Error in MergeBamAlignment

rafayrafay PakistanMember
sudo java -jar ../picard/build/libs/picard.jar MergeBamAlignment ALIGNED= IonXpress_001.bam UNMAPPED=IonXpress_001_rawlib.basecaller.bam O=IonXpressMerge_alignments.bam R=../reference/hg19/hg19.fasta

22:13:45.558 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/rafay/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Apr 17 22:13:58 PKT 2018] MergeBamAlignment UNMAPPED_BAM=IonXpress_001_rawlib.basecaller.bam ALIGNED_BAM=[IonXpress_001.bam] OUTPUT=IonXpressMerge_alignments.bam REFERENCE_SEQUENCE=../reference/hg19/hg19.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Tue Apr 17 22:13:58 PKT 2018] Executing as [email protected] on Linux 4.13.0-37-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_151-8u151-b12-0ubuntu0.17.10.2-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 2.17.11-5-geed3ea5-SNAPSHOT
INFO 2018-04-17 22:13:58 SamAlignmentMerger Processing SAM file(s): [IonXpress_001.bam]
[Tue Apr 17 22:13:59 PKT 2018] picard.sam.MergeBamAlignment done. Elapsed time: 0.23 minutes.
Runtime.totalMemory()=32440320
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///home/rafay/gatkTest/../reference/hg19/hg19.fasta
at htsjdk.variant.utils.SAMSequenceDictionaryExtractor$TYPE$1.extractDictionary(SAMSequenceDictionaryExtractor.java:55)
at htsjdk.variant.utils.SAMSequenceDictionaryExtractor.extractDictionary(SAMSequenceDictionaryExtractor.java:149)
at picard.sam.SamAlignmentMerger.getDictionaryForMergedBam(SamAlignmentMerger.java:192)
at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:363)
at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:181)
at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:356)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

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