[svtoolkit-help] An recalibration problem

[sunchangyue <cha...@ho...>]

Hi,Why do I still get this erro even though all reads have RG tag in sam.
##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/share/data/staff/sunchy/BFC2011010/HL040/GATK/test_HL040_1_pair_NM2_header.sorted.rmdup.bam} is malformed: The input .bam file contains reads with no read group. First observed at read with name = HWI-ST298:171:81MJKABXX:6:1101:11277:2454 Users must set both the default read group using the --default_read_group <String> argument and the default platform using the --default_platform <String> argument.
and here is the  sam:@SQ     SN:1    LN:249250621@SQ     SN:2    LN:243199373@SQ     SN:3    LN:198022430@SQ     SN:4    LN:191154276@SQ     SN:5    LN:180915260@SQ     SN:6    LN:171115067@SQ     SN:7    LN:159138663@SQ     SN:8    LN:146364022@SQ     SN:9    LN:141213431@SQ     SN:10   LN:135534747@SQ     SN:11   LN:135006516@SQ     SN:12   LN:133851895@SQ     SN:13   LN:115169878@SQ     SN:14   LN:107349540@SQ     SN:15   LN:102531392@SQ     SN:16   LN:90354753@SQ     SN:17   LN:81195210@SQ     SN:18   LN:78077248@SQ     SN:19   LN:59128983@SQ     SN:20   LN:63025520@SQ     SN:21   LN:48129895@SQ     SN:22   LN:51304566@SQ     SN:X    LN:155270560@SQ     SN:Y    LN:59373566HWI-ST298:171:81MJKABXX:6:1101:1664:2484        83      10      42832500        37      63M     =       42832371        -192    AATTATATTTAGTAAAGCTTAACAACCAATAAAAGGCTTTACCACATTCTTCGAATTTGTAAG  DC<48**?0*@?**?B9*??3@GFCAE9IIIIGEEHGEHCF9B<<GHGHGHHHBHFFFFFCC@ RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:1  SM:i:37 AM:i:0  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:6G56        RG:Z:READ_GROUP_1HWI-ST298:171:81MJKABXX:6:1101:1664:2484        163     10      42832371        36      50M     =       42832500        192     AGCTTTGCCACATTCTTCACATTTGCAGGGTTTCTCTCCCGTACGAATTC       @@BDFB>?B?BHHIFEGCEHF9EE><AFEGCEH9<???F*00))00?FHG      RG:Z:FLOWCELL1-LINE1    XT:A:R  NM:i:1  SM:i:0  AM:i:0  X0:i:5  X1:i:3  XM:i:1  XO:i:0  XG:i:0  MD:Z:43T6       RG:Z:READ_GROUP_1HWI-ST298:171:81MJKABXX:6:1101:2442:2401        99      13      101256483       60      49M     =       101256650       230     GTAACAAAAATAAAGATGTGAGGCTGCCTGCTCTTGCCTAAAGCATGGC        @@@FFFFDDDHHHBHBGGC4AFGICB;AFG>3?<D@F;CD@GH**09?@       RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:49 RG:Z:READ_GROUP_1HWI-ST298:171:81MJKABXX:6:1101:2442:2401        147     13      101256650       60      63M     =       101256483       -230    GAGAAAAGCATATAGATATTCTATGTTAAAACTTCCATTCCTCATTCGATTATTTGCCCTATT  HC83<GFB899FB499?00*EFGF>GB???1HEEGE9E@EIHHCGGFCCAFADD;;FFFD@@< RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:2  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:1G17A43     RG:Z:READ_GROUP_1HWI-ST298:171:81MJKABXX:6:1101:2496:2427        83      20      49195046        60      65M     =       49194943        -168    TCTTTTCAAAGTCCGAGAGTCAGGGTCACTCAGCCCGGAGCACGGGCCCGTTGTGGTGCACTGCA        ?:5(55;3ABA:FFCBECHC?>>ACDF@IGHBF6IJJJJIGGGGHBHJIGHGFGHHHDDDFFC@@       RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:0  XO:i:0   XG:i:0  MD:Z:65HWI-ST298:171:81MJKABXX:6:1101:2496:2427        163     20      49194943        60      60M     =       49195046        168     TTTTTCTCTTTCAGACCCAAGAAACTCGAGAGATCTTACATTTCCACTATACCACATGGC     @@@FFE?DDHFFFGDEEBEE;BCE<C9CAC@F19CF**:*?****0*00?9B9B328B>D    RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:60  RG:Z:READ_GROUP_1
My commander line is :/usr/java/jdk1.6.0_16/bin/java -jar /share/apps/GenomeAnalysisTK-1.0.5777/GenomeAnalysisTK.jar -l INFO -R /share/data/staff/sunchy/data/GATK/human_g1k_v37.fasta --DBSNP /share/data/staff/sunchy/data/GATK/dbsnp_129_b37.rod -I sorted.rmdup.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile var.csv
Thank you                                       Cheo