Hi Kristian,
Your read_structure parameter tells ExtractIlluminaBarcodes to do exactly what
you’re suspecting. 101T8B101T states that there is only one barcode read.
Perhaps it should be 101T8B8B101T?
-t
On Jun 15, 2014, at 6:31 PM, Kristian Andersen <kga1...@gmail.com> wrote:
> Hi All,
>
> I have run into the following problem that I was hoping somebody could help
> me with.
>
> I have been trying to demultiplex some Illumina (101bp PE, dual barcoded)
> libraries using Picard - e.g.:
>
> java -Xmx2g -jar /seq/software/picard/1.626/bin/ExtractIlluminaBarcodes.jar
> BASECALLS_DIR=/analysis/140615/_temp/140615.H9FT9ADXX/Data/Intensities/BaseCalls/
> LANE=2 READ_STRUCTURE=101T8B101T BARCODE_FILE=/analysis/140615/barcodeData.2
> METRICS_FILE=/analysis/140615/_logs/barcode.metrics.H9FT9ADXX.2.txt
> MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=25 NUM_PROCESSORS=1
>
> I have done this a million times before, but with these new libraries I keep
> getting the following error messages:
>
> Barcode AGGCAGAA specified more than once in /analysis/140615/barcodeData.2
> Barcode CAGAGAGG specified more than once in /analysis/140615/barcodeData.2
> Barcode CAGAGAGG specified more than once in /analysis/140615/barcodeData.2
> .
> .
> .
>
> I have never seen this happen before and I have tried everything (I can think
> of...) to fix the problem. Basically it appears as if Picard isn’t accepting
> the dual barcodes and just treats them individually - which is strange, since
> I have demultiplexed many runs that were dual barcoded. If I just to try to
> demultiplex samples where both barcodes are different, then everything goes
> through.
>
> My barcode data files look like this:
> barcode_name library_name barcode_sequence_1 barcode_sequence_2
> H9FT9ADXX-EM-096_NuGEN EM-096_NuGEN AGGCAGAA TATCCTCT
> H9FT9ADXX-EM-098_NuGEN EM-098_NuGEN AGGCAGAA AGAGTAGA
> H9FT9ADXX-EM-095B_NuGEN EM-095B_NuGEN CAGAGAGG TAGATCGC
> H9FT9ADXX-G3691-1_NuGEN G3691-1_NuGEN CAGAGAGG CTCTCTAT
> H9FT9ADXX-K562B_NuGEN K562B_NuGEN CAGAGAGG CTAAGCCT
> H9FT9ADXX-EM-095_NuGEN EM-095_NuGEN CTCTCTAC CTAAGCCT
> H9FT9ADXX-G3670-1_NuGEN G3670-1_NuGEN CTCTCTAC TAGATCGC
> H9FT9ADXX-G3679-1_NuGEN G3679-1_NuGEN CTCTCTAC TATCCTCT
> H9FT9ADXX-G3680-1_NuGEN G3680-1_NuGEN CTCTCTAC AGAGTAGA
> H9FT9ADXX-G3681-1_NuGEN G3681-1_NuGEN CTCTCTAC GTAAGGAG
> H9FT9ADXX-G3682-1_NuGEN G3682-1_NuGEN CTCTCTAC ACTGCATA
> H9FT9ADXX-G3683-1_NuGEN G3683-1_NuGEN CTCTCTAC AAGGAGTA
> H9FT9ADXX-G3686-1_NuGEN G3686-1_NuGEN GGACTCCT ACTGCATA
> H9FT9ADXX-G3676-1_NuGEN G3676-1_NuGEN TAGGCATG AAGGAGTA
> H9FT9ADXX-G3676-2_NuGEN G3676-2_NuGEN TAGGCATG CTAAGCCT
> H9FT9ADXX-G3677-1_NuGEN G3677-1_NuGEN TAGGCATG GTAAGGAG
> H9FT9ADXX-G3677-2_NuGEN G3677-2_NuGEN TAGGCATG ACTGCATA
> H9FT9ADXX-G3687-1_NuGEN G3687-1_NuGEN TAGGCATG TAGATCGC
>
> Any idea how to fix this? It's driving me potty.
>
> Thanks very much in advance,
> Kristian
>
>
>
>
>
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HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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