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PROBLEM: "A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary"

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firat zahid

Hello there, 
Im trying to run "PreprocessIntervals" but I get this error: 

PROBLEM: "A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary"
Can you please provide

I have generated reference.dict and reference.fasta.fai properly and my bed file looks like this (tab-delimited): 

chr1 69090 70008 OR4F5_1 0 +
chr1 367658 368597 OR4F29_1 0 -
chr1 621095 622034 OR4F16_1 0 -
chr1 861321 861393 SAMD11_1 0 +
chr1 865534 865716 SAMD11_2 0 +
chr1 866418 866469 SAMD11_3 0 +
chr1 871151 871276 SAMD11_4 0 +
chr1 874419 874509 SAMD11_5 0 +
chr1 874654 874840 SAMD11_6 0 +
chr1 876523 876686 SAMD11_7 0 +
chr1 877515 877631 SAMD11_8 0 +
chr1 877789 877868 SAMD11_9 0 +
chr1 877938 878438 SAMD11_10 0 +
chr1 878632 878757 SAMD11_11 0 +
chr1 879077 879188 SAMD11_12 0 +
chr1 879287 879533 SAMD11_13 0 +
chr1 880073 880180 NOC2L_19 0 -
chr1 880436 880526 NOC2L_18 0 -
chr1 880897 881033 NOC2L_17 0 -
chr1 881552 881666 NOC2L_16 0 -
chr1 881781 881925 NOC2L_15 0 -
chr1 883510 883612 NOC2L_14 0 -
chr1 883869 883983 NOC2L_13 0 -
chr1 886506 886618 NOC2L_12 0 -
chr1 887379 887519 NOC2L_11 0 -
chr1 887791 887980 NOC2L_10 0 -

Thanks in advance

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  • Avatar
    Dr N Ch
    • Edited

    Hi,

    @preprocessintervals - A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "home/Reference_Sequences/xxxx.bed" is not valid for this input.

     

    I am using  the fasta sequences, index files from GATK server itself.. can u help to rectify the error. 

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  • Avatar
    Tiffany Miller

    Can you paste the commands you used to get this error? What reference are you using? You may have a mismatch with the way you are naming intervals in your bed file and the reference you are using. 

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  • Avatar
    firat zahid

    My genome reference is "hg19_v0_Homo_sapiens_assembly19" that I downloaded it from bundle
    and my command is: 

    gatk PreprocessIntervals \
        -R hg19_v0_Homo_sapiens_assembly19.fasta \
        --bin-length 0 \
        -L mybed.bed \
        -imr OVERLAPPING_ONLY \
        -O targets.interval_list
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  • Avatar
    Tiffany Miller

    Thanks. Can you send the contents of your reference dict? Basically, you need to make sure that every input (bed file and reference files) is following the same way of naming the contigs...either chr1 or 1. 

    For example, looking at the reference dictionary for hg19 and hg38 from this public reference bucket, 

    you can see how the contigs are named differently:

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  • Avatar
    firat zahid

    Thank you for your answer Tiffany
    my reference.dict file looks like :

     

    and mybed.bed file looks likes : 

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  • Avatar
    Tiffany Miller

    Ok, are you still getting the issue? If so, try using the fasta reference files available here and let me know if the same error occurs. 

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  • Avatar
    vivekruhela
    • Edited

    Tiffany Miller: I am also facing the exact same issue. First I was using hg19 from UCSC golden path, the I also tried with the fasta reference files (and .dict file) but still gatting the same error (command and errror is shown below):

    12:09:27.234 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/akansha/vivekruhela/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    Jan 12, 2021 12:09:27 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    12:09:27.532 INFO GenomicsDBImport - ------------------------------------------------------------
    12:09:27.532 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.9.0
    12:09:27.532 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
    12:09:27.532 INFO GenomicsDBImport - Executing as akansha@sbilab on Linux v4.4.0-169-generic amd64
    12:09:27.533 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~16.04-b01
    12:09:27.533 INFO GenomicsDBImport - Start Date/Time: January 12, 2021 12:09:27 PM IST
    12:09:27.533 INFO GenomicsDBImport - ------------------------------------------------------------
    12:09:27.533 INFO GenomicsDBImport - ------------------------------------------------------------
    12:09:27.533 INFO GenomicsDBImport - HTSJDK Version: 2.23.0
    12:09:27.533 INFO GenomicsDBImport - Picard Version: 2.23.3
    12:09:27.534 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    12:09:27.534 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    12:09:27.534 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    12:09:27.534 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    12:09:27.534 INFO GenomicsDBImport - Deflater: IntelDeflater
    12:09:27.534 INFO GenomicsDBImport - Inflater: IntelInflater
    12:09:27.534 INFO GenomicsDBImport - GCS max retries/reopens: 20
    12:09:27.534 INFO GenomicsDBImport - Requester pays: disabled
    12:09:27.534 INFO GenomicsDBImport - Initializing engine
    12:09:32.225 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/akansha/vivekruhela/hg19_v0_HybSelOligos_whole_exome_illumina_coding_v1_whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list
    12:09:32.259 INFO GenomicsDBImport - Shutting down engine
    [January 12, 2021 12:09:32 PM IST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.08 minutes.
    Runtime.totalMemory()=2767716352
    ***********************************************************************

    A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig 1 given as location, but this contig isn't present in the Fasta sequence dictionary

