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VariantFiltration - log4j:WARN

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


I have ran this script:

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 -Xmx10g -jar /share/apps/bio/gatk- VariantFiltration -R /home/shared/resources/hgRef/hg38/Homo_sapiens_assembly38.fasta -V WES_HChg38noG_49x150_4x100_rawSNP.vcf --filter-expression QD < 2.0 || MQ < 40.0 || FS > 60.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || ExcessHet > 54.69 --filter-name HF_snp_filter_w_ExHet -O WES_HChg38noG_49x150_4x100_HF-SNP.vcf

18:39:06.282 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/apps/bio/gatk-!/com/intel/gkl/native/libgkl_compression.so
18:39:06.454 INFO VariantFiltration - ------------------------------------------------------------
18:39:06.454 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.0.3.0
18:39:06.454 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
18:39:06.455 INFO VariantFiltration - Executing as [email protected] on Linux v3.5.0-36-generic amd64
18:39:06.455 INFO VariantFiltration - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_91-b14
18:39:06.456 INFO VariantFiltration - Start Date/Time: April 4, 2018 6:39:06 PM CEST
18:39:06.456 INFO VariantFiltration - ------------------------------------------------------------
18:39:06.456 INFO VariantFiltration - ------------------------------------------------------------
18:39:06.457 INFO VariantFiltration - HTSJDK Version: 2.14.3
18:39:06.457 INFO VariantFiltration - Picard Version: 2.17.2
18:39:06.457 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:39:06.457 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:39:06.458 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:39:06.458 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:39:06.458 INFO VariantFiltration - Deflater: IntelDeflater
18:39:06.458 INFO VariantFiltration - Inflater: IntelInflater
18:39:06.458 INFO VariantFiltration - GCS max retries/reopens: 20
18:39:06.458 INFO VariantFiltration - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
18:39:06.459 INFO VariantFiltration - Initializing engine
18:39:07.805 INFO FeatureManager - Using codec VCFCodec to read file file:///home/manolis/GATK4/IlluminaExomePairEnd/6.vcf/filtered/WES_HChg38noG_49x150_4x100_rawSNP.vcf
18:39:08.392 INFO VariantFiltration - Done initializing engine
18:39:08.659 INFO ProgressMeter - Starting traversal
18:39:08.660 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
log4j:WARN No appenders could be found for logger (org.apache.commons.jexl2.JexlEngine).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
18:39:18.697 INFO ProgressMeter - chr1:65116577 0.2 179000 1070147.5

Do you have any suggestion about who to fix this WARN? I found some treads including this error but I missed the solution...

Many thanks

Issue · Github
by Sheila

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