BaseRecalibrator - no suitable codecs

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Rhodri Smith

• April 01, 2020 09:59

Can you please provide
a) GATK version use: 4.1.4.1
b) Exact GATK commands used
c) The entire error log if applicable.

Hi Team

I'm fairly new to GATK and very new to posting on here so apologies in advance

I'm having a problem getting BaseRecalibrator function to work for me using input RNA seq data in bam format that has been through splitntrim as per workflow. I am using vcf 00-All.vcf(.gz) downloaded from https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/#table-1

I keeping getting "a no suitable codecs problem"

I found a post from April 2017 with same error but alas  have not been able to get this working

Error in full:

Command line:

gatk BaseRecalibrator -I /users/rlsmith/sharedscratch/split/RA003_split.bam -R genome.fa --known-sites /mnt/lustre/users/hlwright/00-All.vcf.tbi -O RA003_recal.table

Currently Loaded Modulefiles:
1) apps/star/2.7.3a
Using GATK jar /mnt/data1/users/software/GATK/gatk-4.1.4.1/gatk-package-4.1.4.1-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 /mnt/data1/users/software/GATK/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar BaseRecalibrator -I /users/rlsmith/sharedscratch/split/RA003_split.bam -R genome.fa --known-sites 00-All.vcf.tbi -O RA003_recal.table
10:56:24.194 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/data1/users/software/GATK/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 01, 2020 10:56:24 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:56:24.544 INFO BaseRecalibrator - ------------------------------------------------------------
10:56:24.545 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.4.1
10:56:24.545 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
10:56:24.546 INFO BaseRecalibrator - Executing as rlsmith@node062.pri.barkla.alces.network on Linux v3.10.0-1062.9.1.el7.x86_64 amd64
10:56:24.546 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_232-b09
10:56:24.546 INFO BaseRecalibrator - Start Date/Time: 01 April 2020 10:56:23 BST
10:56:24.546 INFO BaseRecalibrator - ------------------------------------------------------------
10:56:24.546 INFO BaseRecalibrator - ------------------------------------------------------------
10:56:24.547 INFO BaseRecalibrator - HTSJDK Version: 2.21.0
10:56:24.547 INFO BaseRecalibrator - Picard Version: 2.21.2
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:56:24.547 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:56:24.547 INFO BaseRecalibrator - Deflater: IntelDeflater
10:56:24.547 INFO BaseRecalibrator - Inflater: IntelInflater
10:56:24.547 INFO BaseRecalibrator - GCS max retries/reopens: 20
10:56:24.547 INFO BaseRecalibrator - Requester pays: disabled
10:56:24.547 INFO BaseRecalibrator - Initializing engine
10:56:25.131 INFO BaseRecalibrator - Shutting down engine
[01 April 2020 10:56:25 BST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2216165376
***********************************************************************

A USER ERROR has occurred: Cannot read file:///mnt/lustre/users/rlsmith/hg38/Bowtie2Index/00-All.vcf.tbi because no suitable codecs found

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

******

I have tried running both the zipped and unzipped, and have tried indexing and running the .tbi file with no luck

If I run the vcf (un indexed) then iI get the error: A USER ERROR has occurred: Input /mnt/lustre/users/hlwright/00-All.vcf must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

Any help to advise me on my errors would be much appreciated

With thanks

 

1

• 

  Bhanu Gandham

  • April 03, 2020 17:40

  Hi,

   

  The input for knownsites argument should be a vcf file and you are providing it a vcf-index file. Take a look at the tools docs: https://gatk.broadinstitute.org/hc/en-us/articles/360041850511-BaseRecalibrator

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• 

  Rhodri Smith

  • April 04, 2020 14:08

  Hi Bhanu 

  Thanks for your reply

  I think I initially got errors with my vcf file as it was in a different folder to my index file and that was the problem. I then started using the index files as you identified. I have now got it working. Many thanks for your time and help

