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Input files reference and reads have incompatible contigs

zillurbmb51zillurbmb51 USAMember

Hello,
I was trying to run haplotypecaller ;

  • /usr/libexec/java_home -v 1.8.0_221 --exec java -jar ../gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar HaplotypeCaller -R hg38.fa -I new.bams -O gatk.haplo.raw.vcf (new.bams is a list of bam files)

But getting incompatible contigs between reference and reads. I used bowtie2 and same reference fasta file for mapping, then why it is incompatible? attached is the header of one sample bam and the contigs in reference. Any help will be greatly appreciated. This error happened previously when mapping fasta was different. But why it is happening for same fasta and what is the fix? Best, Zillur

Answers

  • Tiffany_at_BroadTiffany_at_Broad admin Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @zillurbmb51 , your contigs do match between the two files you posted.
    Can you share the full error message, please?

  • zillurbmb51zillurbmb51 USAMember

    Sure. Thank you. Here it is;

    (base) rcmi-29:snpcall mzillur$ /usr/libexec/java_home -v 1.8.0_221 --exec java -jar ../gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar HaplotypeCaller -R hg38.fa -I new.bams -O gatk.haplo.raw.vcf
    16:20:17.047 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Volumes/Macintosh%20HD2/data/UPR_CANCER_2/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
    Jul 31, 2019 4:20:18 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    16:20:18.108 INFO HaplotypeCaller - ------------------------------------------------------------
    16:20:18.108 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.2.0
    16:20:18.108 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
    16:20:18.109 INFO HaplotypeCaller - Executing as [email protected] on Mac OS X v10.12.6 x86_64
    16:20:18.109 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_221-b11
    16:20:18.109 INFO HaplotypeCaller - Start Date/Time: July 31, 2019 4:20:16 PM AST
    16:20:18.109 INFO HaplotypeCaller - ------------------------------------------------------------
    16:20:18.109 INFO HaplotypeCaller - ------------------------------------------------------------
    16:20:18.110 INFO HaplotypeCaller - HTSJDK Version: 2.19.0
    16:20:18.110 INFO HaplotypeCaller - Picard Version: 2.19.0
    16:20:18.110 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    16:20:18.110 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    16:20:18.110 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    16:20:18.110 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    16:20:18.110 INFO HaplotypeCaller - Deflater: IntelDeflater
    16:20:18.110 INFO HaplotypeCaller - Inflater: IntelInflater
    16:20:18.110 INFO HaplotypeCaller - GCS max retries/reopens: 20
    16:20:18.110 INFO HaplotypeCaller - Requester pays: disabled
    16:20:18.110 INFO HaplotypeCaller - Initializing engine
    16:20:18.756 INFO HaplotypeCaller - Shutting down engine
    [July 31, 2019 4:20:18 PM AST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.03 minutes.
    Runtime.totalMemory()=633339904


