Hey Matthew,
as a short-term fix, could you try re-running with a similarly old release
of Picard?
N
On Fri, Oct 17, 2014 at 12:46 PM, Ducar, Matthew D. <
matthewd_du...@dfci.harvard.edu> wrote:
> 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
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
> ------------------------------------------------------------------------------
> Comprehensive Server Monitoring with Site24x7.
> Monitor 10 servers for $9/Month.
> Get alerted through email, SMS, voice calls or mobile push notifications.
> Take corrective actions from your mobile device.
> http://p.sf.net/sfu/Zoho
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
