils.getSAMFileSamples(ReadUtils.java:70)
    at org.broadinstitute.gatk.engine.samples.SampleDBBuilder.addSamplesFromSAMHeader(SampleDBBuilder.java:66)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeSampleDB(GenomeAnalysisEngine.java:846)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:296)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
    ERROR
    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 http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭
    edited July 2015

    @mpmachado
    Hi Miguel Machado,

    Have a look at this article to see what the input bam file requires: http://gatkforums.broadinstitute.org/discussion/1317/collected-faqs-about-bam-files
    You can use Picard's Add or Replace Read Groups to add any missing information. http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups

    For the second error, Picard's Fix Mate Information may help. http://broadinstitute.github.io/picard/command-line-overview.html#FixMateInformation

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    P.S.

    If you want all the sites emitted, --output_mode EMIT_ALL_SITES does not work. You should use Haplotype Caller in -ERC GVCF or -ERC BP_RESOLUTION mode then run GenotypeGVCFs with the -allSites option. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php#--includeNonVariantSites

    -Sheila

  • agrothbergagrothberg Member

    I am seeing a similar exception:

    ##### ERROR stack trace 
    java.lang.NullPointerException
        at java.util.TreeMap.compare(TreeMap.java:1188)
        at java.util.TreeMap.put(TreeMap.java:531)
        at java.util.TreeSet.add(TreeSet.java:255)
        at org.broadinstitute.gatk.utils.sam.ReadUtils.getSAMFileSamples(ReadUtils.java:70)
        at org.broadinstitute.gatk.engine.samples.SampleDBBuilder.addSamplesFromSAMHeader(SampleDBBuilder.java:66)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeSampleDB(GenomeAnalysisEngine.java:846)
        at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:296)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
    

    I am not sure if this is related:

    java -jar picard.jar ValidateSamFile INPUT=/output/ecoli.bam
    ERROR: File /output/ecoli.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:b5771143 PU:/input/ecoli.fastq   PL:PACBIO   DS:READTYPE=SUBREAD;BINDINGKIT=;SEQUENCINGKIT=;BASECALLERVERSION=
    ERROR: Header version: 1.5 does not match any of the acceptable versions: 1.0, 1.4, 1.3
    
    samtools view -H /output/ecoli.bam
    @HD VN:1.5  SO:coordinate   pb:3.0b7
    @SQ SN:chr1 LN:4641652  M5:482a2b04485ec8c4b5f4eaba2c2002da
    @RG ID:b5771143 PU:/input/ecoli.fastq   PL:PACBIO   DS:READTYPE=SUBREAD;BINDINGKIT=;SEQUENCINGKIT=;BASECALLERVERSION=
    @PG ID:1    PN:BLASR    VN:2.0.0    CL:blasr /input/ecoli.fastq /input-ref/ecoli_k12_reference.fasta -sam -out /output/ecoli.sam 
    
  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @agrothberg
    Hi,

    Can you please tell me the version of GATK you are using and the exact command you ran to get the first error?

    For the Validate Sam File error, the problem is that you do not have sample names specified in the bam header. You can use Picard's Add or Replace Read Groups to fix that.

    These articles may help as well:
    http://gatkforums.broadinstitute.org/discussion/42/pacbio-data-processing-guidelines

    https://www.broadinstitute.org/gatk/guide/article?id=1317

    -Sheila

  • jdlimjdlim South AfricaMember

    Hi I am having a similar issue with files I generate using SMALT alignment. I'm using GATK version 3.5 and I get an vcf containing only a header and no variants.

    java -Xmx12g -jar picard.jar ValidateSamFile \
            INPUT="Test_SMALT_sorted_dedup_realigned_sorted.bam" \
            OUTPUT="valid.txt"
    

    "ERROR: Header version: 1.5 does not match any of the acceptable versions: 1.0, 1.4, 1.3"

    samtools view -H "Test_SMALT_sorted_dedup_realigned_sorted.bam"