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

    Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
    Using GATK jar /home/akansha/vivekruhela/gatk-4.1.9.0/gatk-package-4.1.9.0-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 /home/akansha/vivekruhela/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar GenomicsDBImport -R /home/akansha/vivekruhela/gatk_bundle/hg19_v0_Homo_sapiens_assembly19.fasta -V /home/akansha/vivekruhela/PON/SRR1566827.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566831.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566833.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566835.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566859.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566889.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566901.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566928.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566933.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566957.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566967.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566985.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1606005.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1606009.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1606035.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1606043.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1606045.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1606068.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128443.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128462.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128495.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128507.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128517.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128529.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128531.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128544.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128570.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128646.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128650.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128654.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128704.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128752.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128950.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128952.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128954.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128962.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128969.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2128995.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129015.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129022.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129031.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129042.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129072.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129091.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129142.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129150.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129220.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129222.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129229.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129259.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2182804.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2182806.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3162947.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3162978.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163146.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163205.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163605.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163648.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163652.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163653.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163678.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163680.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163705.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163711.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4188892.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4188955.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189328.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189350.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189588.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189593.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189594.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189597.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189602.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189605.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189606.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189699.vcf.gz -V /home/akansha/vivekruhela/PON/SRR4189725.vcf.gz -V /home/akansha/vivekruhela/PON/SRR1566955.vcf.gz -V /home/akansha/vivekruhela/PON/SRR2129174.vcf.gz -V /home/akansha/vivekruhela/PON/SRR3163666.vcf.gz --genomicsdb-workspace-path pon_db --tmp-dir /home/akansha/vivekruhela/tmp1 -L /home/akansha/vivekruhela/hg19_v0_HybSelOligos_whole_exome_illumina_coding_v1_whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list

     

    EDIT1: I want to add my next attempt here. This time the prevous error is resolved but GenomicsDBImport is still not working. I have downloaded the hg38 intervals from GATK resource bundle and used UCSC liftover to convert it into hg19 based interval list. The error message is shown below:

    15:36:14.002 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/akansha/vivekruhela/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    Jan 12, 2021 3:36:14 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    15:36:14.265 INFO GenomicsDBImport - ------------------------------------------------------------
    15:36:14.266 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.9.0
    15:36:14.266 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
    15:36:14.266 INFO GenomicsDBImport - Executing as akansha@sbilab on Linux v4.4.0-169-generic amd64
    15:36:14.266 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~16.04-b01
    15:36:14.266 INFO GenomicsDBImport - Start Date/Time: January 12, 2021 3:36:13 PM IST
    15:36:14.266 INFO GenomicsDBImport - ------------------------------------------------------------
    15:36:14.267 INFO GenomicsDBImport - ------------------------------------------------------------
    15:36:14.267 INFO GenomicsDBImport - HTSJDK Version: 2.23.0
    15:36:14.267 INFO GenomicsDBImport - Picard Version: 2.23.3
    15:36:14.267 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    15:36:14.267 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    15:36:14.267 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    15:36:14.268 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    15:36:14.268 INFO GenomicsDBImport - Deflater: IntelDeflater
    15:36:14.268 INFO GenomicsDBImport - Inflater: IntelInflater
    15:36:14.268 INFO GenomicsDBImport - GCS max retries/reopens: 20
    15:36:14.268 INFO GenomicsDBImport - Requester pays: disabled
    15:36:14.268 INFO GenomicsDBImport - Initializing engine
    15:36:18.805 INFO FeatureManager - Using codec BEDCodec to read file file:///home/akansha/vivekruhela/gatk_bundle/hglft_genome_3bc14_d6f440.bed
    15:36:18.810 INFO IntervalArgumentCollection - Processing 0 bp from intervals
    15:36:18.847 INFO GenomicsDBImport - Done initializing engine
    15:36:19.417 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.3.2-e18fa63
    15:36:19.418 INFO GenomicsDBImport - Vid Map JSON file will be written to /home/akansha/vivekruhela/pon_db/vidmap.json
    15:36:19.418 INFO GenomicsDBImport - Callset Map JSON file will be written to /home/akansha/vivekruhela/pon_db/callset.json
    15:36:19.418 INFO GenomicsDBImport - Complete VCF Header will be written to /home/akansha/vivekruhela/pon_db/vcfheader.vcf
    15:36:19.418 INFO GenomicsDBImport - Importing to workspace - /home/akansha/vivekruhela/pon_db
    15:36:19.418 INFO ProgressMeter - Starting traversal
    15:36:19.418 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
    15:36:19.467 INFO GenomicsDBImport - Shutting down engine
    [January 12, 2021 3:36:19 PM IST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.09 minutes.
    Runtime.totalMemory()=2850029568
    java.lang.IndexOutOfBoundsException: Index: 0
    at java.util.Collections$EmptyList.get(Collections.java:4456)
    at org.genomicsdb.model.GenomicsDBImportConfiguration$ImportConfiguration.getColumnPartitions(GenomicsDBImportConfiguration.java:2083)
    at org.genomicsdb.importer.GenomicsDBImporter.<init>(GenomicsDBImporter.java:203)
    at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.traverse(GenomicsDBImport.java:745)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    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)

    Kindly suggest. Thanks.

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  • Avatar
    Genevieve Brandt (she/her)

    Hi vivekruhela, could you make a new post about this issue? The user above is running PreProcessIntervals but you are running GenomicsDBImport, so it may be a different issue. Please see this document about what to include in your post: https://gatk.broadinstitute.org/hc/en-us/articles/360053424571-How-to-Write-a-Post

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  • Avatar
    Pamela Bretscher

    Hi Dr N Ch,

    It looks like this error is occurring because the tool is unable to recognize the file you provided as a proper interval list. Can you provide the full command that you ran and take a look at this article on interval lists to ensure yours is in the proper format?

    Kind regards,

    Pamela

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