    A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
    reference contigs = [chr1, chr10, chr11, chr11_KI270721v1_random, chr12, chr13, chr14, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr15, chr15_KI270727v1_random, chr16, chr16_KI270728v1_random, chr17, chr17_GL000205v2_random, chr17_KI270729v1_random, chr17_KI270730v1_random, chr18, chr19, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2, chr20, chr21, chr22, chr22_KI270731v1_random, chr22_KI270732v1_random, chr22_KI270733v1_random, chr22_KI270734v1_random, chr22_KI270735v1_random, chr22_KI270736v1_random, chr22_KI270737v1_random, chr22_KI270738v1_random, chr22_KI270739v1_random, chr2_KI270715v1_random, chr2_KI270716v1_random, chr3, chr3_GL000221v1_random, chr4, chr4_GL000008v2_random, chr5, chr5_GL000208v1_random, chr6, chr7, chr8, chr9, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr1_KI270762v1_alt, chr1_KI270766v1_alt, chr1_KI270760v1_alt, chr1_KI270765v1_alt, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270764v1_alt, chr1_KI270763v1_alt, chr1_KI270759v1_alt, chr1_KI270761v1_alt, chr2_KI270770v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270769v1_alt, chr2_GL383521v1_alt, chr2_KI270772v1_alt, chr2_KI270775v1_alt, chr2_KI270771v1_alt, chr2_KI270768v1_alt, chr2_GL582966v2_alt, chr2_GL383522v1_alt, chr2_KI270776v1_alt, chr2_KI270767v1_alt, chr3_JH636055v2_alt, chr3_KI270783v1_alt, chr3_KI270780v1_alt, chr3_GL383526v1_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270781v1_alt, chr3_KI270779v1_alt, chr3_KI270782v1_alt, chr3_KI270784v1_alt, chr4_KI270790v1_alt, chr4_GL383528v1_alt, chr4_KI270787v1_alt, chr4_GL000257v2_alt, chr4_KI270788v1_alt, chr4_GL383527v1_alt, chr4_KI270785v1_alt, chr4_KI270789v1_alt, chr4_KI270786v1_alt, chr5_KI270793v1_alt, chr5_KI270792v1_alt, chr5_KI270791v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270794v1_alt, chr5_GL339449v2_alt, chr5_GL383530v1_alt, chr5_KI270796v1_alt, chr5_GL383531v1_alt, chr5_KI270795v1_alt, chr6_GL000250v2_alt, chr6_KI270800v1_alt, chr6_KI270799v1_alt, chr6_GL383533v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KB021644v2_alt, chr6_KI270797v1_alt, chr6_KI270798v1_alt, chr7_KI270804v1_alt, chr7_KI270809v1_alt, chr7_KI270806v1_alt, chr7_GL383534v2_alt, chr7_KI270803v1_alt, chr7_KI270808v1_alt, chr7_KI270807v1_alt, chr7_KI270805v1_alt, chr8_KI270818v1_alt, chr8_KI270812v1_alt, chr8_KI270811v1_alt, chr8_KI270821v1_alt, chr8_KI270813v1_alt, chr8_KI270822v1_alt, chr8_KI270814v1_alt, chr8_KI270810v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270817v1_alt, chr8_KI270816v1_alt, chr8_KI270815v1_alt, chr9_GL383539v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270823v1_alt, chr10_GL383545v1_alt, chr10_KI270824v1_alt, chr10_GL383546v1_alt, chr10_KI270825v1_alt, chr11_KI270832v1_alt, chr11_KI270830v1_alt, chr11_KI270831v1_alt, chr11_KI270829v1_alt, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270827v1_alt, chr11_KI270826v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270837v1_alt, chr12_GL383549v1_alt, chr12_KI270835v1_alt, chr12_GL383550v2_alt, chr12_GL383552v1_alt, chr12_GL383553v2_alt, chr12_KI270834v1_alt, chr12_GL383551v1_alt, chr12_KI270833v1_alt, chr12_KI270836v1_alt, chr13_KI270840