I'm trying to validate a set of cram files, however, I'm getting the error shown below. I'm not sure if it is because I'm using a CRAM file, I have problems with the htsjdk library or the cram files are corrupted
[Tue Jul 05 16:49:12 BST 2016] picard.sam.ValidateSamFile INPUT=19743.cramFiles/19743_1.1.cram MODE=SUMMARY MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Jul 05 16:49:12 BST 2016] Executing as jga on Linux 3.2.0-75-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_74-b02; Picard version: 2.4.1(7c4d36e011df1aec4689b51efcada44e92d1817f_1464389670) JdkDeflater
[Tue Jul 05 16:49:13 BST 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=759693312
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.cram.CRAMException: Contig chr1 not found in the reference file.
at htsjdk.samtools.CRAMIterator.nextContainer(CRAMIterator.java:171)
at htsjdk.samtools.CRAMIterator.hasNext(CRAMIterator.java:257)
at htsjdk.samtools.SamReader$AssertingIterator.hasNext(SamReader.java:568)
at htsjdk.samtools.SamFileValidator.validateSamRecordsAndQualityFormat(SamFileValidator.java:268)
at htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:200)
at htsjdk.samtools.SamFileValidator.validateSamFileSummary(SamFileValidator.java:128)
at picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:187)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Any help will be much appreciated.
Thanks!