Sequence dictionary and index contain different numbers of contigs

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rahelp

• December 09, 2020 07:19

Dear GATK,

I am trying to run GATK to detect somatic copy number variants. Workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035531092--How-to-part-I-Sensitively-detect-copy-ratio-alterations-and-allelic-segments

I get an error when I try to run: 
gatk PreprocessIntervals     -L targets_C.interval_list     -R Homo_sapiens_assembly19.fasta     --bin-length 0     --interval-merging-rule OVERLAPPING_ONLY     -O sandbox/targets_C.preprocessed.interval_list

I am using GATK docker image 4.1.3.0.

Error:

07:02:56.434 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Dec 09, 2020 7:02:57 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

07:02:57.600 INFO  PreprocessIntervals - ------------------------------------------------------------

07:02:57.601 INFO  PreprocessIntervals - The Genome Analysis Toolkit (GATK) v4.1.3.0

07:02:57.601 INFO  PreprocessIntervals - For support and documentation go to https://software.broadinstitute.org/gatk/

07:02:57.601 INFO  PreprocessIntervals - Executing as root@7645dd8077e3 on Linux v5.4.39-linuxkit amd64

07:02:57.601 INFO  PreprocessIntervals - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12

07:02:57.601 INFO  PreprocessIntervals - Start Date/Time: December 9, 2020 7:02:56 AM UTC

07:02:57.601 INFO  PreprocessIntervals - ------------------------------------------------------------

07:02:57.602 INFO  PreprocessIntervals - ------------------------------------------------------------

07:02:57.602 INFO  PreprocessIntervals - HTSJDK Version: 2.20.1

07:02:57.602 INFO  PreprocessIntervals - Picard Version: 2.20.5

07:02:57.602 INFO  PreprocessIntervals - HTSJDK Defaults.COMPRESSION_LEVEL : 2

07:02:57.602 INFO  PreprocessIntervals - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

07:02:57.602 INFO  PreprocessIntervals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

07:02:57.602 INFO  PreprocessIntervals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

07:02:57.602 INFO  PreprocessIntervals - Deflater: IntelDeflater

07:02:57.603 INFO  PreprocessIntervals - Inflater: IntelInflater

07:02:57.603 INFO  PreprocessIntervals - GCS max retries/reopens: 20

07:02:57.603 INFO  PreprocessIntervals - Requester pays: disabled

07:02:57.603 INFO  PreprocessIntervals - Initializing engine

07:02:57.640 INFO  PreprocessIntervals - Shutting down engine

[December 9, 2020 7:02:57 AM UTC] org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals done. Elapsed time: 0.02 minutes.

Runtime.totalMemory()=148373504

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

 

A USER ERROR has occurred: Couldn't read file file:///gatk/USZ_melanoma/Homo_sapiens_assembly19.fasta. Error was: Sequence dictionary and index contain different numbers of contigs

I am using this reference file: https://storage.cloud.google.com/genomics-public-data/references/b37/Homo_sapiens_assembly19.fasta.gz

However, the dict and fai files are not available for this genome version, therefore I created them with the following commands:

• samtools faidx Homo_sapiens_assembly19.fasta

• gatk CreateSequenceDictionary -R Homo_sapiens_assembly19.fasta
  

 

I am open to any suggestions on how to solve these issues.

Thank you.

0

• 

  Genevieve Brandt (she/her)

  • December 11, 2020 20:48

  Hi rahelp, there could have been an issue when you downloaded the files and created the index and dictionary files. Check for errors in those processes and/or re-do them to confirm the files do not have issues.

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• 

  Genevieve Brandt (she/her)

  • February 10, 2021 18:29

  rahelp another user is seeing this same error message. Did you end up solving this problem? If so, what was your solution?

  Thank you,

  Genevieve

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  rahelp

  • February 11, 2021 10:21

  Dear Genevieve,

  The issue was that CreateSequenceDictionary was not working properly.

  For it to work properly:

  • google authentication completed
  • Docker default memory is only 2 GB. This needs to be set to higher (I set it to 100).
  • change java options: 
    

    gatk --java-options -Xmx12g CreateSequenceDictionary -R Homo_sapiens_assembly19.fasta

  I hope this helps.

  Good luck!

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  Genevieve Brandt (she/her)

  • February 11, 2021 16:48

  Thank you so much, rahelp!

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