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MuTect2 ->Reference name for '1283' not found in sequence dictionary

t1000t1000 Member
edited November 2017 in Ask the GATK team

Hi, I am trying to run
java -jar GenomeAnalysisTK.jar -T MuTect2 -R ucsc.hg19.fasta -I:tumor tumor_rg.bam -I:normal normal_rg.bam -o output.vcf

I am using ucsc.hg19.fasta as a reference and I used:
1. samtools faidx to create the ucsc.hg19.fasta.fai file
2. java -jar picard.jar CreateSequenceDictionary REFERENCE=ucsc.hg19.fasta OUTPUT=ucsc.hg19.fasta.dict

I added a ReadGroup to my two BAM Files:
java -jar picard.jar AddOrReplaceReadGroups I=normal.bam O=normal_rg.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20

I also validated the BAM files

Now I get the following error:

##### ERROR MESSAGE: SAM/BAM/CRAM file /analysis/tumnormalor.bam is malformed. Error details: Reference name for '1283' not found in sequence dictionary.

If I exchange the tumor and normal .bam files as command line arguments I get the error
##### ERROR MESSAGE: SAM/BAM/CRAM file /analysis/tumor.bam is malformed. Error details: Reference name for '1283' not found in sequence dictionary.

I tried to google it and found nothing. Can someone give me a clue where to look ?

Is the file ucsc.hg19.fasta.dict the sequence dictionary ?

Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @t1000
    Hi,

    Can you post the BAM file header and the FASTA dict file here? Specifically, I need to see if the @SQ lines in the BAM file match the ones in your dict file.

    Thanks,
    Sheila

  • michaelmcmichaelmc Member

    Hi,

    I'm having a similar issue with MuTect2 (GATK version 4.0.3.0).

    I'm trying to run:

    gatk Mutect2 \
     -R human_g1k_v37_decoy.fasta \
     -I ${TUMOUR}.recal.bam \
     -tumor ${TUMOUR} \
     -I ${NORMAL}.recal.bam \
     -normal ${NORMAL} \
     --germline-resource af-only-gnomad.raw.sites.b37.vcf \
     --af-of-alleles-not-in-resource 0.00003125 \
     -O ${TUMOUR}_${NORMAL}.vcf
    

    And I'm getting this error, with a different number after reference name each time:

    [August 8, 2018 3:55:11 PM BST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.14 minutes.
    Runtime.totalMemory()=2076049408
    java.lang.IllegalArgumentException: Reference name for '3223094' not found in sequence dictionary.
            at htsjdk.samtools.SAMRecord.resolveNameFromIndex(SAMRecord.java:569)
            at htsjdk.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:422)
            at htsjdk.samtools.BAMRecord.<init>(BAMRecord.java:87)
            at htsjdk.samtools.DefaultSAMRecordFactory.createBAMRecord(DefaultSAMRecordFactory.java:42)
            at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:210)
            at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:829)
            at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:981)
            at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:803)
            at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:963)
            at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:918)
            at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:575)
            at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528)
            at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400)
            at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:125)
            at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:66)
            at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:404)
            at org.broadinstitute.hellbender.engine.ReadsDataSource.iterator(ReadsDataSource.java:330)
            at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134)
            at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:109)
            at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286)
            at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271)
            at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)
            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134)
            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
            at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
            at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
            at org.broadinstitute.hellbender.Main.main(Main.java:289)
    

    I've checked the @SQ lines of both the .dict file and the .bam files, but can't see any obvious differences. Here is my .dict file:

    @HD     VN:1.0  SO:unsorted
    @SQ     SN:1    LN:249250621    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
    @SQ     SN:2    LN:243199373    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:a0d9851da00400dec1098a9255ac712e
    @SQ     SN:3    LN:198022430    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:fdfd811849cc2fadebc929bb925902e5
    @SQ     SN:4    LN:191154276    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:23dccd106897542ad87d2765d28a19a1
    @SQ     SN:5    LN:180915260    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:0740173db9ffd264d728f32784845cd7
    @SQ     SN:6    LN:171115067    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1d3a93a248d92a729ee764823acbbc6b
    @SQ     SN:7    LN:159138663    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:618366e953d6aaad97dbe4777c29375e
    @SQ     SN:8    LN:146364022    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:96f514a9929e410c6651697bded59aec
    @SQ     SN:9    LN:141213431    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:3e273117f15e0a400f01055d9f393768
    @SQ     SN:10   LN:135534747    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:988c28e000e84c26d552359af1ea2e1d
    @SQ     SN:11   LN:135006516    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:98c59049a2df285c76ffb1c6db8f8b96
    @SQ     SN:12   LN:133851895    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:51851ac0e1a115847ad36449b0015864
    @SQ     SN:13   LN:115169878    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:283f8d7892baa81b510a015719ca7b0b
    @SQ     SN:14   LN:107349540    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:98f3cae32b2a2e9524bc19813927542e
    @SQ     SN:15   LN:102531392    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:e5645a794a8238215b2cd77acb95a078
    @SQ     SN:16   LN:90354753     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:fc9b1a7b42b97a864f56b348b06095e6
    @SQ     SN:17   LN:81195210     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:351f64d4f4f9ddd45b35336ad97aa6de
    @SQ     SN:18   LN:78077248     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
    @SQ     SN:19   LN:59128983     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1aacd71f30db8e561810913e0b72636d
    @SQ     SN:20   LN:63025520     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:0dec9660ec1efaaf33281c0d5ea2560f
    @SQ     SN:21   LN:48129895     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:2979a6085bfe28e3ad6f552f361ed74d
    @SQ     SN:22   LN:51304566     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:a718acaa6135fdca8357d5bfe94211dd
    @SQ     SN:X    LN:155270560    UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:7e0e2e580297b7764e31dbc80c2540dd
    @SQ     SN:Y    LN:59373566     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1fa3474750af0948bdf97d5a0ee52e51
    @SQ     SN:MT   LN:16569        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:c68f52674c9fb33aef52dcf399755519
    @SQ     SN:GL000207.1   LN:4262 UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:f3814841f1939d3ca19072d9e89f3fd7
    @SQ     SN:GL000226.1   LN:15008        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1c1b2cd1fccbc0a99b6a447fa24d1504
    @SQ     SN:GL000229.1   LN:19913        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:d0f40ec87de311d8e715b52e4c7062e1
    @SQ     SN:GL000231.1   LN:27386        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:ba8882ce3a1efa2080e5d29b956568a4
    @SQ     SN:GL000210.1   LN:27682        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:851106a74238044126131ce2a8e5847c
    @SQ     SN:GL000239.1   LN:33824        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:99795f15702caec4fa1c4e15f8a29c07
    @SQ     SN:GL000235.1   LN:34474        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:118a25ca210cfbcdfb6c2ebb249f9680
    @SQ     SN:GL000201.1   LN:36148        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:dfb7e7ec60ffdcb85cb359ea28454ee9
    @SQ     SN:GL000247.1   LN:36422        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:7de00226bb7df1c57276ca6baabafd15
    @SQ     SN:GL000245.1   LN:36651        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:89bc61960f37d94abf0df2d481ada0ec
    @SQ     SN:GL000197.1   LN:37175        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:6f5efdd36643a9b8c8ccad6f2f1edc7b
    @SQ     SN:GL000203.1   LN:37498        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:96358c325fe0e70bee73436e8bb14dbd
    @SQ     SN:GL000246.1   LN:38154        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:e4afcd31912af9d9c2546acf1cb23af2
    @SQ     SN:GL000249.1   LN:38502        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1d78abec37c15fe29a275eb08d5af236
    @SQ     SN:GL000196.1   LN:38914        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:d92206d1bb4c3b4019c43c0875c06dc0
    @SQ     SN:GL000248.1   LN:39786        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:5a8e43bec9be36c7b49c84d585107776
    @SQ     SN:GL000244.1   LN:39929        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:0996b4475f353ca98bacb756ac479140
    @SQ     SN:GL000238.1   LN:39939        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:131b1efc3270cc838686b54e7c34b17b
    @SQ     SN:GL000202.1   LN:40103        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:06cbf126247d89664a4faebad130fe9c
