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GATK- GetPileupSummaries "No suitable codecs found" error


I am trying to run the contamination pipeline for GATK- If I use somatic-hg38_af-only-gnomad.hg38.vcf as reference, I get out of memory errors, exactly as detailed in a previous thread (https://gatkforums.broadinstitute.org/gatk/discussion/23931/getpileupsummaries-runs-out-of-memory).

So, I take the suggestion of davidben at the end of the thread "In our best practices we recommend using gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz for the Contamination pipeline....". I downloaded the vcf file from gatk website (https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38?project=broad-dsde-outreach&pli=1). However, I get "No suitable codecs found" error. How do I get around this issue?

My command:

gatk --java-options "-Xmx200g" GetPileupSummaries \ -I ${id}-T/${id}-T.recal.bam \ -V ${REFDIR}/small_exac_common_3.hg38.vcf.gz \ -L ${REFDIR}/small_exac_common_3.hg38.vcf.gz \ -O ${id}-T/${id}-T.recal.pileups.table \

The error I get:

`05:32:19.408 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/beegfs/v1/star/sw/star/Pkgs/GATK/!/com/intel/gkl/native/libgkl_compression.so
Dec 29, 2019 5:32:21 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
05:32:21.668 INFO GetPileupSummaries - ------------------------------------------------------------
05:32:21.669 INFO GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.1.3.0
05:32:21.670 INFO GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/
05:32:21.672 INFO GetPileupSummaries - Executing as [email protected] on Linux v3.10.0-1062.9.1.el7.x86_64 amd64
05:32:21.673 INFO GetPileupSummaries - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_111-b14
05:32:21.674 INFO GetPileupSummaries - Start Date/Time: December 29, 2019 5:32:19 AM EST
05:32:21.675 INFO GetPileupSummaries - ------------------------------------------------------------
05:32:21.676 INFO GetPileupSummaries - ------------------------------------------------------------
05:32:21.679 INFO GetPileupSummaries - HTSJDK Version: 2.20.1
05:32:21.680 INFO GetPileupSummaries - Picard Version: 2.20.5
05:32:21.681 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
05:32:21.682 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
05:32:21.683 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
05:32:21.684 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
05:32:21.685 INFO GetPileupSummaries - Deflater: IntelDeflater
05:32:21.686 INFO GetPileupSummaries - Inflater: IntelInflater
05:32:21.687 INFO GetPileupSummaries - GCS max retries/reopens: 20
05:32:21.688 INFO GetPileupSummaries - Requester pays: disabled
05:32:21.689 WARN GetPileupSummaries -

[1m[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Warning: GetPileupSummaries is a BETA tool and is not yet ready for use in production


05:32:21.690 INFO GetPileupSummaries - Initializing engine
05:32:24.001 INFO GetPileupSummaries - Shutting down engine
[December 29, 2019 5:32:24 AM EST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.08 minutes.

A USER ERROR has occurred: Cannot read file:///home/bsmith/data/references/gatk- 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.
Using GATK jar /mnt/beegfs/v1/star/sw/star/Pkgs/GATK/
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 -Xmx400g -jar /mnt/beegfs/v1/star/sw/star/Pkgs/GATK/ GetPileupSummaries -I 4P-T/4P-T.recal.bam -V /home/bsmith/data/references/gatk- -L /home/bsmith/data/references/gatk- -O 4P-T/4P-T.recal.pileups.table

What do I need to do to get around this?


Best Answer


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