CheckFingerprint (Picard) error message

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Heba B abusamra

• September 16, 2020 05:25

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 

gatk-4.1.8.1

b) Exact command used:

/app/Genome/gatk-4.1.8.1/gatk CheckFingerprint \
--DETAIL_OUTPUT PBG-561-20R_S6-FingerPrint \
--INPUT PBG-561-20R_S6.bam \
--GENOTYPES PBG-561-20R_S6.vcf \
--HAPLOTYPE_MAP hg19_v0_Homo_sapiens_assembly19.haplotype_database.txt \
--SUMMARY_OUTPUT PBG-561-20R_S6-Fi.tsv

c) Entire error log:

 

Using GATK jar /app/Genome/gatk-4.1.8.1/gatk-package-4.1.8.1-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 /app/Genome/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar CheckFingerprint --DETAIL_OUTPUT PBG-561-20R_S6-FingerPrint --INPUT PBG-561-20R_S6.bam --GENOTYPES PBG-561-20R_S6.vcf --HAPLOTYPE_MAP hg19_v0_Homo_sapiens_assembly19.haplotype_database.txt --SUMMARY_OUTPUT PBG-561-20R_S6-Fi.tsv
08:15:59.593 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/app/Genome/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Sep 16 08:15:59 AST 2020] CheckFingerprint --INPUT PBG-561-20R_S6.bam --SUMMARY_OUTPUT PBG-561-20R_S6-Fi.tsv --DETAIL_OUTPUT PBG-561-20R_S6-FingerPrint --GENOTYPES PBG-561-20R_S6.vcf --HAPLOTYPE_MAP hg19_v0_Homo_sapiens_assembly19.haplotype_database.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Sep 16, 2020 8:15:59 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Wed Sep 16 08:15:59 AST 2020] Executing as habusamra@kdata1 on Linux 2.6.32-358.23.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_66-b17; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.8.1
[Wed Sep 16 08:15:59 AST 2020] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=595066880
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match: 0/16571/chrM/UR=D:\Data\Repository\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa 0/249250621/chr1
at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:272)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:334)
at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:249)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
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 have this indexing error when Im using fingerPrint in GATK, how can I solve this ?

0

• 

  Genevieve Brandt (she/her)

  • September 16, 2020 19:54

  This is an error with your index. Please check that it was made with the same file you are using now and is up to date. You can also look through your index to confirm that the files you are using match.

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• 

  Heba B abusamra

  • September 17, 2020 04:16

  Thank you for your reply 

  what do you mean  by "your index" is it  the PBG-561-20R_S6.bam.bai  or reference dictionary file?

  actually the same sample was  aligned and used with haplotypeCaller without any error.

  Also I tried to change the order of contig in the reference dictionary but it didn't work.

  Another question please:

  --GENOTYPES PBG-561-20R_S6.vcf , I'm not sure about the genotypes here is it the genotypes specific for the sample because I'm using vcf file generated form haplotypeCaller  since it has a genotypes

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  Genevieve Brandt (she/her)

  • September 17, 2020 21:46

  Heba B abusamra The problem could be in your dict file or bai file. Have you indexed your files with the correct file? The error message indicates that there is a problem with matching: 

  Sequences at index 0 don't match: 0/16571/chrM/UR=D:\Data\Repository\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa 0/249250621/chr1

  You can check out our tool IndexFeatureFile. There is also a similar post on biostars about this issue: https://www.biostars.org/p/344620/

  The most up to date information on how to use CheckFingerPrint and the genotypes file is on the ToolDocs page: https://gatk.broadinstitute.org/hc/en-us/articles/360047216131-CheckFingerprint-Picard-

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• 

  Yuan Zhou

  • April 16, 2021 20:42

  Hi Heba B abusamra,

  Could you please tell me where you download the hg19_v0_Homo_sapiens_assembly19.haplotype_database.txt? Thanks!

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• 

  Genevieve Brandt (she/her)

  • July 13, 2021 23:00

  Yuan Zhou, it looks like that file is something Heba B abusamra created. You can read more about how to build a haplotype map here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format

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