Hi Stathis,
Could you try running CheckIlluminaDirectory on one of the basecalling dirs
and send us the output? It looks like it can't find any .locs or analogous
files.
-Matt
On Wed, Dec 3, 2014 at 10:58 AM, Kanterakis, Efstathios <
ekantera...@illumina.com> wrote:
> Hello,
>
> I’m running the following command from picard-tools-1.125 (jre1.7.0):
>
> java -Xmx2g -jar picard.jar CollectHiSeqXPfFailMetrics
> BASECALLS_DIR=Data/Intensities/BaseCalls LANE=1 OUTPUT=out.txt
> VALIDATION_STRINGENCY=LENIENT
>
>
>
> and get:
>
> Exception in thread "main" picard.PicardException: Could not find a format
> with available files for the following data types: Position
>
> at
> picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:172)
>
> at
> picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:127)
>
> at
> picard.illumina.quality.CollectHiSeqXPfFailMetrics.doWork(CollectHiSeqXPfFailMetrics.java:127)
>
> at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
>
> at
> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
>
> at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
>
>
>
> I’ve tried it on a number of HiSeqX runs (2x36, 2x151, 2x151 indexed) and
> they all failed.
>
>
>
> Any ideas?
>
>
>
> Thank you,
>
> Stathis
>
>
>
>
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