Picard ExtractIlluminaBarcodes return NullPointerException error
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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Please post the exact commands you used and the entire error log.
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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_metricsMy barcode file looks like this (all tab-separated):barcode_name library_name barcode_sequence_1 barcode_sequence_2JAZE5 Twist_IDT CCGCGGTTNNNNNNNNN AGCGCTAGJAZE3 Twist_IDT TTATAACCNNNNNNNNN GATATCGAJAZE1 Twist_IDT GGACTTGGNNNNNNNNN CGCAGACGJAZE13 Twist_IDT AAGTCCAANNNNNNNNN TATGAGTAHG Twist_IDT ATCCACTGNNNNNNNNN AGGTGCGTJA Twist_IDT GCTTGTCANNNNNNNNN GAACATACBH Twist_IDT CAAGCTAGNNNNNNNNN ACATAGCGOH Twist_IDT TGGATCGANNNNNNNNN GTGCGATA -
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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Thank you for sharing your workaround Martin Szyska
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