ImportGVCFs error message "Failed to create reader from file"

Hello,

I am using joint-discovery-gatk4.wdl + joint-discovery-gatk4.hg38.wgs.inputs.json to run “Generic germline short variant joint genotyping” pipeline with GATK 4.0.3.0 on my local computer.
I got an error message: “A USER ERROR has occurred: Failed to create reader from file:///home/carl/temp/NA12878.g.vcf.gz” when running the task “ImportGVCFs”. What dose this message mean and how about the solution?

**Here is the content of cromwell-executions/JointGenotyping/…/call-ImportGVCFs/shard-1/execution/sterr: **

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/JointGenotyping/e584fd7e-1bb8-46ee-8daa-5630351324c2/call-ImportGVCFs/shard-1/tmp.ad3e936f
13:39:13.501 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/build/libs/gatk-package-4.0.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
13:39:13.723 INFO GenomicsDBImport - ------------------------------------------------------------
13:39:13.723 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.3.0
13:39:13.723 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
13:39:13.724 INFO GenomicsDBImport - Executing as [email protected] on Linux v4.13.0-38-generic amd64
13:39:13.724 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11
13:39:13.724 INFO GenomicsDBImport - Start Date/Time: April 11, 2018 1:39:13 PM UTC
13:39:13.724 INFO GenomicsDBImport - ------------------------------------------------------------
13:39:13.724 INFO GenomicsDBImport - ------------------------------------------------------------
13:39:13.725 INFO GenomicsDBImport - HTSJDK Version: 2.14.3
13:39:13.725 INFO GenomicsDBImport - Picard Version: 2.17.2
13:39:13.725 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:39:13.725 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:39:13.725 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:39:13.725 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:39:13.725 INFO GenomicsDBImport - Deflater: IntelDeflater
13:39:13.725 INFO GenomicsDBImport - Inflater: IntelInflater
13:39:13.725 INFO GenomicsDBImport - GCS max retries/reopens: 20
13:39:13.725 INFO GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
13:39:13.725 INFO GenomicsDBImport - Initializing engine
13:39:13.747 INFO GenomicsDBImport - Shutting down engine
[April 11, 2018 1:39:13 PM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=4116185088


A USER ERROR has occurred: Failed to create reader from file:///home/carl/temp/NA12878.g.vcf.gz


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 /gatk/build/libs/gatk-package-4.0.3.0-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 -Xmx4g -Xms4g -jar /gatk/build/libs/gatk-package-4.0.3.0-local.jar GenomicsDBImport --genomicsdb-workspace-path genomicsdb --batch-size 50 -L chr2:1-242193529 --sample-name-map /cromwell-executions/JointGenotyping/e584fd7e-1bb8-46ee-8daa-5630351324c2/call-ImportGVCFs/shard-1/inputs/home/carl/WDL/NA12878.sample_map --reader-threads 5 -ip 500

**And here is the code of “joint-discovery-gatk4.hg38.wgs.inputs.json”: **

{
"##_COMMENT1": "INPUT GVCFs & COHORT -- DATASET-SPECIFC, MUST BE ADAPTED",
"JointGenotyping.callset_name": "NA12878",
"JointGenotyping.sample_name_map": "/home/carl/WDL/NA12878.sample_map",

"##_COMMENT2": "REFERENCE FILES",
"JointGenotyping.ref_fasta": "/home/carl/GATK4/hg38/Homo_sapiens_assembly38.fasta",
"JointGenotyping.ref_fasta_index": "/home/carl/GATK4/hg38/Homo_sapiens_assembly38.fasta.fai",
"JointGenotyping.ref_dict": "/home/carl/GATK4/hg38/Homo_sapiens_assembly38.dict",

"##_COMMENT3": "INTERVALS",
"JointGenotyping.eval_interval_list": "/home/carl/WDL/wgs_evaluation_regions.hg38.interval_list",
"JointGenotyping.unpadded_intervals_file": "/home/carl/WDL/hg38.even.handcurated.20k.intervals",

"##_COMMENT4": "RESOURCE FILES",
"JointGenotyping.dbsnp_vcf": "/home/carl/GATK4/hg38/Homo_sapiens_assembly38.dbsnp138.vcf",
"JointGenotyping.dbsnp_vcf_index": "/home/carl/GATK4/hg38/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"JointGenotyping.one_thousand_genomes_resource_vcf": "/home/carl/GATK4/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"JointGenotyping.one_thousand_genomes_resource_vcf_index": "/home/carl/GATK4/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"JointGenotyping.omni_resource_vcf": "/home/carl/GATK4/hg38/1000G_omni2.5.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf_index": "/home/carl/GATK4/hg38/1000G_omni2.5.hg38.vcf.gz.tbi",
"JointGenotyping.mills_resource_vcf": "/home/carl/GATK4/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"JointGenotyping.mills_resource_vcf_index": "/home/carl/GATK4/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"JointGenotyping.axiomPoly_resource_vcf": "/home/carl/GATK4/hg38/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
"JointGenotyping.axiomPoly_resource_vcf_index": "/home/carl/GATK4/hg38/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
"JointGenotyping.hapmap_resource_vcf": "/home/carl/GATK4/hg38/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.hapmap_resource_vcf_index": "/home/carl/GATK4/hg38/hapmap_3.3.hg38.vcf.gz.tbi",

