Picard ExtractIlluminaBarcodes return NullPointerException error

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Jing Lin

• March 20, 2020 21:52

Hi,

I am trying to use Picard 2.22.1 for demultiplexing dual-index Illumina sequencing data.

I was playing with the "ExtractIlluminaBarcodes" function, and got the following error message:

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)

 

Any advice is appreciated!

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• 

  Bhanu Gandham

  • March 21, 2020 05:34

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

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  Martin Szyska

  • April 14, 2020 05:57

  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

  • April 14, 2020 06:06

  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

  • April 15, 2020 16:44

  Thank you for sharing your workaround Martin Szyska

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