Cannot use Picard MergeBamAlignment on International Genomes Project alignments

Question

[godth13teen]

Hi, I used samtools to save just the intervals of international genomes project alignments (both mapped and unmapped bam file), then I used Picard MergeBamAlignment to merge them, but I got this error

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, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605, hs37d5] and [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249].
        at htsjdk.samtools.SAMSequenceDictionary.mergeDictionaries(SAMSequenceDictionary.java:322)
        at picard.sam.SamAlignmentMerger.getDictionaryForMergedBam(SamAlignmentMerger.java:197)
        at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:370)
        at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:186)
        at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:358)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

this is my command:

MergeBamAlignment -ALIGNED aln/HG02142.mapped.ILLUMINA.bwa.KHV.low_coverage.20130415.bam -UNMAPPED aln/HG02142.unmapped.ILLUMINA.bwa.KHV.low_coverage.20130415.bam -O HG02142/preprocessing/HG02142_hg38_merged.bam -R /ref38/hg19.fasta -TMP_DIR tmp

it seems like there are mismatch between two files, but I'm pretty sure that I got it from internationa genome project ftp. The command I used to get these files:

samtools view -h [URL] -L gene_padding.bed -M -o ${URLl##*/}

Any help and advice is warmly welcome

Edit 1: I have tried this again with full bam file, the error from Picard still persists

[Pierre Lindenbaum]

are you using the very same REFERence fasta sequence wth the -R param ?

PS:

/ref38/hg19.fasta

looks very wrong to me . It looks like you put the hg19.fa (GHRCh37) into the hg38 folder (GHRCh38)

[Pierre Lindenbaum]

I reopened this post. Why did you close it ?

[ATpoint]

See follow-up: Picard - MergeBamAlignment: Reads remaining on alignment iterator