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  • Error in IlluminaBasecallsToSam.jar

    Hi All,

    I run the following command

    Code:
    java -Xmx2g -Dsnappy.disable=true -jar /idi/sabeti-scratch/kandersen/bin/picard/IlluminaBasecallsToSam.jar BASECALLS_DIR=/broad/hptmp/andersen/130130.C1E4YACXX/Data/Intensities/BaseCalls/ LANE=5 READ_STRUCTURE=101T8B101T LIBRARY_PARAMS=/idi/sabeti-data/kandersen/analysis/130130_sarah_rerun/_logs/library_params.txt SEQUENCING_CENTER=Broad RUN_BARCODE=C1E4YACXX NUM_PROCESSORS=4 ADAPTERS_TO_CHECK=PAIRED_END MAX_READS_IN_RAM_PER_TILE=100000 MAX_RECORDS_IN_RAM=100000 FORCE_GC=false
    but I keep getting the following error:

    Code:
    [Wed Jan 30 16:07:56 EST 2013] net.sf.picard.illumina.IlluminaBasecallsToSam BASECALLS_DIR=/broad/hptmp/andersen/130130.C1E4YACXX/Data/Intensities/BaseCalls LANE=5 RUN_BARCODE=C1E4YACXX SEQUENCING_CENTER=Broad READ_STRUCTURE=101T8B101T LIBRARY_PARAMS=/idi/sabeti-data/kandersen/analysis/130130_sarah_rerun/_logs/library_params.txt ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM, PAIRED_END] NUM_PROCESSORS=4 FORCE_GC=false MAX_READS_IN_RAM_PER_TILE=100000 MAX_RECORDS_IN_RAM=100000    PLATFORM=illumina VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false
    [Wed Jan 30 16:07:56 EST 2013] Executing as [email protected] on Linux 2.6.18-194.8.1.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_35-b10; Picard version: 1.84(1332)
    INFO	2013-01-30 16:07:56	IlluminaBasecallsToSam	DONE_READING STRUCTURE IS 101T8B101T
    [Wed Jan 30 16:07:56 EST 2013] net.sf.picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes.
    Runtime.totalMemory()=125435904
    FAQ:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
    Exception in thread "main" java.lang.NullPointerException
    	at net.sf.samtools.util.StringUtil.join(StringUtil.java:54)
    	at net.sf.picard.illumina.IlluminaBasecallsToSam.populateWritersFromLibraryParams(IlluminaBasecallsToSam.java:962)
    	at net.sf.picard.illumina.IlluminaBasecallsToSam.initialize(IlluminaBasecallsToSam.java:839)
    	at net.sf.picard.illumina.IlluminaBasecallsToSam.doWork(IlluminaBasecallsToSam.java:754)
    	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    	at net.sf.picard.illumina.IlluminaBasecallsToSam.main(IlluminaBasecallsToSam.java:1038)
    I have tried different versions of the program, with and without 'snappy' and checked that all the required files are there (e.g. library_params.txt) and point to the correct directories, etc. Everything appears to be correct.

    Before this command I extract barcodes using:

    Code:
    java -Xmx2g -jar /seq/software/picard/1.465/bin/ExtractIlluminaBarcodes.jar BASECALLS_DIR=/broad/hptmp/andersen/130130.C1E4YACXX/Data/Intensities/BaseCalls/ LANE=5 READ_STRUCTURE=101T8B101T BARCODE_FILE=/idi/sabeti-data/kandersen/analysis/130130_sarah_rerun/_logs/barcodeData.5 METRICS_FILE=/idi/sabeti-data/kandersen/analysis/130130_sarah_rerun/_logs/barcode.metrics.txt MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=25 NUM_PROCESSORS=1
    which completes and generates bar-code files correctly (as far as I can tell).

    Any ideas what is going on here?

    Thanks

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