Funcotator Error, incompatible contigs

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J LoPiccolo

• September 28, 2021 23:41

I am trying to run Funcotator as follows and getting an error which I think means that my reference and source data is not compatible, yet both are hg38. Can you provide insight as to the issue? Thanks 

! gatk Funcotator \
--variant ../1-3-Generate-Sample-Map-HG38_2021-09-07T19-59-00.vcf.gz \
--reference Homo_sapiens_assembly38.fasta \
--ref-version hg38 \
--data-sources-path funcotator_dataSources.v1.7.20200521g \
--output variants090721.funcotated.vcf \
--output-file-format VCF

Using GATK jar /etc/gatk-4.2.0.0/gatk-package-4.2.0.0-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 /etc/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar Funcotator --variant ../1-3-Generate-Sample-Map-HG38_2021-09-07T19-59-00.vcf.gz --reference Homo_sapiens_assembly38.fasta --ref-version hg38 --data-sources-path ../funcotator_dataSources.v1.7.20200521g --output variants090721.funcotated.vcf --output-file-format VCF
23:35:41.840 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/etc/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:35:42.034 INFO  Funcotator - ------------------------------------------------------------
23:35:42.034 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.2.0.0
23:35:42.034 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
23:35:42.035 INFO  Funcotator - Executing as jupyter@006276791b8d on Linux v5.4.104+ amd64
23:35:42.035 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_292-8u292-b10-0ubuntu1~18.04-b10
23:35:42.035 INFO  Funcotator - Start Date/Time: September 28, 2021 11:35:41 PM UTC
23:35:42.035 INFO  Funcotator - ------------------------------------------------------------
23:35:42.035 INFO  Funcotator - ------------------------------------------------------------
23:35:42.036 INFO  Funcotator - HTSJDK Version: 2.24.0
23:35:42.036 INFO  Funcotator - Picard Version: 2.25.0
23:35:42.036 INFO  Funcotator - Built for Spark Version: 2.4.5
23:35:42.036 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:35:42.036 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:35:42.036 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:35:42.036 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:35:42.037 INFO  Funcotator - Deflater: IntelDeflater
23:35:42.037 INFO  Funcotator - Inflater: IntelInflater
23:35:42.037 INFO  Funcotator - GCS max retries/reopens: 20
23:35:42.037 INFO  Funcotator - Requester pays: disabled
23:35:42.037 INFO  Funcotator - Initializing engine
23:35:42.639 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/jupyter/notebooks/PROACTIVE-WGS_JL%20correct%20billing%20acct/edit/../1-3-Generate-Sample-Map-HG38_2021-09-07T19-59-00.vcf.gz
23:35:43.149 INFO  Funcotator - Done initializing engine
23:35:43.149 INFO  Funcotator - Validating sequence dictionaries...
23:35:43.225 INFO  Funcotator - Shutting down engine
[September 28, 2021 11:35:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=414711808
***********************************************************************

A USER ERROR has occurred: Input files Reference and Driving Variants have incompatible contigs: Dictionary Reference is missing contigs found in dictionary Driving Variants.  Missing contigs: 

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  Genevieve Brandt (she/her)

  • October 20, 2021 14:11

  I believe there are no current issues about uploading to the FTP server, please share more information if you are encountering some sort of bug.

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  J LoPiccolo

  • October 20, 2021 14:43

  I am trying to upload the files using Finder on my Mac. I am connected to the server (folder is gsapubftp@ftp.broadinstitute.org), but it will not let me drag/drop any files. 

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  Genevieve Brandt (she/her)

  • October 20, 2021 15:23

  I would recommend a solution such as FileZilla, I've used it successfully before: https://filezilla-project.org/

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  J LoPiccolo

  • October 21, 2021 11:59

  Sorry I just tried that, and it didnt work. can we find some other way, this is becoming very difficult!

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  Genevieve Brandt (she/her)

  • October 22, 2021 17:37

  I was able to successfully see the VCF file and found the HPV contigs do in fact exist in your VCF header. You'll want to update your VCF header to match your reference, this can be done with the GATK Tool UpdateVCFSequenceDictionary. Give a bam file for the source dictionary and use the option --replace=true. 

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