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  • #1

    ReorderSam.jar in picard and GATK

    Dear community members,

    I have tried to reorder several exome-sequencing bam files with "ReorderSam.jar," which is in the most recent version of picard, on Hg18 reference sequence. A weird thing is that some of the bam files were "successfully" reordered with the "ReorderSam.jar", while this tool also fails to reorder other bam files.

    A main error message that I have is:
    ------------------------------------------------------------
    [Mon Dec 12 10:06:02 CST 2011] net.sf.picard.sam.ReorderSam done. Elapsed time: 0.27 minutes.
    Runtime.totalMemory()=2274099200
    Exception in thread "main" java.lang.IllegalArgumentException: Reference index 1701670503 not found in sequence dictionary.
    at net.sf.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:353)
    at net.sf.samtools.BAMRecord.<init>(BAMRecord.java:82)
    at net.sf.samtools.DefaultSAMRecordFactory.createBAMRecord(DefaultSAMRecordFactory.java:30)
    at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:189)
    at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:514)
    at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:621)
    at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:488)
    at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:604)
    at net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:554)
    at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:315)
    at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:356)
    at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:110)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:176)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
    at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
    Caused by: java.lang.NullPointerException
    at net.sf.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:351)
    ------------------------------------------------------------

    I really appreciate it if some one help me understand why this tool makes these errors and how to avoid them.

