Question: Gatk Alignertargetcreator Error
gravatar for Leandro Batista
8.6 years ago by
Leandro Batista100 wrote:


I'm performing for the first time SNP calling using GATK. I'm following the pipeline proposed in , although I haven't run the first steps since the BAM files were already available and sorted for the whole genome sequencing. I'm giving here some more detail of what I have done until now:

1) split whole genome BAM file by chromosomal location with samtools, I'm interested only in mouse chromosome 11;

2) produced the correspondent .bai file;

3) used AlignerTargetCreator (GATK) to identify target regions for realignement: - reference chr11 in fasta (.fa) from UCSC mouse assembly database; - fasta index file with samtools - .dict file with picard

Then, when running the AlignerTargetCreator: $ java -jar Software/GenomeAnalysisTK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R Genomes/Reference/chr11.fasta -I Genomes/Bam/PWK/chr11.bam -o Genomes/Bam/PWK/chr11.intervals

I got the following error:

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR A USER ERROR has occurred (version 1.4-37-g0b29d54):</h5> <h5>ERROR The invalid arguments or inputs must be corrected before the GATK can proceed</h5> <h5>ERROR Please do not post this error to the GATK forum</h5> <h5>ERROR</h5> <h5>ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.</h5> <h5>ERROR Visit our wiki for extensive documentation</h5> <h5>ERROR Visit our forum to view answers to commonly asked questions</h5> <h5>ERROR</h5> <h5>ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found.</h5> <h5>ERROR reads contigs = [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 3, 4, 5, 6, 7, 8, 9, MT, X, Y, NT_166325, NT_166464, NT_166452, NT_166480, NT_166448, NT_166458, NT_166443, NT_166466, NT_166476, NT_166479, NT_166478, NT_166474, NT_166471, NT_166445, NT_166465, NT_166457, NT_166470, NT_166454, NT_166472, NT_166449, NT_166481, NT_166337, NT_166459, NT_166456, NT_166473, NT_166461, NT_166475, NT_166462, NT_166444, NT_166453, NT_166446, NT_166469, NT_072868, NT_166335, NT_166467, NT_166283, NT_166338, NT_166340, NT_166442, NT_166334, NT_166286, NT_166451, NT_166336, NT_166339, NT_166290, NT_053651, NT_166450, NT_166447, NT_166468, NT_166460, NT_166477, NT_166455, NT_166291, NT_166463, NT_166433, NT_166402, NT_166327, NT_166308, NT_166309, NT_109319, NT_166282, NT_166314, NT_166303, NT_112000, NT_110857, NT_166280, NT_166375, NT_166311, NT_166307, NT_166310, NT_166323, NT_166437, NT_166374, NT_166364, NT_166439, NT_166328, NT_166438, NT_166389, NT_162750, NT_166436, NT_166372, NT_166440, NT_166326, NT_166342, NT_166333, NT_166435, NT_166434, NT_166341, NT_166376, NT_166387, NT_166281, NT_166313, NT_166380, NT_166360, NT_166441, NT_166359, NT_166386, NT_166356, NT_166357, NT_166423, NT_166384, NT_161879, NT_161928, NT_166388, NT_161919, NT_166381, NT_166367, NT_166392, NT_166406, NT_166365, NT_166379, NT_166358, NT_161913, NT_166378, NT_166382, NT_161926, NT_166345, NT_166385, NT_165789, NT_166368, NT_166405, NT_166390, NT_166373, NT_166361, NT_166348, NT_166369, NT_161898, NT_166417, NT_166410, NT_166383, NT_166362, NT_165754, NT_166366, NT_166363, NT_161868, NT_166407, NT_165793, NT_166352, NT_161925, NT_166412, NT_165792, NT_161924, NT_166422, NT_165795, NT_166354, NT_166350, NT_165796, NT_161904, NT_166370, NT_165798, NT_165791, NT_161885, NT_166424, NT_166346, NT_165794, NT_166377, NT_166418, NT_161877, NT_166351, NT_166408, NT_166349, NT_161906, NT_166391, NT_161892, NT_166415, NT_165790, NT_166420, NT_166353, NT_166344, NT_166371, NT_161895, NT_166404, NT_166413, NT_166419, NT_161916, NT_166347, NT_161875, NT_161911, NT_161897, NT_161866, NT_166409, NT_161872, NT_166403, NT_161902, NT_166414, NT_166416, NT_166421, NT_161923, NT_161937]</h5> <h5>ERROR reference contigs = [chr11]</h5> <h5>ERROR ------------------------------------------------------------------------------------------</h5>

I'm quite new to NGS data analysis. Does anyone know why I'm having this problem and how can I solve it?

gatk snp • 4.2k views
ADD COMMENTlink written 8.6 years ago by Leandro Batista100
gravatar for Raony Guimarães
8.6 years ago by
Dublin / Ireland
Raony Guimarães1.1k wrote:

The problem is that the fasta you are using is not the same one was used to align the reads and produce the BAM file.

The chromossome names are not the same. In your bam file they are: [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 3, 4, 5, 6, 7, 8, 9, MT, X, Y,..]

And in your reference it they are : [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrMT, chrX, chrY, ...]

Change the cromossome names in your reference to [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 3, 4, 5, 6, 7, 8, 9, MT, X, Y,..] or in your bam file to [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrMT, chrX, chrY, ...]

Just a tip, try to use resource bundle always when it's possible!

ADD COMMENTlink written 8.6 years ago by Raony Guimarães1.1k

Thanks, that was the problem indeed. I've already changed the chromosome notation in fasta file, but I forgot the .fai and .dict file.

ADD REPLYlink written 8.6 years ago by Leandro Batista100
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