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CollectSamErrorMetrics not working

Hi, CollectSamErrorMetrics is giving the following error with any --ERROR_METRICS option. Here's an example with --ERROR_METRICS ERROR:READ_ORDINALITY:CYCLE:
java.lang.IllegalArgumentException: Duplicated suffix (error_by_read_ordinality_and_cycle) found in aggregator class picard.sam.SamErrorMetric.BaseErrorAggregation.
at picard.sam.SamErrorMetric.CollectSamErrorMetrics.getAggregatorList(CollectSamErrorMetrics.java:685)
at picard.sam.SamErrorMetric.CollectSamErrorMetrics.initializeAggregationState(CollectSamErrorMetrics.java:456)
at picard.sam.SamErrorMetric.CollectSamErrorMetrics.doWork(CollectSamErrorMetrics.java:468)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @GER

    Please post the exact gatk version you are using, the command and the entire error log.

  • GERGER Member

    gatk CollectSamErrorMetrics -I input.bam -O input.error -R Homo_sapiens_assembly38.fasta -V input.vcf.gz --ERROR_METRICS ERROR:READ_ORDINALITY:CYCLE

    gatk 4.1.4.0

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @GER

    As requested above, can you please post the entire error log.

  • GERGER Member

    Here you go.

    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 /gpfs/data/evronylab/bin/gatk/gatk-package-4.1.4.0-local.jar CollectSamErrorMetrics -I UDP-1401_exome.bam -O UDP-1401_exome.error -R /gpfs/home/evrong01/evronylab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta -V UDP-1401_exome.g.vcf.gz --ERROR_METRICS ERROR:READ_ORDINALITY:CYCLE
    11:33:20.301 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/evronylab/bin/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    [Tue Nov 19 11:33:20 EST 2019] CollectSamErrorMetrics --INPUT UDP-1401_exome.bam --OUTPUT UDP-1401_exome.error --ERROR_METRICS ERROR --ERROR_METRICS ERROR:BASE_QUALITY --ERROR_METRICS ERROR:INSERT_LENGTH --ERROR_METRICS ERROR:GC_CONTENT --ERROR_METRICS ERROR:READ_DIRECTION --ERROR_METRICS ERROR:PAIR_ORIENTATION --ERROR_METRICS ERROR:HOMOPOLYMER --ERROR_METRICS ERROR:BINNED_HOMOPOLYMER --ERROR_METRICS ERROR:CYCLE --ERROR_METRICS ERROR:READ_ORDINALITY --ERROR_METRICS ERROR:READ_ORDINALITY:CYCLE --ERROR_METRICS ERROR:READ_ORDINALITY:HOMOPOLYMER --ERROR_METRICS ERROR:READ_ORDINALITY:GC_CONTENT --ERROR_METRICS ERROR:READ_ORDINALITY:PRE_DINUC --ERROR_METRICS ERROR:MAPPING_QUALITY --ERROR_METRICS ERROR:READ_GROUP --ERROR_METRICS ERROR:MISMATCHES_IN_READ --ERROR_METRICS ERROR:ONE_BASE_PADDED_CONTEXT --ERROR_METRICS OVERLAPPING_ERROR --ERROR_METRICS OVERLAPPING_ERROR:BASE_QUALITY --ERROR_METRICS OVERLAPPING_ERROR:INSERT_LENGTH --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT --ERROR_METRICS INDEL_ERROR --ERROR_METRICS ERROR:READ_ORDINALITY:CYCLE --VCF UDP-1401_exome.g.vcf.gz --REFERENCE_SEQUENCE /gpfs/home/evrong01/evronylab/reference-files/hg38-gatk/Homo_sapiens_assembly38.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
    [Tue Nov 19 11:33:20 EST 2019] Executing as [email protected] on Linux 3.10.0-693.17.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_181-b13; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.4.0
    [Tue Nov 19 11:33:20 EST 2019] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.01 minutes.
    Runtime.totalMemory()=2592079872
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    java.lang.IllegalArgumentException: Duplicated suffix (error_by_read_ordinality_and_cycle) found in aggregator class picard.sam.SamErrorMetric.BaseErrorAggregation.
    at picard.sam.SamErrorMetric.CollectSamErrorMetrics.getAggregatorList(CollectSamErrorMetrics.java:685)
    at picard.sam.SamErrorMetric.CollectSamErrorMetrics.initializeAggregationState(CollectSamErrorMetrics.java:456)
    at picard.sam.SamErrorMetric.CollectSamErrorMetrics.doWork(CollectSamErrorMetrics.java:468)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
    at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
    at org.broadinstitute.hellbender.Main.main(Main.java:292)

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