    For your information, the full logs I received after running the ReorderSam are the following:
    ------------------------------------------------------------
    [Mon Dec 12 10:05:46 CST 2011] net.sf.picard.sam.ReorderSam INPUT=/home/Input.bam OUTPUT=/home/out.bam REFERENCE=/home/GATK_Resources/Homo_sapiens_assembly18.fasta CREATE_INDEX=true ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VER BOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
    [Mon Dec 12 10:05:46 CST 2011] Executing as hkim6@cnode71 on Linux 2.6.18-194.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_23-b05; Picard vers ion: 1.57
    INFO 2011-12-12 10:05:46 ReorderSam SAM/BAM file
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrM16571
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1247249719
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2242951149
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr3199501827
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr4191273063
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr5180857866
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr6170899992
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr7158821424
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr8146274826
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr9140273252
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr10135374737
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr11134452384
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr12132349534
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr13114142980
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr14106368585
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr15100338915
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1688827254
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1778774742
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1876117153
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1963811651
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2062435964
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2146944323
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2249691432
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrX154913754
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrY57772954
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1_random1663265
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2_random185571
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr3_random749256
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr4_random842648
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr5_random143687
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr6_random1875562
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr7_random549659
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr8_random943810
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr9_random1146434
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr10_random113275
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr11_random215294
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr13_random186858
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr15_random784346
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr16_random105485
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr17_random2617613
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr18_random4262
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr19_random301858
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr21_random1679693
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr22_random257318
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrX_random1719168
    INFO 2011-12-12 10:05:46 ReorderSam Reference
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrM16571
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1247249719
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2242951149
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr3199501827
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr4191273063
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr5180857866
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr6170899992
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr7158821424
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr8146274826
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr9140273252
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr10135374737
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr11134452384
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr12132349534
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr13114142980
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr14106368585
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr15100338915
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1688827254
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1778774742
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1876117153
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1963811651
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2062435964
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2146944323
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2249691432
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrX154913754
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrY57772954
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr1_random1663265
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr2_random185571
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr3_random749256
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr4_random842648
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr5_random143687
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr6_random1875562
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr7_random549659
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr8_random943810
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr9_random1146434
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr10_random113275
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr11_random215294
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr13_random186858
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr15_random784346
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr16_random105485
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr17_random2617613
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr18_random4262
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr19_random301858
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr21_random1679693
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchr22_random257318
    INFO 2011-12-12 10:05:46 ReorderSam SN=%s LN=%d%nchrX_random1719168
    INFO 2011-12-12 10:05:46 ReorderSam Reordering SAM/BAM file:
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chrM [index=0] to => ref contig chrM [index=0]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr1 [index=1] to => ref contig chr1 [index=1]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr2 [index=2] to => ref contig chr2 [index=2]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr3 [index=3] to => ref contig chr3 [index=3]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr4 [index=4] to => ref contig chr4 [index=4]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr5 [index=5] to => ref contig chr5 [index=5]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr6 [index=6] to => ref contig chr6 [index=6]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr7 [index=7] to => ref contig chr7 [index=7]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr8 [index=8] to => ref contig chr8 [index=8]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr9 [index=9] to => ref contig chr9 [index=9]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr10 [index=10] to => ref contig chr10 [index=10]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr11 [index=11] to => ref contig chr11 [index=11]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr12 [index=12] to => ref contig chr12 [index=12]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr13 [index=13] to => ref contig chr13 [index=13]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr14 [index=14] to => ref contig chr14 [index=14]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr15 [index=15] to => ref contig chr15 [index=15]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr16 [index=16] to => ref contig chr16 [index=16]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr17 [index=17] to => ref contig chr17 [index=17]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr18 [index=18] to => ref contig chr18 [index=18]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr19 [index=19] to => ref contig chr19 [index=19]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr20 [index=20] to => ref contig chr20 [index=20]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr21 [index=21] to => ref contig chr21 [index=21]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr22 [index=22] to => ref contig chr22 [index=22]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chrX [index=23] to => ref contig chrX [index=23]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chrY [index=24] to => ref contig chrY [index=24]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr1_random [index=25] to => ref contig chr1_random [index=25]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr2_random [index=26] to => ref contig chr2_random [index=26]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr3_random [index=27] to => ref contig chr3_random [index=27]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr4_random [index=28] to => ref contig chr4_random [index=28]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr5_random [index=29] to => ref contig chr5_random [index=29]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr6_random [index=30] to => ref contig chr6_random [index=30]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr7_random [index=31] to => ref contig chr7_random [index=31]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr8_random [index=32] to => ref contig chr8_random [index=32]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr9_random [index=33] to => ref contig chr9_random [index=33]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr10_random [index=34] to => ref contig chr10_random [index=34]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr11_random [index=35] to => ref contig chr11_random [index=35]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr13_random [index=36] to => ref contig chr13_random [index=36]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr15_random [index=37] to => ref contig chr15_random [index=37]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr16_random [index=38] to => ref contig chr16_random [index=38]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr17_random [index=39] to => ref contig chr17_random [index=39]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr18_random [index=40] to => ref contig chr18_random [index=40]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr19_random [index=41] to => ref contig chr19_random [index=41]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr21_random [index=42] to => ref contig chr21_random [index=42]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chr22_random [index=43] to => ref contig chr22_random [index=43]
    INFO 2011-12-12 10:05:46 ReorderSam Reordering read contig chrX_random [index=44] to => ref contig chrX_random [index=44]
    INFO 2011-12-12 10:05:46 ReorderSam Writing reads...
    [Mon Dec 12 10:06:02 CST 2011] net.sf.picard.sam.ReorderSam done. Elapsed time: 0.27 minutes.
    Runtime.totalMemory()=2274099200
    Exception in thread "main" java.lang.IllegalArgumentException: Reference index 1701670503 not found in sequence dictionary.
    at net.sf.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:353)
    at net.sf.samtools.BAMRecord.<init>(BAMRecord.java:82)
    at net.sf.samtools.DefaultSAMRecordFactory.createBAMRecord(DefaultSAMRecordFactory.java:30)
    at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:189)
    at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:514)
    at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:621)
    at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:488)
    at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:604)
    at net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:554)
    at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:315)
    at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:356)
    at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:110)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:176)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
    at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
    Caused by: java.lang.NullPointerException
    at net.sf.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:351)
    Tags: None
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