CollectSamErrorMetrics error

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Joe Georgeson

• October 10, 2022 17:41

Dear GATK community,

I would like to run 'picard CollectSamErrorMetrics' but receive the below error. Can anyone offer advice?

REQUIRED for all errors and issues:
a) GATK version used:

Picard version: Version:2.27.5

b) Exact command used:

java -jar picard.jar CollectSamErrorMetrics --INPUT ./myBAM_Aligned.sortedByCoord.out.bam --OUTPUT ./myBAM_Aligned.sortedByCoord.out.bam.errorMetrics.txt --VCF ./gnomad.exomes.r2.0.2.sites.vcf --MIN_MAPPING_Q 0 --MIN_BASE_Q 20 --REFERENCE_SEQUENCE ./hg19.fa

c) Entire program log: 

20:27:56.348 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:~/picard.jar!/com/intel/gkl/native/libgkl_compression.so

[Mon Oct 10 20:27:56 IDT 2022] CollectSamErrorMetrics --INPUT ./myBAM_Aligned.sortedByCoord.out.bam --OUTPUT ./myBAM_Aligned.sortedByCoord.out.bam.errorMetrics.txt --VCF ./gnomad.exomes.r2.0.2.sites.vcf --MIN_MAPPING_Q 0 --MIN_BASE_Q 20 --REFERENCE_SEQUENCE ./hg19.fa --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 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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

[Mon Oct 10 20:27:56 IDT 2022] Executing as user@place on Linux 3.10.0-514.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.27.5

INFO 2022-10-10 20:27:56 CollectSamErrorMetrics Getting SamLocusIterator

INFO 2022-10-10 20:27:56 CollectSamErrorMetrics Using 26 aggregators.

INFO 2022-10-10 20:27:56 CollectSamErrorMetrics Starting iteration over loci

INFO 2022-10-10 20:27:56 CollectSamErrorMetrics Really starting iteration now.

[Mon Oct 10 20:36:31 IDT 2022] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 8.59 minutes.

Runtime.totalMemory()=3184525312

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

Exception in thread "main" java.lang.NullPointerException

at picard.sam.SamErrorMetric.ReadBaseStratification.stratifyReadGroup(ReadBaseStratification.java:1210)

at picard.sam.SamErrorMetric.ReadBaseStratification$2.stratify(ReadBaseStratification.java:171)

at picard.sam.SamErrorMetric.ReadBaseStratification$RecordStratifier.stratify(ReadBaseStratification.java:105)

at picard.sam.SamErrorMetric.ReadBaseStratification$CollectionStratifier.stratify(ReadBaseStratification.java:242)

at picard.sam.SamErrorMetric.BaseErrorAggregation.addBase(BaseErrorAggregation.java:55)

at picard.sam.SamErrorMetric.CollectSamErrorMetrics.addRecordAndOffset(CollectSamErrorMetrics.java:624)

at picard.sam.SamErrorMetric.CollectSamErrorMetrics.addLocusBases(CollectSamErrorMetrics.java:694)

at picard.sam.SamErrorMetric.CollectSamErrorMetrics.processData(CollectSamErrorMetrics.java:395)

at picard.sam.SamErrorMetric.CollectSamErrorMetrics.doWork(CollectSamErrorMetrics.java:509)

at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:309)

at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)

at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

0

• 

  Anthony DiCi

  • October 13, 2022 16:49

  Hi Joe Georgeson,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.

  I brought this issue to our developers and received some feedback and things for you to try. The crash seems to have occurred in a part of Picard where it’s trying to get the read group ID. It could be because either the bam didn’t have it set or it was set to something Picard didn’t like. 

  You can verify whether there is a problem with your bam file by running our GATK tool ValidateSamFile. Assuming the issue is a missing read group, you may be able to repair it by using either --samtools addreplacerg or --picard AddOrReplaceReadGroups.

  I hope this helps! Please let me know if this leads you to success. If you have any other questions in the meantime, please do not hesitate to reach out.

  Best,
  Anthony

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  Joe Georgeson

  • October 13, 2022 18:25

  Hi Anthony DiCi

  Thank you for the reply, after adding read groups this function works fine.

  Best,

  Joe

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• 

  Anthony DiCi

  • October 13, 2022 19:04

  Hi Joe Georgeson,

  Great! Happy to hear that. Thank you again for contributing to the GATK forum. Please do not hesitate to reach out with any other questions that pop up in the future.

  Best,

  Anthony

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