GenotypeGVCFs 4.0.5.0 error

manolismanolis Member ✭✭
edited June 2018 in Ask the GATK team

Hi,

do you have any idea what is this error?

06:43:19.441 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by defau

java: tpp.c:63: __pthread_tpp_change_priority: Assertion new_prio == -1 || (new_prio >= __sched_fifo_min_prio && new_prio <= __sched_fifo_max_prio)' failed.`

The full log file...

Using GATK jar /share/apps/bio/gatk-4.0.5.0/gatk-package-4.0.5.0-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 -Dsamj
dk.compression_level=2 -Xmx10g -jar /share/apps/bio/gatk-4.0.5.0/gatk-package-4.0.5.0-local.jar GenotypeGVCFs -R /home/shared/resources/hgRef
/hg38/Homo_sapiens_assembly38.fasta -O /home/manolis/GATK4/IlluminaExomePairEnd/6.vcf/processing/WESx3_WgWgCC_prova01_01.vcf -G StandardAnnot
ation --only-output-calls-starting-in-intervals -new-qual -V gendb://WESx3_WgWgCC_prova01/01 -L chr1
06:43:19.441 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by defau
lt
06:43:19.578 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/apps/bio/gatk-4.0.5.0/gatk-package-4.0.5.0-local.
jar!/com/intel/gkl/native/libgkl_compression.so
06:43:19.865 INFO  GenotypeGVCFs - ------------------------------------------------------------
06:43:19.866 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.0.5.0
06:43:19.866 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
06:43:19.867 INFO  GenotypeGVCFs - Executing as [email protected] on Linux v3.5.0-36-generic amd64
06:43:19.867 INFO  GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_91-b14
06:43:19.867 INFO  GenotypeGVCFs - Start Date/Time: June 12, 2018 6:43:19 AM CEST
06:43:19.867 INFO  GenotypeGVCFs - ------------------------------------------------------------
06:43:19.868 INFO  GenotypeGVCFs - ------------------------------------------------------------
06:43:19.869 INFO  GenotypeGVCFs - HTSJDK Version: 2.15.1
06:43:19.869 INFO  GenotypeGVCFs - Picard Version: 2.18.2
06:43:19.869 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
06:43:19.869 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
06:43:19.869 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
06:43:19.869 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
06:43:19.869 INFO  GenotypeGVCFs - Deflater: IntelDeflater
06:43:19.870 INFO  GenotypeGVCFs - Inflater: IntelInflater
06:43:19.870 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
06:43:19.870 INFO  GenotypeGVCFs - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
06:43:19.870 INFO  GenotypeGVCFs - Initializing engine
WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
06:43:22.800 INFO  IntervalArgumentCollection - Processing 248956422 bp from intervals
06:43:22.909 INFO  GenotypeGVCFs - Done initializing engine
06:43:23.225 INFO  ProgressMeter - Starting traversal
06:43:23.226 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
06:43:35.787 INFO  ProgressMeter -           chr1:17703              0.2                  1000           4776.7
06:43:38.536 INFO  GenotypeGVCFs - Shutting down engine
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.3484763260000022,Cpu time(s),0.27263762600000135
java: tpp.c:63: __pthread_tpp_change_priority: Assertion `new_prio == -1 || (new_prio >= __sched_fifo_min_prio && new_prio <= __sched_fifo_max_prio)' failed.

Many thanks

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Best Answers

  • manolismanolis ✭✭
    Accepted Answer

    using the same input files, with GATK4.0.4.0 I don't have those Warning.

    Best

  • manolismanolis ✭✭
    Accepted Answer

    Hi!

    No I did not used yet 4.0.5.1.
    Now, from fastq to gVCFs with v4.0.5.0; from GenomicsDBImport up to the end of the pipeline, post-VQSR, with v4.0.4.0.

    I will try the last one, 4.0.5.1.

    Thank you

Answers

  • manolismanolis Member ✭✭
    Accepted Answer

    using the same input files, with GATK4.0.4.0 I don't have those Warning.

    Best

  • manolismanolis Member ✭✭
    Accepted Answer

    Hi!

    No I did not used yet 4.0.5.1.
    Now, from fastq to gVCFs with v4.0.5.0; from GenomicsDBImport up to the end of the pipeline, post-VQSR, with v4.0.4.0.

    I will try the last one, 4.0.5.1.

    Thank you

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