Badly formed genome loc

moranmoran The BroadMember
edited October 2013 in Ask the GATK team

Hello,

Trying to run diagnoseTargets with a list of genes as intervals: java -jar GenomeAnalysisTK.jar -T DiagnoseTargets -R Final.HMP.fasta -o genes.output.new.vcf -I bam.list -L gene.intervals.list

ERROR MESSAGE: Badly formed genome loc: Contig '@SQ SN:lcl|NZ_ABYJ02000001.1 LN' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

However, this sequence exists in the dictionary:
grep "lcl|NZ_ABYJ02000001.1" Final.HMP.dict

@SQ SN:lcl|NZ_ABYJ02000001.1 LN:27533 UR:file:/seq/msctmp/moran/RISK/HMP.katz/Final.HMP.fasta M5:a492998ddf8c8b4f9d6aad4d7d4c26d5

And in the header of the interval files:
grep "lcl|NZ_ABYJ02000001.1" ../Raw/HMP649/gene.intervals.list

@SQ SN:lcl|NZ_ABYJ02000001.1 LN:27533

I'm sorry, but have been working on this for hours, can't figure it out.

any idea?

Thanks!

Answers

  • moranmoran The BroadMember

    found the problem!! in the interval list there was one line (of the 52K there) in which the start position was larger than the stop position.

    Too bad this is the error message you get for this though..

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The error looks more like there was a formatting issue in the header of your intervals list. There is a specific error for when the start/stop don't make sense. Is it possible that the formatting error got fixed while you were fixing the coordinates issue?

  • moranmoran The BroadMember

    don't think so. I got to the point where adding that line in the interval has evoked the above error, and when removing it from the interval list, all was well.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    That's weird, shouldn't happen like that. I'm glad your problem is fixed of course. I'll keep an eye out for any other similar issues; if someone else experiences an issue like that we'll debug.

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