    @SQ     SN:GL000234.1   LN:40531        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:93f998536b61a56fd0ff47322a911d4b
    @SQ     SN:GL000232.1   LN:40652        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:3e06b6741061ad93a8587531307057d8
    @SQ     SN:GL000206.1   LN:41001        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:43f69e423533e948bfae5ce1d45bd3f1
    @SQ     SN:GL000240.1   LN:41933        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:445a86173da9f237d7bcf41c6cb8cc62
    @SQ     SN:GL000236.1   LN:41934        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:fdcd739913efa1fdc64b6c0cd7016779
    @SQ     SN:GL000241.1   LN:42152        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:ef4258cdc5a45c206cea8fc3e1d858cf
    @SQ     SN:GL000243.1   LN:43341        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:cc34279a7e353136741c9fce79bc4396
    @SQ     SN:GL000242.1   LN:43523        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:2f8694fc47576bc81b5fe9e7de0ba49e
    @SQ     SN:GL000230.1   LN:43691        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:b4eb71ee878d3706246b7c1dbef69299
    @SQ     SN:GL000237.1   LN:45867        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:e0c82e7751df73f4f6d0ed30cdc853c0
    @SQ     SN:GL000233.1   LN:45941        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:7fed60298a8d62ff808b74b6ce820001
    @SQ     SN:GL000204.1   LN:81310        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:efc49c871536fa8d79cb0a06fa739722
    @SQ     SN:GL000198.1   LN:90085        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:868e7784040da90d900d2d1b667a1383
    @SQ     SN:GL000208.1   LN:92689        UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:aa81be49bf3fe63a79bdc6a6f279abf6
    @SQ     SN:GL000191.1   LN:106433       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:d75b436f50a8214ee9c2a51d30b2c2cc
    @SQ     SN:GL000227.1   LN:128374       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:a4aead23f8053f2655e468bcc6ecdceb
    @SQ     SN:GL000228.1   LN:129120       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:c5a17c97e2c1a0b6a9cc5a6b064b714f
    @SQ     SN:GL000214.1   LN:137718       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:46c2032c37f2ed899eb41c0473319a69
    @SQ     SN:GL000221.1   LN:155397       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:3238fb74ea87ae857f9c7508d315babb
    @SQ     SN:GL000209.1   LN:159169       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:f40598e2a5a6b26e84a3775e0d1e2c81
    @SQ     SN:GL000218.1   LN:161147       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:1d708b54644c26c7e01c2dad5426d38c
    @SQ     SN:GL000220.1   LN:161802       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:fc35de963c57bf7648429e6454f1c9db
    @SQ     SN:GL000213.1   LN:164239       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:9d424fdcc98866650b58f004080a992a
    @SQ     SN:GL000211.1   LN:166566       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:7daaa45c66b288847b9b32b964e623d3
    @SQ     SN:GL000199.1   LN:169874       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:569af3b73522fab4b40995ae4944e78e
    @SQ     SN:GL000217.1   LN:172149       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:6d243e18dea1945fb7f2517615b8f52e
    @SQ     SN:GL000216.1   LN:172294       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:642a232d91c486ac339263820aef7fe0
    @SQ     SN:GL000215.1   LN:172545       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:5eb3b418480ae67a997957c909375a73
    @SQ     SN:GL000205.1   LN:174588       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:d22441398d99caf673e9afb9a1908ec5
    @SQ     SN:GL000219.1   LN:179198       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:f977edd13bac459cb2ed4a5457dba1b3
    @SQ     SN:GL000224.1   LN:179693       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:d5b2fc04f6b41b212a4198a07f450e20
    @SQ     SN:GL000223.1   LN:180455       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:399dfa03bf32022ab52a846f7ca35b30
    @SQ     SN:GL000195.1   LN:182896       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:5d9ec007868d517e73543b005ba48535
    @SQ     SN:GL000212.1   LN:186858       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:563531689f3dbd691331fd6c5730a88b
    @SQ     SN:GL000222.1   LN:186861       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:6fe9abac455169f50470f5a6b01d0f59
    @SQ     SN:GL000200.1   LN:187035       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:75e4c8d17cd4addf3917d1703cacaf25
    @SQ     SN:GL000193.1   LN:189789       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:dbb6e8ece0b5de29da56601613007c2a
    @SQ     SN:GL000194.1   LN:191469       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:6ac8f815bf8e845bb3031b73f812c012
    @SQ     SN:GL000225.1   LN:211173       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:63945c3e6962f28ffd469719a747e73c
    @SQ     SN:GL000192.1   LN:547496       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:325ba9e808f669dfeee210fdd7b470ac
    @SQ     SN:NC_007605    LN:171823       UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:6743bd63b3ff2b5b8985d8933c53290a
    @SQ     SN:hs37d5       LN:35477943     UR:file:/humgen/1kg/reference/human_g1k_v37_decoy.fasta M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1
    

