Running Gatk Baserecalibrator

Question

[Saket Choudhary]

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

[Neilfws]

This is very difficult to read. You can make it more readable if you indent lines with 4 spaces.

Answer 1

[Neilfws]

I think these are the key parts of the error message:

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

You did something wrong.

ERROR Please do not post this error to the GATK forum

It's a common mistake and they don't want to hear about it.

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 commonly asked questions

Read the manual.

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

This is what you did wrong.

[vdauwera]

Excellent parsing of the GATK error message :D

Answer 2

[vdauwera]

Answered here:

http://gatkforums.broadinstitute.org/discussion/1736/running-baserecalibrator