Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary

Answered
0

5 comments

  • Avatar
    Genevieve Brandt (she/her)

    Yeah, you'll need to make sure to use the same reference for DepthofCoverage that was used for read mapping.

    1
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Hi Maha Tageldein,

    Have you tried to create a new sequence dictionary for your fasta file? The tool may be using an old version without this contig. You can use the tool CreateSequenceDictionary.

    Let me know if that works.

    Best,

    Genevieve

    0
    Comment actions Permalink
  • Avatar
    Maha Tageldein

    Hi Genevieve-Brandt-she-her,


    Thank you for the suggestion. I confirmed that "chr1_KI270762v1_alt" was present in the fasta file then used CreateSequenceDictionary to create a new sequence dictionary using:

    java -jar picard.jar CreateSequenceDictionary R=hg38.fasta O=hg38.dict

    When I run the command now (old .dict file deleted from the directory) like this: 

    gatk DepthOfCoverage -R hg38.fasta -I sample.final.bam -O DepthOfCoverage -L hg38.interval_list

    I encounter the same error. Please find the logs below:

     

    Using GATK jar /Applications/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar

    Running:

        java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar DepthOfCoverage -R hg38.fasta -I IR_MN_3.final.bam -O DepthOfCoverage -L hg38.interval_list

    11:51:35.169 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.dylib

    11:51:35.497 INFO  DepthOfCoverage - ------------------------------------------------------------

    11:51:35.498 INFO  DepthOfCoverage - The Genome Analysis Toolkit (GATK) v4.2.6.1

    11:51:35.498 INFO  DepthOfCoverage - For support and documentation go to https://software.broadinstitute.org/gatk/

    11:51:35.500 INFO  DepthOfCoverage - Executing as maha@Mahas-MacBook-Pro.local on Mac OS X v11.4 x86_64

    11:51:35.500 INFO  DepthOfCoverage - Java runtime: Java HotSpot(TM) 64-Bit Server VM v16.0.2+7-67

    11:51:35.501 INFO  DepthOfCoverage - Start Date/Time: June 6, 2022 at 11:51:35 a.m. EDT

    11:51:35.501 INFO  DepthOfCoverage - ------------------------------------------------------------

    11:51:35.501 INFO  DepthOfCoverage - ------------------------------------------------------------

    11:51:35.503 INFO  DepthOfCoverage - HTSJDK Version: 2.24.1

    11:51:35.503 INFO  DepthOfCoverage - Picard Version: 2.27.1

    11:51:35.503 INFO  DepthOfCoverage - Built for Spark Version: 2.4.5

    11:51:35.503 INFO  DepthOfCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 2

    11:51:35.503 INFO  DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

    11:51:35.503 INFO  DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

    11:51:35.503 INFO  DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

    11:51:35.503 INFO  DepthOfCoverage - Deflater: IntelDeflater

    11:51:35.503 INFO  DepthOfCoverage - Inflater: IntelInflater

    11:51:35.504 INFO  DepthOfCoverage - GCS max retries/reopens: 20

    11:51:35.504 INFO  DepthOfCoverage - Requester pays: disabled

    11:51:35.506 WARN  DepthOfCoverage - 

     

       !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

     

       Warning: DepthOfCoverage is a BETA tool and is not yet ready for use in production

     

       !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

     

     

    11:51:35.506 INFO  DepthOfCoverage - Initializing engine

    11:51:36.355 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///Volumes/My%20Passport%20for%20Mac/Experiments-%20raw%20data/1041%20WGS%20Kate_MN%20sequencing%20experiments_20210917/20200409_Sequencing%20IR%20MN%20HeLa_Novogene_rep1/WGS_202004/hg38.interval_list

    11:51:36.513 INFO  IntervalArgumentCollection - Processing 2982123250 bp from intervals

    11:51:36.526 INFO  DepthOfCoverage - Done initializing engine

    11:51:36.662 INFO  ProgressMeter - Starting traversal

    11:51:36.663 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute

    11:51:36.671 INFO  DepthOfCoverage - Shutting down engine

    [June 6, 2022 at 11:51:36 a.m. EDT] org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage done. Elapsed time: 0.03 minutes.

    Runtime.totalMemory()=119537664

    ***********************************************************************

     

    A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary

     

    ***********************************************************************

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

     

     

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Thanks Maha Tageldein! Could you confirm that chr1_KI270762v1_alt is the header sequence dictionary of your BAM file? https://gatk.broadinstitute.org/hc/en-us/articles/360035890791-SAM-or-BAM-or-CRAM-Mapped-sequence-data-formats

    0
    Comment actions Permalink
  • Avatar
    Maha Tageldein

    Hi Genevieve-Brandt-she-her,

    It turns out 'chr1_KI270762v1_alt' is not in the header of my BAM file. Does this mean I should use a different fasta file as a reference?

    Thank you

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk