I got this error message, when trying to use a file to specify at which positions to emit variants:
ERROR MESSAGE: Couldn't read file /lustre/scratch109/sanger/tc9/agv/wgs/pipeline/union4x.positions because The interval file /lustre/scratch109/sanger/tc9/agv/wgs/pipeline/union4x.positions does not have one of the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). Please rename your file with the appropriate extension. Is there a GATK page describing those 5 file formats? Some of them are unknown to me; e.g. .list.
I asked my question here, but please ignore it: http://gatkforums.broadinstitute.org/discussion/2219/l-option
Thanks a lot.
Also, the error message does not mention support for vcf files, but the documentation does. Are vcf files supported?
Hello,
During running of the depthOfCoverage tool, I get the error: /tmp/RsQHCt1W: No space left on device
I have tried changing the TMPDIR environment variable (and exporting) but eventually I get the same error. Is there a way to change the temporary directory that GATK uses?
I'm running GATK v2.1-8-g5efb575 on a Linux system.
Thanks, Rick
Hi I´ve a strange problem with the GATK. Everytime I try to run it my Console shows the following error Message.
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR ------------------------------------------------------------------------------------------
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR A USER ERROR has occurred (version 2.1-13-g0f021e6):
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR Please do not post this error to the GATK forum
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR Visit our website and forum for extensive documentation and answers to
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR MESSAGE: Argument with name '--analysis_type' (-T) is missing.
30.10.12 15:10:06 [0x0-0xe20e2].com.apple.JarLauncher[1114] ##### ERROR ------------------------------------------------------------------------------------------
Can you show me my mistakes please? With regards Oliver
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 ------------------------------------------------------------------------------------------
hi all! I'm trying to complete my first GATK run, I'm doing the step in the "EXECUTION STEP" following section.
please tell me if the step execution are globally correct.
------------------------------------------------------------------ERRORS----------------------------------------------------------------
the step 4.1 isn't executed without -maxCycle 1500.
when try to execute 4.2 step I got the following error:
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Key 1036 is too large for dimension 2 (max is 1001)
at org.broadinstitute.sting.utils.collections.NestedIntegerArray.put(NestedIntegerArray.java:128)
at org.broadinstitute.sting.utils.recalibration.RecalibrationReport.parseAllCovariatesTable(RecalibrationReport.java:157)
at org.broadinstitute.sting.utils.recalibration.RecalibrationReport.
---------------------------------------------------------------EXECUTION STEP---------------------------------------------------------
2 MARKING PCR DUPLICATE
java -Xmx4g -Djava.io.tmpdir=/tmp -jar MarkDuplicates.jar INPUT=M9.bam OUTPUT=m9.marked.bam METRICS_FILE=metrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT
3 LOCAL REALIGNMENT AROUND INDEL
3.1
java -Xmx4g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ucsc.hg19.fasta -knowndbsnp_137.hg19.vcf -o m9.list -I m9.marked.bam
3.2
java -Xmx4g -Djava.io.tmpdir=/tmp -jar GenomeAnalysisTK.jar -I m9.marked.bam -R ucsc.hg19.fasta -T IndelRealigner -targetIntervals m9.list -known dbsnp_137.hg19.vcf -o m9.marked.realigned.bam
3.2.1
java -Xmx4g -jar GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T ReduceReads -I m9.marked.realigned.bam -o m9.marked.realigned.reduce.bam
3.3
java -Djava.io.tmpdir=/tmp/flx-auswerter -Xmx4g -jar FixMateInformation.jar INPUT=m9.marked.realigned.reduce.bam OUTPUT=m9.marked.realigned.reduce.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
4 QUALITY SCORE RECALIBRATION
4.1
java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R ucsc.hg19.fasta -knownSites dbsnp_137.hg19.vcf -I m9.marked.realigned.reduce.fixed.bam -T BaseRecalibrator -maxCycle 1500 -cov ReadGroupCovariate -cov QualityScoreCovariate -o m9.recal_data.grp
4.2 ***********************************
java -Xmx4g -jar GenomeAnalysisTK.jar -T PrintReads -R ucsc.hg19.fasta -I m9.marked.realigned.reduce.fixed.bam -BQSR m9.recal_data.grp -o m9.marked.realigned.reduce.fixed.recal.bam
5 SNP CALLING
5.1
java -Xmx4g -jar GenomeAnalysisTK.jar -nct 4 --num_threads 4 -glm BOTH
-R ucsc.hg19.fasta
-T UnifiedGenotyper
--sample_ploidy 5
-I m9.marked.realigned.reduce.fixed.bam
-D dbsnp_137.hg19.vcf
-o m9.vcf
-stand_call_conf 20.0
-stand_emit_conf 20.0
-A DepthOfCoverage
-A AlleleBalance