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GATK4.0 HaplotypeCaller: Input files reference and reads have incompatible contigs

Hi,

When I use GATK4.0 HaplotypeCaller, it present a similar errorA USER ERROR has occurred:
**Input files reference and reads have incompatible contigs: Found contigs with the same name but different lengths:
contig reference = NC_008484.2 / 14966190
contig reads = NC_008484.2 / 14966191.
reference contigs = [NC_008467.2, NC_008468.2, NC_008469.2, NC_008470.2, NC_008475.2, NC_008471.2, NC_008472.2, NC_008473.2, NC_008474.2, NC_008476.2, NC_008477.2, NC_008478.2, NC_008479.2, NC_008480.2, NC_008485.2, NC_008481.2, NC_008482.2, NC_008483.2, NC_008484.2]
reads contigs = [NC_008467.2, NC_008468.2, NC_008469.2, NC_008470.2, NC_008475.2, NC_008471.2, NC_008472.2, NC_008473.2, NC_008474.2, NC_008476.2, NC_008477.2, NC_008478.2, NC_008479.2, NC_008480.2, NC_008485.2, NC_008481.2, NC_008482.2, NC_008483.2, NC_008484.2]

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

The reference genome my sequence data was aligned to and the reference genome the known sites I used is the same file:**/mnt/hgfs/D/analysis/populus/Populus.fasta **

My command is
java -jar /home/wang/Documents/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar HaplotypeCaller -R /mnt/hgfs/D/analysis/populus/Populus.fasta -I p1_aln.sorted.dedup.bam -O p1_output_raw_snps_indels.g.vcf

I repeat the processes, but the error really exsited.

Best Answers

Answers

  • eryaerya Member

    After I remove the sequence NC_008484.2, a similar error occured:


    A USER ERROR has occurred: Input files reference and reads have incompatible contigs: Found contigs with the same name but different lengths:
    contig reference = NC_008483.2 / 14661173
    contig reads = NC_008483.2 / 14661174.
    reference contigs = [NC_008467.2, NC_008468.2, NC_008469.2, NC_008470.2, NC_008475.2, NC_008471.2, NC_008472.2, NC_008473.2, NC_008474.2, NC_008476.2, NC_008477.2, NC_008478.2, NC_008479.2, NC_008480.2, NC_008485.2, NC_008481.2, NC_008482.2, NC_008483.2]
    reads contigs = [NC_008467.2, NC_008468.2, NC_008469.2, NC_008470.2, NC_008475.2, NC_008471.2, NC_008472.2, NC_008473.2, NC_008474.2, NC_008476.2, NC_008477.2, NC_008478.2, NC_008479.2, NC_008480.2, NC_008485.2, NC_008481.2, NC_008482.2, NC_008483.2]


    So, How can I solve this problem.

  • eryaerya Member

    SkyWarrior
    Hi,
    Thank you for your answer, it has worked.

    But a new error occured, When I used GATK4.0 GenotypeGVCFs, the error present as:

    11:05:44.157 INFO GenotypeGVCFs - ------------------------------------------------------------
    11:05:44.157 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.0.2.1
    11:05:44.157 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
    11:05:44.157 INFO GenotypeGVCFs - Executing as [email protected] on Linux v4.13.0-36-generic amd64
    11:05:44.157 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_151-b12
    11:05:44.157 INFO GenotypeGVCFs - Start Date/Time: March 14, 2018 11:05:42 AM CST
    11:05:44.157 INFO GenotypeGVCFs - ------------------------------------------------------------
    11:05:44.158 INFO GenotypeGVCFs - ------------------------------------------------------------
    11:05:44.158 INFO GenotypeGVCFs - HTSJDK Version: 2.14.3
    11:05:44.158 INFO GenotypeGVCFs - Picard Version: 2.17.2
    11:05:44.158 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 1
    11:05:44.158 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    11:05:44.158 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    11:05:44.158 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    11:05:44.158 INFO GenotypeGVCFs - Deflater: IntelDeflater
    11:05:44.158 INFO GenotypeGVCFs - Inflater: IntelInflater
    11:05:44.159 INFO GenotypeGVCFs - GCS max retries/reopens: 20
    11:05:44.159 INFO GenotypeGVCFs - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
    11:05:44.159 INFO GenotypeGVCFs - Initializing engine
    11:05:44.398 INFO FeatureManager - Using codec VCFCodec to read file file:///home/wang/Music/snp/p3_output_raw_snps_indels.g.vcf
    11:05:44.434 INFO GenotypeGVCFs - Done initializing engine
    11:05:44.825 INFO ProgressMeter - Starting traversal
    11:05:44.825 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    11:05:44.836 INFO GenotypeGVCFs - Shutting down engine
    [March 14, 2018 11:05:44 AM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.04 minutes.
    Runtime.totalMemory()=456130560


    A USER ERROR has occurred: The list of input alleles must contain as an allele but that is not the case at position 7033; please use the Haplotype Caller with gVCF output to generate appropriate records


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

    My command followed as:
    java -jar /home/wang/Documents/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar GenotypeGVCFs -R /mnt/hgfs/D/analysis/populus/populus.fasta -V p1_output_raw_snps_indels.g.vcf -O p1.vcf

    So which command cause it, and how can I solve it?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Can you check you reference file or the GVCF file for what is shown in position 7033?

  • eryaerya Member

    In the GVCF file, the position 7033 prentent as:

    source=HaplotypeCaller

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT P3

    NC_008467.2 7033 . C A 107.90 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.67;QD=21.58;SOR=1.022 GT:AD:DP:GQ:PL 1/1:0,5:5:15:136,15,0
    NC_008467.2 7123 . T C 107.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.36;SOR=2.833 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0

  • eryaerya Member

    You can read clearly in this picture:

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