  Best wishes 

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  Miaoran ZHANG

  • April 15, 2021 02:38

  hi ,when i use ~/software/gatk-4.2.0.0/gatk FastaAlternateReferenceMaker -R chr1.fa -O chr1gatk.fasta -V variations.vcf.idx to build myown reference fasta file, I meet an error like this:

  A USER ERROR has occurred: Cannot read file:///data/zhangmr/peng/modifref/variations.vcf.idx because no suitable codecs found

  the full log is here:

  Using GATK jar /home/zhangmr/software/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 /home/zhangmr/software/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar FastaAlternateReferenceMaker -R chr1.fa -O chr1gatk.fasta -V /data/zhangmr/peng/modifref/variations.vcf.idx
  10:34:28.181 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/zhangmr/software/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  Apr 15, 2021 10:34:35 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
  INFO: Failed to detect whether we are running on Google Compute Engine.
  10:34:35.402 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
  10:34:35.403 INFO FastaAlternateReferenceMaker - The Genome Analysis Toolkit (GATK) v4.2.0.0
  10:34:35.403 INFO FastaAlternateReferenceMaker - For support and documentation go to https://software.broadinstitute.org/gatk/
  10:34:35.403 INFO FastaAlternateReferenceMaker - Executing as zhangmr@centaur on Linux v4.15.0-128-generic amd64
  10:34:35.403 INFO FastaAlternateReferenceMaker - Java runtime: OpenJDK 64-Bit Server VM v11.0.10+9-Ubuntu-0ubuntu1.18.04
  10:34:35.404 INFO FastaAlternateReferenceMaker - Start Date/Time: April 15, 2021 at 10:34:28 AM CST
  10:34:35.404 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
  10:34:35.404 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------
  10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Version: 2.24.0
  10:34:35.405 INFO FastaAlternateReferenceMaker - Picard Version: 2.25.0
  10:34:35.405 INFO FastaAlternateReferenceMaker - Built for Spark Version: 2.4.5
  10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  10:34:35.405 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  10:34:35.405 INFO FastaAlternateReferenceMaker - Deflater: IntelDeflater
  10:34:35.405 INFO FastaAlternateReferenceMaker - Inflater: IntelInflater
  10:34:35.406 INFO FastaAlternateReferenceMaker - GCS max retries/reopens: 20
  10:34:35.406 INFO FastaAlternateReferenceMaker - Requester pays: disabled
  10:34:35.406 INFO FastaAlternateReferenceMaker - Initializing engine
  10:34:35.567 INFO FastaAlternateReferenceMaker - Shutting down engine
  [April 15, 2021 at 10:34:35 AM CST] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.12 minutes.
  Runtime.totalMemory()=2155872256
  ***********************************************************************

  A USER ERROR has occurred: Cannot read file:///data/zhangmr/peng/modifref/variations.vcf.idx because no suitable codecs found

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

  could you help me to sovle this problem?

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• 

  Genevieve Brandt (she/her)

  • April 20, 2021 15:35

  Hi Miaoran ZHANG,

  It looks like this error is coming from a file format issue. Here are the tool docs for that tool: FastaAlternateReferenceMaker. The tool needs a VCF input for the -V argument, and you are submitting an index file (/data/zhangmr/peng/modifref/variations.vcf.idx) instead of the VCF file.

  Hope this helps!

  Genevieve

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• 

  Ekin Köni

  • November 06, 2021 17:22

  ey, ı am facing the same error and can't figure it out away. 

  A USER ERROR has occurred: Cannot read file:///mnt/e/thesis/data/hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz because no suitable codecs found

  ı have all there reference related files that ı have installed from resource bundle

  hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi                hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz

  hg38_v0_Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf         hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi

  hg38_v0_Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi  hg38_v0_hapmap_3.3.hg38.vcf

  hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf                             hg38_v0_hapmap_3.3.hg38.vcf.gz.tbi

  hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz                          hg38_v0_wgs_calling_regions.hg38.interval_list                                               hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi                     

  hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.idx                                                               hg38_v0_Homo_sapiens_assembly38.dict                                    

