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Hi! I'm a new GATK user and I've this error..

paolorehopaoloreho Pavia, ItalyMember

I've tried to re-cat the ref genome including all the chromosomes present in the reads contig but I've had the same error..
Maybe there is a way to exclude that chromosome in my bam file, I think I don't need theese infomation in my analysis

Thanks!

ERROR MESSAGE: Input files reads and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.

ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_gl000193_random, chr4_gl000194_random, 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_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]
ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrM, chrX, chrY]

Best Answers

Answers

  • paolorehopaoloreho Pavia, ItalyMember

    Ok, thanks!

    I've controlled my ref genome, before using GATK I've created a .dict and .fa.fai files by following your guide.

    I've decided to keep all contigs.

    Now my error after run GATK is differente, but I think I'm in the right road to solve my problem..(I hope)
    It seem that the only problem is the contigs order of my reads/reference, but I'm sure I'm using the same fasta file during my analysis.
    I've noted that my .dict file is different from your example, it's in the same order like the reference contigs below.
    I think the problem is that!

    ERROR MESSAGE: Input files reads and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.

    ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_gl000193_random, chr4_gl000194_random, 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_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]
    ERROR reference contigs = [chr1, chr1_gl000191_random, chr1_gl000192_random, chr2, chr3, chr4, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6, chr7, chr7_gl000195_random, chr8, chr8_gl000196_random, chr8_gl000197_random, chr9, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr10, chr11, chr11_gl000202_random, chr12, chr13, chr14, chr15, chr16, chr17, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18, chr18_gl000207_random, chr19, chr19_gl000208_random, chr19_gl000209_random, chr20, chr21, chr21_gl000210_random, chr22, chrM, 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, chrX, chrY]
  • paolorehopaoloreho Pavia, ItalyMember

    Done!

    Thank you, now I can continue with my analysis...

    see you next ERROR!!

    Thank you so much!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hah, let's hope there are no more errors ;) Good luck!

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