    @HD VN:1.5 GO:none SO:coordinate
    @SQ SN:gi|448814763|ref|NC_000962.3| LN:4411532
    @RG ID:M_15_A712_F2_R14816_GGAGAAC_L004 PU:truseq LB:library SM:M_15_A712_F2_R14816_GGAGAAC_L004 PL:illumina
    @PG ID:MarkDuplicates VN:1.124(69ecf101f612fdc0f3d555aa2d3cc0b1ea193c68_1415030499) CL:picard.sam.markduplicates.MarkDuplicates INPUT=[/scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_SMALT_sorted.bam] OUTPUT=/scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_SMALT_sorted_dedup.bam METRICS_FILE=/scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_SMALT_sorted_dedup.bam.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PN:MarkDuplicates
    @PG ID:smalt VN:0.7.6 CL:/home/lmbjas002/bin/smalt/src/smalt map -x -c 0.6 -l pe -d 0 -r -1 -n 16 -f sam -o M_15_A712_F2_R14816_GGAGAAC_L004_no_RG_SMALTpair.sam /researchdata/fhgfs/lmbjas002/Server_Version/My_pipeline/references/H37Rv/H37Rv.fasta /scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_forward_paired.fq /scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_reverse_paired.fq PN:smalt
    @PG ID:smalt.1 VN:0.7.6 CL:/home/lmbjas002/bin/smalt/src/smalt map -x -c 0.6 -d 0 -r -1 -n 16 -f sam -o M_15_A712_F2_R14816_GGAGAAC_L004_no_RG_SMALTunF.sam /researchdata/fhgfs/lmbjas002/Server_Version/My_pipeline/references/H37Rv/H37Rv.fasta /scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_forward_unpaired.fq PN:smalt
    @PG ID:smalt.2 VN:0.7.6 CL:/home/lmbjas002/bin/smalt/src/smalt map -x -c 0.6 -d 0 -r -1 -n 16 -f sam -o M_15_A712_F2_R14816_GGAGAAC_L004_no_RG_SMALTunR.sam /researchdata/fhgfs/lmbjas002/Server_Version/My_pipeline/references/H37Rv/H37Rv.fasta /scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_reverse_unpaired.fq PN:smalt
    @PG ID:GATK IndelRealigner VN:3.5-0-g36282e4 CL:knownAlleles=[] targetIntervals=/scratch/lmbjas002/new_pipe_test_data/results/M_15_A712_F2_R14816_GGAGAAC_L004/Temp/M_15_A712_F2_R14816_GGAGAAC_L004_SMALT_sorted_dedup.bam.list LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null

    module load java/jdk-1.7
    java -Xmx12g -jar ~/bin/GenomeAnalysisTK/GenomeAnalysisTK.jar \
        -nt 6 \
        -T UnifiedGenotyper \
        -R "${Ref_name}" \
        -I "${sample}_SMALT_sorted_dedup_realigned_sorted.bam" \
        -ploidy 1 \
        -glm BOTH \
        -stand\_call\_conf "$Call" \
        -stand\_emit\_conf "$Emit" \
        -o "TEST_raw_variants_GATK_unified_genotyper.vcf"
    

    INFO 10:35:19,236 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:35:19,242 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO 10:35:19,242 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 10:35:19,242 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 10:35:19,247 HelpFormatter - Program Args: -nt 6 -T UnifiedGenotyper -R /researchdata/fhgfs/lmbjas002/Server_Version/My_pipeline/references/H37Rv/H37Rv.fasta -I M_15_A712_F2_R14816_GGAGAAC_L004_SMALT_sorted_dedup_realigned_sorted.bam -ploidy 1 -glm BOTH -stand_call_conf 30 -stand_emit_conf 10 -o TEST_DELETE_raw_variants_GATK_unified_genotyper.vcf
    INFO 10:35:19,288 HelpFormatter - Executing as [email protected] on Linux 3.0.101-68-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13.
    INFO 10:35:19,292 HelpFormatter - Date/Time: 2016/02/05 10:35:19
    INFO 10:35:19,292 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:35:19,293 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:35:20,057 GenomeAnalysisEngine - Strictness is SILENT
    INFO 10:35:20,219 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
    INFO 10:35:20,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 10:35:20,356 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
    INFO 10:35:20,548 MicroScheduler - Running the GATK in parallel mode with 6 total threads, 1 CPU thread(s) for each of 6 data thread(s), of 64 processors available on this machine
    INFO 10:35:20,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 10:35:20,935 GenomeAnalysisEngine - Done preparing for traversal
    INFO 10:35:20,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 10:35:20,936 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 10:35:20,937 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    INFO 10:35:20,981 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
    WARN 10:35:20,982 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
    INFO 10:35:20,983 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
    INFO 10:35:28,250 ProgressMeter - done 4411532.0 7.0 s 1.0 s 100.0% 7.0 s 0.0 s
    INFO 10:35:28,256 ProgressMeter - Total runtime 7.31 secs, 0.12 min, 0.00 hours
    INFO 10:35:30,891 GATKRunReport - Uploaded run statistics report to AWS S3

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    To get Picard to run on your bam file, you'll need to upgrade to a more recent version that supports the v1.5 bam spec. Picard 1.141 is the last version that runs on Java 1.7 iirc.

    Once you get that working you'll want to look into our best practices docs to update your workflow, as what you're trying to do right now doesn't appropriately pre-process that data and uses a deprecated caller (UG has been replaced by a more sophisticated caller, HaplotypeCaller).

    Be sure to check also that your aligner produces informative mapping qualities. Consider plotting the distribution of MQ values to check for any issues. That could explain why you're not getting any variants.

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