Unknown reference error using FastaAlternateReferenceMaker

MartinBMartinB Posts: 8Member
edited September 2013 in Ask the GATK team


I tried to run FastaAlternateReferenceMaker and I get the following error:

WARNING 2013-09-18 16:28:28 IntervalList    Ignoring interval for unknown reference: Chr1:3580210-3580286

For all the intervals I submitted. I already looked around on the web, and I did not find any answer, knowing that my chromosome names are all with the 'Chr' format in all the files and that my interval files are tab delimited.

My interval file look like:

@HD     VN:1.4  SO:unsorted
@SQ     SN:Chr1 LN:158337067    UR:file:chromosome_3.1.fasta    M5:0631b350aa263a0f714de8ba9d609eb0
@SQ     SN:Chr2 LN:137060424    UR:file:Chromosome_3.1.fasta    M5:15898469d6142f8bb74f769bfe9b155f
@SQ     SN:Chr3 LN:121430405    UR:file:Chromosome_3.1.fasta    M5:c515c4da7c2cd2d24c9487db8f733cfd
Chr1    3580210 3580286 +       ID=MI0011294_1;accession_number=MI0011294
Chr1    3580220 3580240 +       ID=MIMAT0011792_1;accession_number=MIMAT0011792
Chr1    3607747 3607842 -       ID=MI0014499_1;accession_number=MI0014499
Chr1    3607802 3607822 -       ID=MIMAT0017395_1;accession_number=MIMAT0017395
Chr1    10227277        10227339        -       ID=MI0009752_1;accession_number=MI0009752
Chr1    10227315        10227337        -       ID=MIMAT0009241_1;accession_number=MIMAT0009241
Chr1    19881347        19881431        -       ID=MI0005457_1;accession_number=MI0005457
Chr1    19881398        19881419        -       ID=MIMAT0003539_1;accession_number=MIMAT0003539
Chr1    19930459        19930542        -       ID=MI0005454_1;accession_number=MI0005454
Chr1    19930511        19930532        -       ID=MIMAT0004332_1;accession_number=MIMAT0004332

The header of my interval file is a copy of the Chromosome_3.1.dict I do not know what is misformated and why I get this error



Post edited by Geraldine_VdAuwera on

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