Hello,
I wonder if you can help with the following. I am trying to mark duplicates in a cram file with the following command (picard latest):
'picard-tools MarkDuplicates I=09_1#21.cram O=09_1#21_md.cram M=09_1#21_md.txt'
I keep getting the following errors:
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download
at htsjdk.samtools.cram.ref.ReferenceSource.getDefaultCRAMReferenceSource(ReferenceSource.java:107)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:301)
at picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.openInputs(AbstractMarkDuplicatesCommandLineProgram.java:212)
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:421)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:220)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105
I have also tried with the fasta reference R=in.fasta but nothing..
There is a similar post asking the same question but it doesn't seem to have been solved.
Many thanks in advance,
Carmen