Question: Error with SNPSift while using dbNSFP2.9.txt.gz for annotation
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gravatar for always_learning
3.8 years ago by
Doha, Qatar
always_learning960 wrote:

Dear All,

I have been using SNPSift for annotating VCF with database dbNSFPv_2.6.txt.gz and its working perfectly. Now I am using SNPSift with dbNSFP2.9.txt.gz version for few other annotation like ExAC frequency but getting Null Pointer exception. 

If some one else got same error while trying dbNSFP2.9.txt.gz with SNPSift ? 

Here is command that I am using and associated errors too .

java -jar /gpfs/software/genomics/snpEff/4.1A/SnpSift.jar dbnsfp -v -db /gpfs/data_jrnas1/ref_data/Hsaens/GRCh37/variation/dbNSFP2.9.txt.gz GA_151.GATK.annotated_10000.vcf

00:00:00.000    SnpSift version SnpSift 4.1a (build 2015-01-14), by Pablo Cingolani

00:00:00.003    Command: 'DBNSFP'

00:00:00.003    Reading configuration file 'snpEff.config'

00:00:00.282    done

00:00:00.283    Annotating

    Input file    : 'GA_151.GATK.annotated_10000.vcf'

    Database file : '/gpfs/data_jrnas1/ref_data/Hsapiens/GRCh37/variation/dbNSFP2.9.txt.gz'

Exception in thread "main" java.lang.RuntimeException: java.lang.NullPointerException

    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.annotate(SnpSiftCmdDbNsfp.java:100)

    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.run(SnpSiftCmdDbNsfp.java:423)

    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.run(SnpSiftCmdDbNsfp.java:408)

    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:360)

    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:69)

Caused by: java.lang.NullPointerException

    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.initAnnotate(SnpSiftCmdDbNsfp.java:350)

    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdDbNsfp.annotate(SnpSiftCmdDbNsfp.java:98)

 

snp snpeff annotation snpsift • 1.4k views
ADD COMMENTlink written 3.8 years ago by always_learning960
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