v1_alt, chr13_KI270839v1_alt, chr13_KI270843v1_alt, chr13_KI270841v1_alt, chr13_KI270838v1_alt, chr13_KI270842v1_alt, chr14_KI270844v1_alt, chr14_KI270847v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr15_KI270852v1_alt, chr15_KI270851v1_alt, chr15_KI270848v1_alt, chr15_GL383554v1_alt, chr15_KI270849v1_alt, chr15_GL383555v2_alt, chr15_KI270850v1_alt, chr16_KI270854v1_alt, chr16_KI270856v1_alt, chr16_KI270855v1_alt, chr16_KI270853v1_alt, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr17_GL383563v3_alt, chr17_KI270862v1_alt, chr17_KI270861v1_alt, chr17_KI270857v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_GL383564v2_alt, chr17_GL000258v2_alt, chr17_GL383565v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_GL383566v1_alt, chr17_KI270860v1_alt, chr18_KI270864v1_alt, chr18_GL383567v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr19_KI270868v1_alt, chr19_KI270865v1_alt, chr19_GL383573v1_alt, chr19_GL383575v2_alt, chr19_GL383576v1_alt, chr19_GL383574v1_alt, chr19_KI270866v1_alt, chr19_KI270867v1_alt, chr19_GL949746v1_alt, chr20_GL383577v2_alt, chr20_KI270869v1_alt, chr20_KI270871v1_alt, chr20_KI270870v1_alt, chr21_GL383578v2_alt, chr21_KI270874v1_alt, chr21_KI270873v1_alt, chr21_GL383579v2_alt, chr21_GL383580v2_alt, chr21_GL383581v2_alt, chr21_KI270872v1_alt, chr22_KI270875v1_alt, chr22_KI270878v1_alt, chr22_KI270879v1_alt, chr22_KI270876v1_alt, chr22_KI270877v1_alt, chr22_GL383583v2_alt, chr22_GL383582v2_alt, chrX_KI270880v1_alt, chrX_KI270881v1_alt, chr19_KI270882v1_alt, chr19_KI270883v1_alt, chr19_KI270884v1_alt, chr19_KI270885v1_alt, chr19_KI270886v1_alt, chr19_KI270887v1_alt, chr19_KI270888v1_alt, chr19_KI270889v1_alt, chr19_KI270890v1_alt, chr19_KI270891v1_alt, chr1_KI270892v1_alt, chr2_KI270894v1_alt, chr2_KI270893v1_alt, chr3_KI270895v1_alt, chr4_KI270896v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr6_GL000251v2_alt, chr7_KI270899v1_alt, chr8_KI270901v1_alt, chr8_KI270900v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr12_KI270904v1_alt, chr15_KI270906v1_alt, chr15_KI270905v1_alt, chr17_KI270907v1_alt, chr17_KI270910v1_alt, chr17_KI270909v1_alt, chr17_JH159148v1_alt, chr17_KI270908v1_alt, chr18_KI270912v1_alt, chr18_KI270911v1_alt, chr19_GL949747v2_alt, chr22_KB663609v1_alt, chrX_KI270913v1_alt, chr19_KI270914v1_alt, chr19_KI270915v1_alt, chr19_KI270916v1_alt, chr19_KI270917v1_alt, chr19_KI270918v1_alt, chr19_KI270919v1_alt, chr19_KI270920v1_alt, chr19_KI270921v1_alt, chr19_KI270922v1_alt, chr19_KI270923v1_alt, chr3_KI270924v1_alt, chr4_KI270925v1_alt, chr6_GL000252v2_alt, chr8_KI270926v1_alt, chr11_KI270927v1_alt, chr19_GL949748v2_alt, chr22_KI270928v1_alt, chr19_KI270929v1_alt, chr19_KI270930v1_alt, chr19_KI270931v1_alt, chr19_KI270932v1_alt, chr19_KI270933v1_alt, chr19_GL000209v2_alt, chr3_KI270934v1_alt, chr6_GL000253v2_alt, chr19_GL949749v2_alt, chr3_KI270935v1_alt, chr6_GL000254v2_alt, chr19_GL949750v2_alt, chr3_KI270936v1_alt, chr6_GL000255v2_alt, chr19_GL949751v2_alt, chr3_KI270937v1_alt, chr6_GL000256v2_alt, chr19_GL949752v1_alt, chr6_KI270758v1_alt, chr19_GL949753v2_alt, chr19_KI270938v1_alt, chrM, chrUn_KI270302v1, chrUn_KI270304v1, chrUn_KI270303v1, chrUn_KI270305v1, chrUn_KI270322v1, chrUn_KI270320v1, chrUn_KI270310v1, chrUn_KI270316v1, chrUn_KI270315v1, chrUn_KI270312v1, chrUn_KI270311v1, chrUn_KI270317v1, chrUn_KI270412v1, chrUn_KI270411v1, chrUn_KI270414v1, chrUn_KI270419v1, chrUn_KI270418v1, chrUn_KI270420v1, chrUn_KI270424v1, chrUn_KI270417v1, chrUn_KI270422v1, chrUn_KI270423v1, chrUn_KI270425v1, chrUn_KI270429v1, chrUn_KI270442v1, chrUn_KI270466v1, chrUn_KI270465v1, chrUn_KI270467v1, chrUn_KI270435v1, chrUn_KI270438v1, chrUn_KI270468v1, chrUn_KI270510v1, chrUn_KI270509v1, chrUn_KI270518v1, chrUn_KI270508v1, chrUn_KI270516v1, chrUn_KI270512v1, chrUn_KI270519v1, chrUn_KI270522v1, chrUn_KI270511v1, chrUn_KI270515v1, chrUn_KI270507v1, chrUn_KI270517v1, chrUn_KI270529v1, chrUn_KI270528v1, chrUn_KI270530v1, chrUn_KI270539v1, chrUn_KI270538v1, chrUn_KI270544v1, chrUn_KI270548v1, chrUn_KI270583v1, chrUn_KI270587v1, chrUn_KI270580v1, chrUn_KI270581v1, chrUn_KI270579v1, chrUn_KI270589v1, chrUn_KI270590v1, chrUn_KI270584v1, chrUn_KI270582v1, chrUn_KI270588v1, chrUn_KI270593v1, chrUn_KI270591v1, chrUn_KI270330v1, chrUn_KI270329v1, chrUn_KI270334v1, chrUn_KI270333v1, chrUn_KI270335v1, chrUn_KI270338v1, chrUn_KI270340v1, chrUn_KI270336v1, chrUn_KI270337v1, chrUn_KI270363v1, chrUn_KI270364v1, chrUn_KI270362v1, chrUn_KI270366v1, chrUn_KI270378v1, chrUn_KI270379v1, chrUn_KI270389v1, chrUn_KI270390v1, chrUn_KI270387v1, chrUn_KI270395v1, chrUn_KI270396v1, chrUn_KI270388v1, chrUn_KI270394v1, chrUn_KI270386v1, chrUn_KI270391v1, chrUn_KI270383v1, chrUn_KI270393v1, chrUn_KI270384v1, chrUn_KI270392v1, chrUn_KI270381v1, chrUn_KI270385v1, chrUn_KI270382v1, chrUn_KI270376v1, chrUn_KI270374v1, chrUn_KI270372v1, chrUn_KI270373v1, chrUn_KI270375v1, chrUn_KI270371v1, chrUn_KI270448v1, chrUn_KI270521v1, chrUn_GL000195v1, chrUn_GL000219v1, chrUn_GL000220v1, chrUn_GL000224v1, chrUn_KI270741v1, chrUn_GL000226v1, chrUn_GL000213v1, chrUn_KI270743v1, chrUn_KI270744v1, chrUn_KI270745v1, chrUn_KI270746v1, chrUn_KI270747v1, chrUn_KI270748v1, chrUn_KI270749v1, chrUn_KI270750v1, chrUn_KI270751v1, chrUn_KI270752v1, chrUn_KI270753v1, chrUn_KI270754v1, chrUn_KI270755v1, chrUn_KI270756v1, chrUn_KI270757v1, chrUn_GL000214v1, chrUn_KI270742v1, chrUn_GL000216v2, chrUn_GL000218v1, chrX, chrY, chrY_KI270740v1_random]
    reads contigs = []


    Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

  • zillurbmb51zillurbmb51 USAMember

    Hello, Is there any fix for this problem?

  • Tiffany_at_BroadTiffany_at_Broad admin Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @zillurbmb51 ,
    The error message shows how the reference contigs are displayed, but your bam contigs display nothing...
    reads contigs = []

    Your bam is not being recognized by the tool.
    Try renaming your input new.bams to .bam and rerun.
    In addition ensure the bam is valid by running ValidateSamFile.

  • SkyWarriorSkyWarrior ✭✭✭ TurkeyMember ✭✭✭

    Looks like @zillurbmb51 tried to feed the bam files in a single list file which gatk HaplotypeCaller does not recognize.

    He needs to input individual bam files to -I switch one by one.

  • Tiffany_at_BroadTiffany_at_Broad admin Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Thanks for your input @SkyWarrior !

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