[Samtools-help] Cannot add sequence that already exists in SAMSequenceDictionary

[Banh, P. (PHO) <Phi...@oa...>]

Hi there,

I currently have a problem whenever I'm running my BAM file with any of the tools. I tried using ValidateSam and the same problem comes up, below is the error message I've received multiple times.

Here are some of the commands I've used:

java -jar -Xmx2g ValidateSamFile.jar MODE=SUMMARY INPUT=~.bam OUTPUT=~_2.bam

java -jar -Xmx2g SamToFastq.jar INCLUDE_NON_PF_READS=True VALIDATION_STRINGENCY=SILENT INPUT=$current_dir/unmapped6.bam FASTQ=$current_dir/~.1.fq SECOND_END_FASTQ=~.2.fq

I get some the same error message when trying to run either of these .jar files. I've also tried it with the 'CleanSam.jar' and I still recieve the same error message. I've checked the header and printed it out, I know the '~_genome' is duplicated so I assume that is causing the problem. However, how do I removed it or change it so it fixes the problem? I've done this SAM to FASTQ conversion a few times already and never had a problem. I am assuming this reference genome I was using could be causing a problem? Any ideas will be helpful...

Thanks,
Philip


[Thu Oct 17 15:59:19 EDT 2013] net.sf.picard.sam.ValidateSamFile INPUT= ~.bam OUTPUT=~_2.bam MODE=SUMMARY    MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Oct 17 15:59:19 EDT 2013] Executing as pbanh@pho-cnpl-02 on Linux 2.6.32-279.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: 1.100(1571)
[Thu Oct 17 15:59:19 EDT 2013] net.sf.picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=759758848
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary:
~_genome
    at net.sf.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:62)
    at net.sf.samtools.SAMSequenceDictionary.<init>(SAMSequenceDictionary.java:40)
    at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:110)
    at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:428)
    at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:158)
    at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:117)
    at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:560)
    at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:180)
    at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:135)
    at net.sf.picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:131)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    at net.sf.picard.sam.ValidateSamFile.main(ValidateSamFile.java:100)

***
CentOS - java version "1.6.0_24"
Picard Tools 1.100