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Picard ExtractIlluminaBarcodes return NullPointerException error

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4 comments

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    Bhanu Gandham

    Please post the exact commands you used and the entire error log.

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    Martin Szyska

    Hi same here, 

    I got exactly the same output with version 2.22.3.

    As there is no verbosity in this error message, any help would be appreciated!

     

    Thanks,

    Martin

     

     

    Exception in thread "main" java.lang.NullPointerException

    at picard.illumina.parser.IlluminaFileUtil.<init>(IlluminaFileUtil.java:82)

    at picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:174)

    at picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:138)

    at picard.illumina.ExtractIlluminaBarcodes.customCommandLineValidation(ExtractIlluminaBarcodes.java:474)

    at picard.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:363)

    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:223)

    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)

    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

    The command I used was:

    picard ExtractIlluminaBarcodes BASECALLS_DIR=Data BARCODE_FILE=run2_barcodes.csv LANE=1 READ_STRUCTURE=151T8B9M8B151T OUTPUT_DIR=../../NGSData/Twist2picard METRICS_FILE=../../NGSData/Twist2picard/barcode_metrics
     
    My barcode file looks like this (all tab-separated):
    barcode_name library_name barcode_sequence_1 barcode_sequence_2
    JAZE5 Twist_IDT CCGCGGTTNNNNNNNNN AGCGCTAG
    JAZE3 Twist_IDT TTATAACCNNNNNNNNN GATATCGA
    JAZE1 Twist_IDT GGACTTGGNNNNNNNNN CGCAGACG
    JAZE13 Twist_IDT AAGTCCAANNNNNNNNN TATGAGTA
    HG Twist_IDT ATCCACTGNNNNNNNNN AGGTGCGT
    JA Twist_IDT GCTTGTCANNNNNNNNN GAACATAC
    BH Twist_IDT CAAGCTAGNNNNNNNNN ACATAGCG
    OH Twist_IDT TGGATCGANNNNNNNNN GTGCGATA
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    Martin Szyska

    In my case, I solved the issue by providing a BASECALLS_DIR deeper within the folder structure. In my case changing the top raw data folder to <myfolder>/Data/Intensities/BaseCalls did the trick. 

    Hope that helps!

     

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    Bhanu Gandham

    Thank you for sharing your workaround Martin Szyska

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