                                                        hg38_v0_Homo_sapiens_assembly38.fasta                                   

  hg38_v0_Homo_sapiens_assembly38.fasta.64.alt                            

  hg38_v0_Homo_sapiens_assembly38.fasta.64.amb                            

  hg38_v0_Homo_sapiens_assembly38.fasta.64.ann                            

  hg38_v0_Homo_sapiens_assembly38.fasta.64.bwt                             

  hg38_v0_Homo_sapiens_assembly38.fasta.64.pac                             hg38_v0_1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf      hg38_v0_Homo_sapiens_assembly38.fasta.64.sa                              hg38_v0_1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.idx  hg38_v0_Homo_sapiens_assembly38.fasta.fai                                hg38_v0_1000G_omni2.5.hg38.vcf                                          hg38_v0_Homo_sapiens_assembly38.known_indels.vcf                         hg38_v0_1000G_omni2.5.hg38.vcf.gz.tbi                                   hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz                      hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf                      hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz.tbi                  hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz                   hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf            

   

  ı used the bgzip command to convert my vcf files to vcf.gz as it is the proper way.

  but still, ı'm facing the same error.

  the command that ı run is;

   

  gatk BaseRecalibrator \

     -I mySample68snc.bam \

     -R hg38_v0_Homo_sapiens_assembly38.fasta \

     --known-sites hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz \

     --known-sites hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz \

     --known-sites hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz \

     --known-sites hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \

     -O recal_data1.table

   

   

  so if you have a suggestion ıt would make me so happy. Thank you...

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• 

  Pamela Bretscher

  • November 08, 2021 18:15

  Hi Ekin Köni,

  This error typically indicates that the input file is not being recognized properly as a vcf file. Could you try running "gzcat vcf | head -1" for the file that is causing the issue and paste the header line here? (example "##fileformat=VCFv4.2").

  Kind regards,

  Pamela

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  Ekin Köni

  • November 08, 2021 18:31

  ##fileformat=VCFv4.1

   

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  Pamela Bretscher

  • November 08, 2021 20:19

  Ekin Köni, okay thank you for providing this. What version of GATK are you using?

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  Ekin Köni

  • November 08, 2021 20:21

  The Genome Analysis Toolkit (GATK) v4.2.3.0

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  Pamela Bretscher

  • November 08, 2021 21:04

  Hi Ekin Köni,

  Thank you. It's possible that there is an issue with how this file was compressed, causing it to be malformed. Could you try running PrintBGZFBlockInformation on the file? If there is an error, you may need to retry running bgzip on the vcf.

  Kind regards,

  Pamela

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  Ekin Köni

  • November 08, 2021 21:07

  ı will try this suggestion thank you. 

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• 

  Rea Kalampaliki

  • February 08, 2022 23:08
  • Edited

  Hello! I am receiving the exact error with the file: hg19_v0_Homo_sapiens_assembly19.dbsnp138.vcf

  Please help:)

  ref_snps='./reference_genome/hg19_v0_Homo_sapiens_assembly19.dbsnp138.vcf'
  ref_indels='./reference_genome/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf'
  ref='./reference_genome/hg19_v0_Homo_sapiens_assembly19.fasta'
  
  #..more lines with code..
  ./gatk BaseRecalibrator \
                  -I $bam_marked_dup \
                  -R $ref \
                  --known-sites $ref_snps \
                  --known-sites $ref_indels \
                  -O $recal_table \
  # ..result..
  A USER ERROR has occurred: Cannot read file:///home/user/gatk_project/gatk-4.2.5.0/./reference_genome/hg19_v0_Homo_sapiens_assembly19.dbsnp138.vcf because no suitable codecs found

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• 

  Genevieve Brandt (she/her)

  • February 09, 2022 15:39

  Ekin Köni, do you have any suggestions that might help out Rea Kalampaliki?

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  Genevieve Brandt (she/her)

  • February 16, 2022 18:50

  Rea Kalampaliki if you are still having issues with this file, go ahead and make a new post so we can walk you through the troubleshooting steps.

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