MESSAGE: Code exception (see stack trace for error itself)

Hi GATK Team,

I am running RealignerTargetCreator on my BAM file, sorted, with ReadsGroup added, and indexed. I have no interval file created while doing this command line:
java -jar ../apps/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T RealignerTargetCreator -R Bathycoccus_genome_FINAL_RELEASE.fasta -o ReadsConcat_Bathy_Sensitive_bowtie2_sorted_readsgroup.intervals -I ReadsConcat_Bathy_Sensitive_bowtie2_sorted_readsgroup.bam

And then, I have the following error messages and
INFO 13:55:09,832 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:55:09,838 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 13:55:09,838 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:55:09,838 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:55:09,842 HelpFormatter - Program Args: -T RealignerTargetCreator -R Bathycoccus_genome_FINAL_RELEASE.fasta -o ReadsConcat_Bathy_Sensitive_bowtie2_sorted_readsgroup.intervals -I ReadsConcat_Bathy_Sensitive_bowtie2_sorted_readsgroup.bam
INFO 13:55:09,847 HelpFormatter - Executing as [email protected] on Linux 3.0.101-0.46-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 13:55:09,848 HelpFormatter - Date/Time: 2015/08/24 13:55:09
INFO 13:55:09,848 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:55:09,848 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:55:10,906 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:55:11,041 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:55:11,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:55:11,074 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 13:55:11,180 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 13:55:11,219 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:55:11,219 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:55:11,219 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:55:11,220 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 13:55:21,992 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException
at java.nio.ByteBuffer.allocate(ByteBuffer.java:334)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:195)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:329)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:150)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:126)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
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 3.4-46-gbc02625):
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 ------------------------------------------------------------------------------------------

An idea of what is happening here? My reference fasta file is indexed in .dict and in .fai, and they are located in the same folder. Same for my bam file which had been indexed and is located in the same folder.

Thanks in advance for your help.

Nathalie.

Best Answer

Answers

  • abhijeetabhijeet FinlandMember
    edited November 2015

    Hi GATK team!

    I believe this error is back in the nightly builds! Any specific nightly builds which are known to work ?

    Best,
    Abhijeet

    INFO  17:11:26,641 HelpFormatter - ---------------------------------------------------------------------------------------------
    INFO  17:11:26,643 HelpFormatter - The Genome Analysis Toolkit (GATK) vnightly-2015-11-25-g65608a7, Compiled 2015/11/25 00:01:28
    INFO  17:11:26,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  17:11:26,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  17:11:26,647 HelpFormatter - Program Args: -T HaplotypeCaller -R mouse_contigs_with_atleast2indi_SNPs.fasta -I all_sample_merged_2SNPs.bam -o all_36_samples_mouse_2SNPs_raw.vcf -hets 0.01 -nct 8
    INFO  17:11:26,666 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.8.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-mockbuild_2015_10_21_19_56-b00.
    INFO  17:11:26,666 HelpFormatter - Date/Time: 2015/11/25 17:11:26
    INFO  17:11:26,667 HelpFormatter - ---------------------------------------------------------------------------------------------
    INFO  17:11:26,667 HelpFormatter - ---------------------------------------------------------------------------------------------
    INFO  17:11:26,782 GenomeAnalysisEngine - Strictness is SILENT
    INFO  17:12:23,148 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
    INFO  17:12:23,158 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO  17:13:33,563 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 70.40
    INFO  17:13:39,662 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
    INFO  17:13:43,569 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### 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)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version nightly-2015-11-25-g65608a7):
    ##### 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, Moderator admin

    @abhijeet
    Hi Abhijeet,

    Can you confirm the error occurs when you do not use -nct 8? Also, can you run ValidateSamFile on your input bam file? http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile

    -Sheila

  • abhijeetabhijeet FinlandMember

    @Sheila
    Hi Shelia,

    The error is persistent if I do not use the flag -nct 8. See console output below.

    INFO  11:46:00,279 HelpFormatter - --------------------------------------------------------------------------------
    INFO  11:46:00,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO  11:46:00,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  11:46:00,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  11:46:00,285 HelpFormatter - Program Args: -T HaplotypeCaller -R mouse_contigs_with_atleast2indi_SNPs.fasta -I all_sample_merged_2SNPs.bam -o all_36_samples_mouse_2SNPs_raw.vcf -hets 0.01
    INFO  11:46:00,295 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.8.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-mockbuild_2015_10_21_19_56-b00.
    INFO  11:46:00,296 HelpFormatter - Date/Time: 2015/11/26 11:46:00
    INFO  11:46:00,296 HelpFormatter - --------------------------------------------------------------------------------
    INFO  11:46:00,296 HelpFormatter - --------------------------------------------------------------------------------
    INFO  11:46:00,403 GenomeAnalysisEngine - Strictness is SILENT
    INFO  11:46:04,528 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
    INFO  11:46:04,535 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO  11:46:12,684 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 8.15
    INFO  11:46:30,907 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
    INFO  11:46:36,408 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### 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)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    ##### 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 ------------------------------------------------------------------------------------------
    

    ValidateSAMFile from picard-tools reported that the read group sample tag (@RG SM) was missing (see below). Will adding this field help or this error is unrelated?

    Thank You!

    Best,
    Abhijeet

    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel25    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel25-75B32716   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel21    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel21-2E9B3CF8   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel26    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel26-37BB9962   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel22    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel22-21F73933   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel27    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel27-3C684C2B   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel23    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel23-6B08FC7A   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel28    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel28-7BACE4E2   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel24    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel24-32A37F8B   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel29    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel29-59567763   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel30    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel30-3B3B662F   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel31    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel31-771F2933   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel32    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel32-6CC9967A   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel33    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel33-53DAFCC3   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel34    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel34-35317808   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel35    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel35-42BAC4AC   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel36    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel36-5AF7DB40   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel1 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel1-48423EF2    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel2 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel2-6CB78892    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel3 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel3-212E5842    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel4 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel4-786077BA    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel5 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel5-22289735    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel6 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel6-29EEAEFC    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel7 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel7-3DC4AF8D    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel8 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel8-59E5CA68    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel9 PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel9-50E53D75    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel10    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel10-707E2B15   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel11    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel11-5C44A8C3   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel12    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel12-5310CE67   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel13    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel13-C7F3037    LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel14    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel14-55EECD4A   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel15    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel15-609B1CBB   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel16    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel16-65718376   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel17    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel17-61AC1CA2   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel18    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel18-45B05EAB   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel19    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel19-34CEC6EA   LB:mouse    PL:ILLUMINA
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel20    PL:ILLUMINA LB:mouse
    ERROR: File /external/data/PNAS_paper_working/mouse_genotypes_test/mouse_2SNPs/all_sample_merged_2SNPs.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG ID:hel20-68E955F4   LB:mouse    PL:ILLUMINA
    
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yes, that should help. I'm not sure why you're getting a code exception instead of a civilized error message, but for sure GATK will not run properly on data that is missing SM.

  • abhijeetabhijeet FinlandMember

    Hi @Sheila and @Geraldine_VdAuwera ,

    GATK-3.5 is working fine after setting the ReadGroups correctly.

    Thank You !

    Best Wishes,
    Abhijeet

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