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 ------------------------------------------------------------------------------------------