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GenotypeGVCFs 3.8 fails

tommycarstensentommycarstensen United KingdomMember ✭✭✭
edited October 2017 in Ask the GATK team

I had the same problem as described in thread 10004:

ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in

Except my issue was with HaplotypeCaller. I upgraded from version 3.8 to the nightly build, but it still fails. Now I just don't get the ERROR message in stderr.

Here is my Linux version:

uname -a
Linux vr-2-2-02 3.2.0-105-generic #146-Ubuntu SMP Fri Jun 10 20:10:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

Here is my command:

/software/jre1.8.0_74/bin/java -Djava.io.tmpdir=tmp -Xmx${memMB}m -XX:+UseSerialGC  \
 -jar GenomeAnalysisTK-nightly-2017-10-06-g1994025.jar \
 --analysis_type GenotypeGVCFs \
 --reference_sequence Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa \
 --num_cpu_threads_per_data_thread $nct \
 --num_threads $nt \
 -L $chrom \
 -V lists/GenotypeGVCFs.$chrom.list \
 -o $out \
 --annotation InbreedingCoeff \
 --annotation FisherStrand \
 --annotation StrandOddsRatio \
 --annotation QualByDepth \
 --annotation ChromosomeCounts \
 --annotation GenotypeSummaries \
 --annotation MappingQualityRankSumTest \
 --annotation ReadPosRankSumTest \
 -A StrandBiasBySample \
 -A VariantType \
 --standard_min_confidence_threshold_for_calling 30 \
 --dbsnp dbsnp_human_9606_b147_GRCh38p2_All_20160527.vcf.gz \

The number of threads --num_threads/-nt is greater than 1. I just tried with -nct and -nt both equal to 1. It still fails.

Thanks for any help you provide.

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Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭
    edited October 2017

    I solved it. I will not delete the issue though. I removed this from my command -XX:+UseSerialGC. The reason I had added it in the first place, is because HaplotypeCaller in GVCF mode sometimes makes the compute cluster complain that I'm using more than one thread despite setting -nt and -nct equal to 1. It happens randomly.

    Now I just need to look into these WARNings, which seem to be related to changes that happened between 3.8 and 3.4, when I last used GATK.

    WARN  11:23:02,627 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  11:23:02,627 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  11:23:03,416 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail. 
WARN  11:23:03,419 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail. 
WARN  11:23:06,063 AnnotationUtils - SB annotation will not be calculated, must be called from HaplotypeCaller or MuTect2, not GenotypeGVCFs 
WARN  11:23:06,268 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not GenotypeGVCFs 
WARN  11:23:29,760 ExactAFCalculator - This tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr18: 71569 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.
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  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    I didn't solve it. Removing -XX:+UseSerialGC just caused the error to be delayed. It still happens after approximately 60 minutes. Ahhh, actually it doesn't happen with the nightly, but it does happen with 3.8. OK, all solved then.

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  • SheilaSheila Broad InstituteMember, Broadie admin

    @tommycarstensen
    Hi Tommy,

    Okay, thanks for telling us :smile:
    Glad to hear the latest nightly solves everything.

    -Sheila

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  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    Sorry about crying wolf again, but the problem remains with GenotypeGVCFs. Even with the nightlies 2017-10-06-g1994025 and 2017-11-07-g45c474f. I posted in thread 13053.

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  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    That is unfortunate @tommycarstensen. Sheila is away for a workshop so I will followup in the other thread.

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  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    With GenotypeGVCFs3.8 I lowered -nt and -Xmx from 24 and 64GB to 8 and 16GB, respectively. That seemed to do the trick. My solution/answer is also posted here.

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