Hi,
I'm having to dig back through our archives and reprocess several older runs
back through our pipeline. Everything was going well until I tried one of our
oldest runs from April 2011. For this run, ExtractIlluminaBarcodes gave me the
following error:
Exception in thread "main" net.sf.picard.PicardException: Could not find a
format with available files for the following data types: PF
at
net.sf.picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:139)
at
net.sf.picard.illumina.ExtractIlluminaBarcodes.customCommandLineValidation(ExtractIlluminaBarcodes.java:301)
at
net.sf.picard.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:236)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:123)
at
net.sf.picard.illumina.ExtractIlluminaBarcodes.main(ExtractIlluminaBarcodes.java:327)
Although our pipeline does not have the latest Picard version (1.122), I did
download the latest version and ran CheckIlluminaDirectory and received the
same error message.
I suspect that it has something to do with changing versions of Illumina's RTA
software (this run uses version 1.7.48) because the next run used a newer RTA
version and put the .filter files in a different location. They are also in a
different format because copying the existing .format files to the now-expected
location & Picard complained about the format being wrong.
Is there any way to processes these older format run directories through Picard?
-Matt
--
Matthew Ducar
Group Leader Clinical Bioinformatics
Center for Cancer Genome Discovery (CCGD)
Dana Farber Cancer Institute, Dana 840B
44 Binney St. Boston, MA 02115
Tel: 617 582-9704
Mailing address:
Dana Farber Cancer Institute
450 Brookline Ave, Boston, MA 02215
matthewd_du...@dfci.harvard.edu
www.cancergenomediscovery.com
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