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BQSR- Issue in generating intervals

nithanitha indiaMember

Hi
I am using GATK latest version is 4.1.2.0. While I am running BQSR for the output file of MarkDuplicate, the intervals are not generating. Moreover, the command was executed without errors.

Command used:

MarkDuplicate command used:

/root/Work/GATK_4.1.2.0/gatk-4.1.2.0/gatk MarkDuplicates --ASSUME_SORT_ORDER "queryname" --INPUT /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_sorted.bam --OUTPUT /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_MarkDuplicate.bam --METRICS_FILE /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_MarkDuplicateMatrics.txt --TMP_DIR /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/Temp

BQSR command used

/root/Work/GATK_4.1.2.0/gatk-4.1.2.0/gatk BaseRecalibrator --input /data1/anupriya_work/Topmed/anu/topmed_variant_calling/examples/bwa/BP89773041JP_MarkDuplicate.bam --reference /data1/anupriya_work/Topmed/anu/topmed_variant_calling/examples/resources/ref/hs38DH.fa --known-sites /data1/anupriya_work/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf --known-sites /data1/anupriya_work/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data1/anupriya_work/SNV-file/Homo_sapiens_assembly38.known_indels.vcf.gz --preserve-qscores-less-than 6 --output /data1/anupriya_work/Topmed/anu/topmed_variant_calling/examples/bwa/BP89773041JP_BQSR.table

Logfile of BQSR:

/root/Work/GATK_4.1.2.0/gatk-4.1.2.0/gatk BaseRecalibrator --input /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_MarkDuplicate.bam --reference /data1/a_work/Topmed/AP/topmed_variant_calling/examples/resources/ref/hs38DH.fa --known-sites /data1/a_work/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf --known-sites /data1/a_work/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data1/a_work/SNV-file/Homo_sapiens_assembly38.known_indels.vcf.gz --preserve-qscores-less-than 6 --tmp-dir Temp/ --output /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_BQSR_pq6.table
Using GATK jar /root/Work/GATK_4.1.2.0/gatk-4.1.2.0/gatk-package-4.1.2.0-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 /root/Work/GATK_4.1.2.0/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar BaseRecalibrator --input /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_MarkDuplicate.bam --reference /data1/a_work/Topmed/AP/topmed_variant_calling/examples/resources/ref/hs38DH.fa --known-sites /data1/a_work/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf --known-sites /data1/a_work/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data1/a_work/SNV-file/Homo_sapiens_assembly38.known_indels.vcf.gz --preserve-qscores-less-than 6 --tmp-dir Temp/ --output /data1/a_work/Topmed/AP/topmed_variant_calling/examples/bwa/BP89773041JP_BQSR_pq6.table
11:58:59.967 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/root/Work/GATK_4.1.2.0/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 30, 2019 11:59:45 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:59:45.568 INFO BaseRecalibrator - ------------------------------------------------------------
11:59:45.570 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.2.0
11:59:45.570 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
11:59:45.571 INFO BaseRecalibrator - Executing as [email protected] on Linux v3.10.0-514.el7.x86_64 amd64
11:59:45.571 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_201-b09
11:59:45.571 INFO BaseRecalibrator - Start Date/Time: July 30, 2019 11:58:59 AM IST
11:59:45.571 INFO BaseRecalibrator - ------------------------------------------------------------
11:59:45.571 INFO BaseRecalibrator - ------------------------------------------------------------
11:59:45.572 INFO BaseRecalibrator - HTSJDK Version: 2.19.0
11:59:45.573 INFO BaseRecalibrator - Picard Version: 2.19.0
11:59:45.573 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:59:45.573 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:59:45.573 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:59:45.573 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:59:45.573 INFO BaseRecalibrator - Deflater: IntelDeflater
11:59:45.573 INFO BaseRecalibrator - Inflater: IntelInflater
11:59:45.573 INFO BaseRecalibrator - GCS max retries/reopens: 20
11:59:45.574 INFO BaseRecalibrator - Requester pays: disabled
11:59:45.574 INFO BaseRecalibrator - Initializing engine
11:59:46.280 INFO FeatureManager - Using codec VCFCodec to read file file:///data1/a_work/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf
11:59:46.673 INFO FeatureManager - Using codec VCFCodec to read file file:///data1/a_work/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
11:59:46.791 INFO FeatureManager - Using codec VCFCodec to read file file:///data1/a_work/SNV-file/Homo_sapiens_assembly38.known_indels.vcf.gz
11:59:46.947 INFO BaseRecalibrator - Done initializing engine
11:59:46.950 INFO BaseRecalibrationEngine - The covariates being used here:
11:59:46.950 INFO BaseRecalibrationEngine - ReadGroupCovariate
11:59:46.950 INFO BaseRecalibrationEngine - QualityScoreCovariate
11:59:46.950 INFO BaseRecalibrationEngine - ContextCovariate
11:59:46.951 INFO BaseRecalibrationEngine - CycleCovariate
11:59:46.995 INFO ProgressMeter - Starting traversal
11:59:46.995 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
12:40:54.979 INFO BaseRecalibrator - 758382002 read(s) filtered by: ((((((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND WellformedReadFilter)
758382002 read(s) filtered by: (((((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
758382002 read(s) filtered by: ((((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
758382002 read(s) filtered by: (((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
758382002 read(s) filtered by: ((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter)
758382002 read(s) filtered by: (MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter)
758382002 read(s) filtered by: MappingQualityNotZeroReadFilter

12:40:54.988 INFO ProgressMeter - unmapped 41.1 0 0.0
12:40:54.988 INFO ProgressMeter - Traversal complete. Processed 0 total reads in 41.1 minutes.
12:40:54.988 INFO BaseRecalibrator - Calculating quantized quality scores...
12:40:55.009 INFO BaseRecalibrator - Writing recalibration report...
12:40:55.066 INFO BaseRecalibrator - ...done!
12:40:55.066 INFO BaseRecalibrator - Shutting down engine
[July 30, 2019 12:40:55 PM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 41.92 minutes.
Runtime.totalMemory()=1917321216

Tool returned:

Could anyone point out where I have to correct the command?

Thanks

Answers

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