Hello there!
I am trying to use picard tools to mark duplicates using a cram format file; however I could not find any documentation to address this problem. How can I pass a valid CRAM reference?
Thanks in advance,
-lili
Sat Feb 06 16:09:42 CST 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=250 INPUT=[/EXOME/gatk/test_10990_bwa_srtd.cram] OUTPUT=EXOME/gatk/test_10990_wes_dupMC.cram METRICS_FILE=/EXOME/gatk/test_10990_wes_dupMC_metrics.txt OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 CREATE_INDEX=true SKIP_PAIRS_WITH_NO_MATE_CIGAR=true BLOCK_SIZE=100000 REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Sat Feb 06 16:09:42 CST 2016] Executing as antunes@gpu10 on Linux 2.6.32-431.29.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b26; Picard version: 2.1.0(25ebc07f7fbaa7c1a4a8e6c130c88c1d10681802_1454776546) IntelDeflater
[Sat Feb 06 16:09:42 CST 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=4116185088
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:98)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:269)
at picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.openInputs(AbstractMarkDuplicatesCommandLineProgram.java:205)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigar.doWork(MarkDuplicatesWithMateCigar.java:118)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)