Tagged with #incompatible-contigs
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Created 2015-11-05 02:36:31 | Updated | Tags: vcf fastaalternatereferencemaker incompatible-contigs

Comments (1)

Hello, I am using FastaAlterenateReferenceMaker to generate new reference genome using SNPs in .vcf file. I used following command: java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R genome.fa -o newgenome.fa -V snps.vcf

I got this error: ##### ERROR ##### ERROR MESSAGE: Input files variant and reference have incompatible contigs: The contig order in variant and referenceis not the same; to fix this please see (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files. ##### ERROR variant contigs = [10, 1, 2, 3, 4, 5, 6, 7, 8, 9, MT, Pt] ##### ERROR reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, MT, Pt]

vfc file contains SNPs for only one genome (ch6) and does not have any contig description line, and using the script in the link didn't work. I tried changing the order of the genome.fa to be same as variant contigs but this time, the chromosomes of the newgenome.fa were wrong (e.g. ch7 had the sequence of ch6, ch1 had the sequence of ch10, etc.)

How can I fix this? Thank you in advance.


Created 2014-09-22 08:02:30 | Updated 2014-09-22 08:03:38 | Tags: depthofcoverage incompatible-contigs

Comments (7)

I am trying to compute mean coverage (using GATK DepthOfCovearge) for a BAM file (targeting sequencing) aligned using reference hg19.

java -Xmx2g -jar GenomeAnalysisTK.jar \
        -R ucsc.hg19.fasta \
        -T DepthOfCoverage \
        -I my_bam.list \
        -L my_targets.bed \
        -o coverage

The problem reported is:

##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR   contig reads = chrM / 16569
##### ERROR   contig reference = chrM / 16571.
##### 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]
##### ERROR   reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, 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_ctg5_hap1, 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 ------------------------------------------------------------------------------------------

Could you please help me to find a solution? Many thanks in advance.


Created 2014-04-06 19:36:24 | Updated 2014-04-06 19:39:05 | Tags: realignertargetcreator error incompatible-contigs

Comments (6)

Hello All,

I am running RealignerTargetCreator using GATK version GenomeAnalysisTK-1.2-4-gd9ea764 and I am getting the following error: `

ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig reads = scaffold69676_size1796 / 3149
ERROR contig reference = scaffold69676_size1796 / 1758.
ERROR reads contigs = [scaffold1_size320545, scaffold2_size291774, scaffold3_size284740..........`

I already checked that I am using the right Reference FASTA file and the correct .bam file, that I have used for alignment before. Therefore, I am clueless why I am getting this error? I would appreciate your help regarding this problem. Any suggestion is welcome?

Thanks, Namrata


Created 2013-08-23 14:16:01 | Updated | Tags: realignertargetcreator realignment incompatible-contigs

Comments (1)

Hello

I am currently trying to run the RealignerTargetCreator on some bam files which were aligned to hg19 howver am getting this error `ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:

ERROR contig known = chrM / 16571
ERROR contig reference = chrM / 16569.`

After some initial investigation I found that the supplied hg19 reference genome which was being used for mapping was using rCRS mtDNA. other then realigning to a different build of hg19 is there any way to easily fix this problem through GATK?


Created 2013-08-14 15:39:16 | Updated | Tags: incompatible-contigs

Comments (1)

ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig reads = chrM / 16569
ERROR contig reference = chrM / 16571.

I'm trying to run some tests and can't because I get this message that my reference is not the same as the input file, even though I've been assured that it is. Is there a way around this? I'm new to this, so step-by-step details would be appreciated, thanks

Rauh Lab