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Running BaseRecalibrator

saketkcsaketkc Member
edited October 2012 in Ask the GATK team

HI When I run Base recabrator with the following command:

java -Xmx4g -jar /usr/bin/GenomeAnalysisTK.jar -T BaseRecalibrator -I realignedBam.bam  -R /data1/human_g1k_v37.fasta --knownSites /data1/snp132.vcf -o recalibration_report.grp

I get the following error :

INFO  07:15:53,380 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: Unrecognized SSL message, plaintext connection? 
INFO  07:15:53,380 HttpMethodDirector - Retrying request 
INFO  07:15:53,386 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: Unrecognized SSL message, plaintext connection? 
INFO  07:15:53,387 HttpMethodDirector - Retrying request 
INFO  07:15:53,393 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: Unrecognized SSL message, plaintext connection? 
INFO  07:15:53,393 HttpMethodDirector - Retrying request 
INFO  07:15:53,398 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: Unrecognized SSL message, plaintext connection? 
INFO  07:15:53,398 HttpMethodDirector - Retrying request 
INFO  07:15:53,405 HttpMethodDirector - I/O exception (javax.net.ssl.SSLException) caught when processing request: Unrecognized SSL message, plaintext connection? 
INFO  07:15:53,405 HttpMethodDirector - Retrying request 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.0-34-g07bda93): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR          Name        FeatureType   Documentation
##### ERROR          BCF2     VariantContext   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_bcf2_BCF2Codec.html
##### ERROR        BEAGLE      BeagleFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_beagle_BeagleCodec.html
##### ERROR           BED         BEDFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_bed_BEDCodec.html
##### ERROR      BEDTABLE       TableFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_table_BedTableCodec.html
##### ERROR EXAMPLEBINARY            Feature   http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_example_ExampleBinaryCodec.html
##### ERROR      GELITEXT    GeliTextFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_gelitext_GeliTextCodec.html
##### ERROR      OLDDBSNP    OldDbSNPFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_dbsnp_OldDbSNPCodec.html
##### ERROR     RAWHAPMAP   RawHapMapFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_hapmap_RawHapMapCodec.html
##### ERROR        REFSEQ      RefSeqFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html
##### ERROR     SAMPILEUP   SAMPileupFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_sampileup_SAMPileupCodec.html
##### ERROR       SAMREAD     SAMReadFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_samread_SAMReadCodec.html
##### ERROR         TABLE       TableFeature   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_table_TableCodec.html
##### ERROR           VCF     VariantContext   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
##### ERROR          VCF3     VariantContext   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
##### ERROR ------------------------------------------------------------------------------------------
Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    edited October 2012 Accepted Answer

    Hi there,

    It looks like you might have two different problems at the same time.

    1. The HttpMethodDirector/SSL gobbledygook suggests that the Phone Home feature is not working (maybe you're running on a machine that can't access the internet?). See the FAQs for the solution to that.

    2. Your knownSites VCF file may be malformed; you should try validating it with the Picard validation tools.

    Incidentally, you're running an older version of the GATK, so I recommend you upgrade. We'll be releasing version 2.2 sometime in the next day, so be sure to grab that when it becomes available.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    edited October 2012 Accepted Answer

    Hi there,

    It looks like you might have two different problems at the same time.

    1. The HttpMethodDirector/SSL gobbledygook suggests that the Phone Home feature is not working (maybe you're running on a machine that can't access the internet?). See the FAQs for the solution to that.

    2. Your knownSites VCF file may be malformed; you should try validating it with the Picard validation tools.

    Incidentally, you're running an older version of the GATK, so I recommend you upgrade. We'll be releasing version 2.2 sometime in the next day, so be sure to grab that when it becomes available.

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