Genome Analysis Toolkit

Tanay Biswas · November 26, 2022 08:21

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

I've hg19 mapped BAM file also. But hg19 gnomad.exome.vcf file is not giving any errors.

REQUIRED for all errors and issues:
a) GATK version used: 4.2.5.0
b) Exact command used: java -jar /home/tbiswas/softwares/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GetPileupSummaries -I /scratch/tbiswas/2/IITK-P6-TD.recal2.bam -V /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf -L /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf -O /scratch/tbiswas/2/IITK-P6-TD_pileups.table
c) Entire program log:

[tbiswas@un02 tbiswas]$ java -jar /home/tbiswas/softwares/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GetPileupSummaries -I /scratch/tbiswas/2/IITK-P6-TD.recal2.bam -V /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf -L /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf -O /scratch/tbiswas/2/IITK-P6-TD_pileups.table

13:35:03.410 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/tbiswas/softwares/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Nov 26, 2022 1:35:03 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

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

13:35:03.540 INFO GetPileupSummaries - ------------------------------------------------------------

13:35:03.541 INFO GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.2.5.0

13:35:03.541 INFO GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/

13:35:03.541 INFO GetPileupSummaries - Executing as tbiswas@un02 on Linux v3.10.0-327.el7.x86_64 amd64

13:35:03.541 INFO GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_65-b17

13:35:03.541 INFO GetPileupSummaries - Start Date/Time: 26 November, 2022 1:35:03 PM IST

13:35:03.541 INFO GetPileupSummaries - ------------------------------------------------------------

13:35:03.542 INFO GetPileupSummaries - ------------------------------------------------------------

13:35:03.542 INFO GetPileupSummaries - HTSJDK Version: 2.24.1

13:35:03.542 INFO GetPileupSummaries - Picard Version: 2.25.4

13:35:03.542 INFO GetPileupSummaries - Built for Spark Version: 2.4.5

13:35:03.542 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2

13:35:03.542 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

13:35:03.542 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

13:35:03.542 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

13:35:03.543 INFO GetPileupSummaries - Deflater: IntelDeflater

13:35:03.543 INFO GetPileupSummaries - Inflater: IntelInflater

13:35:03.543 INFO GetPileupSummaries - GCS max retries/reopens: 20

13:35:03.543 INFO GetPileupSummaries - Requester pays: disabled

13:35:03.543 INFO GetPileupSummaries - Initializing engine

13:35:03.935 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf

13:35:03.960 INFO GetPileupSummaries - Shutting down engine

[26 November, 2022 1:35:03 PM IST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.01 minutes.

Runtime.totalMemory()=2251816960

org.broadinstitute.hellbender.exceptions.GATKException: Error initializing feature reader for path /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf

at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:436)

at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:377)

at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:319)

at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:291)

at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:246)

at org.broadinstitute.hellbender.engine.FeatureManager.initializeFeatureSources(FeatureManager.java:209)

at org.broadinstitute.hellbender.engine.FeatureManager.<init>(FeatureManager.java:156)

at org.broadinstitute.hellbender.engine.GATKTool.initializeFeatures(GATKTool.java:497)

at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:726)

at org.broadinstitute.hellbender.engine.LocusWalker.onStartup(LocusWalker.java:136)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

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)

Caused by: htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /scratch/tbiswas/largefiles/hg38vcfs/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf

at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:263)

at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:102)

at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:127)

at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)

at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:433)

... 15 more

Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file

at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115)

at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)

at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)

at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:261)

... 19 more

[tbiswas@un02 tbiswas]$