MergeBamAlignment Failure

concon PennsylvaniaMember

Hello,

I'm trying to use Picard 2.9.0-1-gf5b9f50-SNAPSHOT's MergeBamAlignment, but get this error:

this command: java -jar ../picard.jar MergeBamAlignment UNMAPPED_BAM=./unaligned_mc_tagged_polyA_filtered.bam ALIGNED_BAM=./aligned.sorted.bam OUTPUT=./merged.bam REFERENCE_SEQUENCE=/home/con/Alex/mm10/mm10.fasta PAIRED_RUN=false INCLUDE_SECONDARY_ALIGNMENTS=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true 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

gives this error:

[Tue Mar 07 09:51:11 EST 2017] picard.sam.MergeBamAlignment UNMAPPED_BAM=./unaligned_mc_tagged_polyA_filtered.bam ALIGNED_BAM=[./aligned.sorted.bam] OUTPUT=./merged.bam REFERENCE_SEQUENCE=/home/con/Alex/mm10/mm10.fasta PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 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=false ADD_MATE_CIGAR=true 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 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE
[Tue Mar 07 09:51:11 EST 2017] Executing as [email protected] on Linux 4.4.0-65-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_121-8u121-b13-0ubuntu1.16.04.2-b13; Picard version: 2.9.0-1-gf5b9f50-SNAPSHOT
INFO 2017-03-07 09:51:11 SamAlignmentMerger Processing SAM file(s): [./aligned.sorted.bam]
[Tue Mar 07 09:51:11 EST 2017] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=124780544
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: Do not use this function to merge dictionaries with different sequences in them. Sequences must be in the same order as well. Found [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 3, 4, 5, 6, 7, 8, 9, CHR_MG117_PATCH, CHR_MG132_PATCH, CHR_MG153_PATCH, CHR_MG184_PATCH, CHR_MG3231_PATCH, CHR_MG3561_PATCH, CHR_MG3562_PATCH, CHR_MG3609_PATCH, CHR_MG3829_PATCH, CHR_MG3833_PATCH, CHR_MG3835_PATCH, CHR_MG4136_PATCH, CHR_MG4151_PATCH, CHR_MG4180_PATCH, CHR_MG4209_PATCH, CHR_MG4211_PATCH, CHR_MG4212_PATCH, CHR_MG4213_PATCH, CHR_MG4214_PATCH, CHR_MG4222_MG3908_PATCH, CHR_MG4248_PATCH, CHR_MG4249_PATCH, CHR_MG4254_PATCH, CHR_MG4255_PATCH, CHR_MG4259_PATCH, CHR_MG4261_PATCH, CHR_MG4264_PATCH, CHR_MG4265_PATCH, CHR_MG4266_PATCH, CHR_MMCHR1_CHORI29_IDD5_1, MT, X, Y, JH584299.1, GL456233.1, JH584301.1, GL456211.1, GL456350.1, JH584293.1, GL456221.1, JH584297.1, JH584296.1, GL456354.1, JH584294.1, JH584298.1, JH584300.1, GL456219.1, GL456210.1, JH584303.1, JH584302.1, GL456212.1, JH584304.1, GL456379.1, GL456216.1, GL456393.1, GL456366.1, GL456367.1, GL456239.1, GL456213.1, GL456383.1, GL456385.1, GL456360.1, GL456378.1, GL456389.1, GL456372.1, GL456370.1, GL456381.1, GL456387.1, GL456390.1, GL456394.1, GL456392.1, GL456382.1, GL456359.1, GL456396.1, GL456368.1, JH584292.1, JH584295.1] and [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1, 1_GL456210_random, 1_GL456211_random, 1_GL456212_random, 1_GL456213_random, 1_GL456221_random, 2, 3, 4, 4_GL456216_random, 4_GL456350_random, 4_JH584292_random, 4_JH584293_random, 4_JH584294_random, 4_JH584295_random, 5, 5_GL456354_random, 5_JH584296_random, 5_JH584297_random, 5_JH584298_random, 5_JH584299_random, 6, 7, 7_GL456219_random, 8, 9, MT, Un_GL456239, Un_GL456359, Un_GL456360, Un_GL456366, Un_GL456367, Un_GL456368, Un_GL456370, Un_GL456372, Un_GL456378, Un_GL456379, Un_GL456381, Un_GL456382, Un_GL456383, Un_GL456385, Un_GL456387, Un_GL456389, Un_GL456390, Un_GL456392, Un_GL456393, Un_GL456394, Un_GL456396, Un_JH584304, X, X_GL456233_random, Y, Y_JH584300_random, Y_JH584301_random, Y_JH584302_random, Y_JH584303_random].
at htsjdk.samtools.SAMSequenceDictionary.mergeDictionaries(SAMSequenceDictionary.java:305)
at picard.sam.SamAlignmentMerger.getDictionaryForMergedBam(SamAlignmentMerger.java:197)
at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:346)
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)

How can I merge the alignments?

Answers

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