    and here are the @SQ lines from the ${TUMOUR}.recal.bam file:

    @SQ     SN:1    LN:249250621
    @SQ     SN:2    LN:243199373
    @SQ     SN:3    LN:198022430
    @SQ     SN:4    LN:191154276
    @SQ     SN:5    LN:180915260
    @SQ     SN:6    LN:171115067
    @SQ     SN:7    LN:159138663
    @SQ     SN:8    LN:146364022
    @SQ     SN:9    LN:141213431
    @SQ     SN:10   LN:135534747
    @SQ     SN:11   LN:135006516
    @SQ     SN:12   LN:133851895
    @SQ     SN:13   LN:115169878
    @SQ     SN:14   LN:107349540
    @SQ     SN:15   LN:102531392
    @SQ     SN:16   LN:90354753
    @SQ     SN:17   LN:81195210
    @SQ     SN:18   LN:78077248
    @SQ     SN:19   LN:59128983
    @SQ     SN:20   LN:63025520
    @SQ     SN:21   LN:48129895
    @SQ     SN:22   LN:51304566
    @SQ     SN:X    LN:155270560
    @SQ     SN:Y    LN:59373566
    @SQ     SN:MT   LN:16569
    @SQ     SN:GL000207.1   LN:4262
    @SQ     SN:GL000226.1   LN:15008
    @SQ     SN:GL000229.1   LN:19913
    @SQ     SN:GL000231.1   LN:27386
    @SQ     SN:GL000210.1   LN:27682
    @SQ     SN:GL000239.1   LN:33824
    @SQ     SN:GL000235.1   LN:34474
    @SQ     SN:GL000201.1   LN:36148
    @SQ     SN:GL000247.1   LN:36422
    @SQ     SN:GL000245.1   LN:36651
    @SQ     SN:GL000197.1   LN:37175
    @SQ     SN:GL000203.1   LN:37498
    @SQ     SN:GL000246.1   LN:38154
    @SQ     SN:GL000249.1   LN:38502
    @SQ     SN:GL000196.1   LN:38914
    @SQ     SN:GL000248.1   LN:39786
    @SQ     SN:GL000244.1   LN:39929
    @SQ     SN:GL000238.1   LN:39939
    @SQ     SN:GL000202.1   LN:40103
    @SQ     SN:GL000234.1   LN:40531
    @SQ     SN:GL000232.1   LN:40652
    @SQ     SN:GL000206.1   LN:41001
    @SQ     SN:GL000240.1   LN:41933
    @SQ     SN:GL000236.1   LN:41934
    @SQ     SN:GL000241.1   LN:42152
    @SQ     SN:GL000243.1   LN:43341
    @SQ     SN:GL000242.1   LN:43523
    @SQ     SN:GL000230.1   LN:43691
    @SQ     SN:GL000237.1   LN:45867
    @SQ     SN:GL000233.1   LN:45941
    @SQ     SN:GL000204.1   LN:81310
    @SQ     SN:GL000198.1   LN:90085
    @SQ     SN:GL000208.1   LN:92689
    @SQ     SN:GL000191.1   LN:106433
    @SQ     SN:GL000227.1   LN:128374
    @SQ     SN:GL000228.1   LN:129120
    @SQ     SN:GL000214.1   LN:137718
    @SQ     SN:GL000221.1   LN:155397
    @SQ     SN:GL000209.1   LN:159169
    @SQ     SN:GL000218.1   LN:161147
    @SQ     SN:GL000220.1   LN:161802
    @SQ     SN:GL000213.1   LN:164239
    @SQ     SN:GL000211.1   LN:166566
    @SQ     SN:GL000199.1   LN:169874
    @SQ     SN:GL000217.1   LN:172149
    @SQ     SN:GL000216.1   LN:172294
    @SQ     SN:GL000215.1   LN:172545
    @SQ     SN:GL000205.1   LN:174588
    @SQ     SN:GL000219.1   LN:179198
    @SQ     SN:GL000224.1   LN:179693
    @SQ     SN:GL000223.1   LN:180455
    @SQ     SN:GL000195.1   LN:182896
    @SQ     SN:GL000212.1   LN:186858
    @SQ     SN:GL000222.1   LN:186861
    @SQ     SN:GL000200.1   LN:187035
    @SQ     SN:GL000193.1   LN:189789
    @SQ     SN:GL000194.1   LN:191469
    @SQ     SN:GL000225.1   LN:211173
    @SQ     SN:GL000192.1   LN:547496
    @SQ     SN:NC_007605    LN:171823
    @SQ     SN:hs37d5       LN:35477943
    

    I did use samtools reheader to change something in the header of my ${NORMAL}.recal.bam file (not the @SQ lines), and I notice that in this topic a ReadGroup was added to the bam file. Could this be the issue?

    Thanks,

    Michael

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @michaelmc
    Hi Michael,

    Can you confirm this happens with the latest version?

    -Sheila

  • michaelmcmichaelmc Member

    Yes, I've tried it with 4.0.8.0 and I get the same error

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited September 2018

    @michaelmc
    Hi Michael,

    Thanks. I need to ask the developer and get back to you.

    -Sheila

    EDIT: This has been resolved in this thread.

    Post edited by Sheila on
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