"##_COMMENT5": "VQSR PARAMETERS",
"JointGenotyping.SNP_VQSR_downsampleFactor": 10,
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 99.7,
"JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.snp_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ],
"JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"],

"##_COMMENT4": "DOCKERS",
"JointGenotyping.python_docker": "python:2.7",
"JointGenotyping.gatk_docker": "broadinstitute/gatk:4.0.3.0",

"##_COMMENT5": "PATHS",
"JointGenotyping.gatk_path": "/gatk/gatk",

"##_COMMENT6": "JAVA OPTIONS",
"JointGenotyping.SNPsVariantRecalibratorScattered.java_opt": "-Xmx3g -Xms3g",
"JointGenotyping.CollectMetricsOnFullVcf.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.IndelsVariantRecalibrator.java_opt": "-Xmx24g -Xms24g",
"JointGenotyping.HardFilterAndMakeSitesOnlyVcf.java_opt": "-Xmx3g -Xms3g",
"JointGenotyping.SNPGatherTranches.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.CollectMetricsSharded.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.SitesOnlyGatherVcf.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.ApplyRecalibration.java_opt": "-Xmx5g -Xms5g",
"JointGenotyping.FinalGatherVcf.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.ImportGVCFs.java_opt": "-Xmx4g -Xms4g",
"JointGenotyping.SNPsVariantRecalibratorCreateModel.java_opt": "-Xmx100g -Xms100g",
"JointGenotyping.GatherMetrics.java_opt": "-Xmx2g -Xms2g",
"JointGenotyping.GenotypeGVCFs.java_opt": "-Xmx5g -Xms5g",

"##_COMMENT7": "MEMORY ALLOCATION",
"JointGenotyping.CollectMetricsSharded.mem_size": "7 GB",
"JointGenotyping.ImportGVCFs.mem_size": "7 GB",
"JointGenotyping.IndelsVariantRecalibrator.mem_size": "26 GB",
"JointGenotyping.ApplyRecalibration.mem_size": "7 GB",
"JointGenotyping.CollectMetricsOnFullVcf.mem_size": "7 GB",
"JointGenotyping.GenotypeGVCFs.mem_size": "7 GB",
"JointGenotyping.FinalGatherVcf.mem_size": "7 GB",
"JointGenotyping.SitesOnlyGatherVcf.mem_size": "7 GB",
"JointGenotyping.SNPsVariantRecalibratorScattered.mem_size": "3.5 GB",
"JointGenotyping.SNPsVariantRecalibratorCreateModel.mem_size": "104 GB",
"JointGenotyping.DynamicallyCombineIntervals.mem_size": "3 GB",
"JointGenotyping.GatherMetrics.mem_size": "3 GB",
"JointGenotyping.HardFilterAndMakeSitesOnlyVcf.mem_size": "3.5 GB",
"JointGenotyping.SNPGatherTranches.mem_size": "7 GB",

"##_COMMENT8": "DISK SIZE ALLOCATION",
"JointGenotyping.small_disk": 100,
"JointGenotyping.medium_disk": 200,
"JointGenotyping.huge_disk": 300,

"##_COMMENT9": "PREEMPTIBLES",
"JointGenotyping.FinalGatherVcf.preemptibles": 5,
"JointGenotyping.IndelsVariantRecalibrator.preemptibles": 5,
"JointGenotyping.SNPsVariantRecalibratorScattered.preemptibles": 5,
"JointGenotyping.HardFilterAndMakeSitesOnlyVcf.preemptibles": 5,
"JointGenotyping.CollectMetricsOnFullVcf.preemptibles": 5,
"JointGenotyping.GatherMetrics.preemptibles": 5,
"JointGenotyping.SNPGatherTranches.preemptibles": 5,
"JointGenotyping.SitesOnlyGatherVcf.preemptibles": 5,
"JointGenotyping.CollectMetricsSharded.preemptibles": 5,
"JointGenotyping.ApplyRecalibration.preemptibles": 5,
"JointGenotyping.ImportGVCFs.preemptibles": 5,
"JointGenotyping.SNPsVariantRecalibratorCreateModel.preemptibles": 5,
"JointGenotyping.GenotypeGVCFs.preemptibles": 5,
"JointGenotyping.DynamicallyCombineIntervals.preemptibles": 5
}

Here is the content of "/home/carl/WDL/NA12878.sample_map" : 

NA12878 /home/carl/temp/NA12878.g.vcf.gz

Best regards,
Carl

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