Hi guys, I think I am missing something with this process (obviously...):
Using latest version of Picard Tools.
Reads are Illumina 100bp single end.
Pre-processing includes de-multiplexing, FastQC and Trimmomatic
I have the uBAMs with read groups added, verified no errors, sorted by query name.
I have the aligned BAMs from BWA-MEM verified with only error "no read groups", sorted by query name.
The header of the uBAM has only the @HD and @RG tags.
The header of the BAM has @HD, multiple @SQ, and @PG tags. No @RG.
I have tried about a dozen times to make this fly but the program ALWAYS throws an ArrayIndexOutOfBoundsException.
Here is the error file from one example:
[Tue May 23 13:41:22 NZST 2017] picard.sam.MergeBamAlignment UNMAPPED_BAM=/project1_APEK1/021.MIA/sorted/C_F1_1.bam ALIGNED_BAM=[/project1_APEK1/022.BWA/sorted/C_F1_1.bam] OUTPUT=/project1_APEK1/022.BWA/MBA/C_F1_1.bam REFERENCE_SEQUENCE=/genome/Peaxi162/Petunia_3000.fasta CLIP_ADAPTERS=false MAX_INSERTIONS_OR_DELETIONS=-1 ATTRIBUTES_TO_RETAIN=[XS] SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true TMP_DIR=[/project1_APEK1/tmp] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=5000000 CREATE_INDEX=true PAIRED_RUN=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue May 23 13:41:22 NZST 2017] Executing as ccd@myserver.com on Linux 3.10.0-514.16.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b11; Picard version: 2.9.2-SNAPSHOT
INFO 2017-05-23 13:41:22 SamAlignmentMerger Processing SAM file(s): [/project1_APEK1/022.BWA/sorted/C_F1_1.bam]
INFO 2017-05-23 13:41:39 AbstractAlignmentMerger Merged 1,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 16s. Last read position: Peaxi162Scf00133:585,031
INFO 2017-05-23 13:42:01 AbstractAlignmentMerger Merged 2,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 21s. Last read position: Peaxi162Scf00376:259,458
INFO 2017-05-23 13:42:14 AbstractAlignmentMerger Merged 3,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 13s. Last read position: Peaxi162Scf00566:712,679
[Tue May 23 13:42:27 NZST 2017] picard.sam.MergeBamAlignment done. Elapsed time: 1.10 minutes.
Runtime.totalMemory()=3898081280
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 96
at htsjdk.samtools.util.SequenceUtil.calculateMdAndNmTags(SequenceUtil.java:910)
at picard.sam.AbstractAlignmentMerger.fixNmMdAndUq(AbstractAlignmentMerger.java:558)
at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:533)
at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:181)
at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:282)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
I would be grateful if you could point me in the right direction to get this going.
Thanks! :-)