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start(0) > (-1) STOP

dcittarodcittaro Posts: 31Member

Hi all, I'm trying to perform BQRS on a bam file I have. Unfortunately I get this error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (0) > (-1) STOP -- this should never happen, please check read: HWI-ST1296:110:C1P16ACXX:8:2116:15747:68300 2/2 101b aligned read. (CIGAR: 5D74M27S)

The culprit appears to be this read pair:

HWI-ST1296:110:C1P16ACXX:8:2116:15747:68300 147 chr2    230419662   24  5D74M27S    =   230419667   -74 GAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGTGAAAGGAAGGGAAAAGAAAAAGGAAAGGAAGGCAATCCCTGCCCAGGTTCTTAATTTTC   #####A>:3CC>;=>DC@;>66;.3@DAA>CA@77.)((./))@FBB.<<??/9*0*******00*?1***1*1)1)<)B3++2+2+22++2222+4++B=   PG:Z:MarkDuplicates RG:Z:GB_L008.1  NM:i:9  AS:i:43 XS:i:45
HWI-ST1296:110:C1P16ACXX:8:2116:15747:68300 99  chr2    230419667   53  83M18S  =   230419662   74  GAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAGAAAGGAAGGAAAAAGAGAAAGGGAAGGAAGGAAATTCATGCTCAGTATCTAATTTTTA   ??;ADDDDHBF3DA=GBGB@D;EFC<3CDHBHICDEGEGIE=@@A@D@;C;;2?@7;=7>>;5>;;@B1<@CB<?>>::4++>@@>CC44>>@DC(:CA##   PG:Z:MarkDuplicates RG:Z:GB_L008.1  NM:i:0  AS:i:83 XS:i:50

Program arguments were:

-R /lustre1/genomes/hg19/fa/hg19.fa -knownSites /lustre1/genomes/hg19/annotation/dbSNP-137.chr.vcf -I GB_dedup.realign.bam -T BaseRecalibrator --covariate QualityScoreCovariate --covariate CycleCovariate --covariate ContextCovariate --covariate ReadGroupCovariate --unsafe ALLOW_SEQ_DICT_INCOMPATIBILITY -nct 64 -o jobdir/GB.grp

I'm running the latest nightbuild of GATK.
Any hint is very much appreciated



Best Answer


  • blueskypyblueskypy Posts: 261Member ✭✭

    Hi, Geraldine,
    I added -rf BadCigar to PrintReads, but still get similar error on the bam file produced from PrintReads. In another threads, you indicated that -rf BadCigar is not needed after PrintReads. I'm using v 2.7.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,560Administrator, Dev admin

    Hi @blueskypy, can you post your command line and the error message you get?

    Geraldine Van der Auwera, PhD

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