Hi, I don't understand why this is not working.
Thanks : Command : /Library/Java/JavaVirtualMachines/jdk1.7.0_79.jdk/Contents/Home/bin/java -jar -Xmx8g ./software/picard-tools/1.131/picard.jar SortVcf INPUT=./refData/dbSNP/138/dbsnp_138.hg19.vcf SEQUENCE_DICTIONARY=./refData/genome/hg19/hg19.dict OUTPUT=./refData/dbSNP/138/dbsnp_138_2.hg19.vcf Ouput : [Wed May 27 15:37:10 CEST 2015] picard.vcf.SortVcf INPUT=[./refData/dbSNP/138/dbsnp_138.hg19.vcf] OUTPUT=./refData/dbSNP/138/dbsnp_138_2.hg19.vcf SEQUENCE_DICTIONARY=./refData/genome/hg19/hg19.dict VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Wed May 27 15:37:10 CEST 2015] Executing as [email protected] on Mac OS X 10.7.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15; Picard version: 1.131(cd60f90fdca902499c70a4472b6162ef37f919ce_1431022382) JdkDeflater [Wed May 27 15:37:10 CEST 2015] picard.vcf.SortVcf done. Elapsed time: 0,00 minutes. Runtime.totalMemory()=128974848 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.IllegalArgumentException: java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected. at picard.vcf.SortVcf.collectFileReadersAndHeaders(SortVcf.java:112) at picard.vcf.SortVcf.doWork(SortVcf.java:81) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) Caused by: java.lang.AssertionError: SAM dictionaries are not the same: SAMSequenceRecord(name=chrM,length=16571,dict_index=0,assembly=hg19) was found when SAMSequenceRecord(name=chr1,length=249250621,dict_index=0,assembly=null) was expected. at htsjdk.samtools.SAMSequenceDictionary.assertSameDictionary(SAMSequenceDictionary.java:145) at picard.vcf.SortVcf.collectFileReadersAndHeaders(SortVcf.java:110) ... 4 more -- *Jean-Philippe Villemin *- Bioinformatics, Software Engineer - Centre Léon Bérard, Cheney C 28 rue Laennec, 69373 Lyon cedex 08, France +33 4 26 55 68 28 JeanPhilippe.VILLEMIN@ <[email protected]>lyon.unicancer.fr <[email protected]>
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