The novoBreak does not work well. Error : region "chr1:66670169-66671169" specifies an unknown reference name.

Question

[seocd74]

Hello.

I'm trying to run novoBreak using human genome in AWS. NovoBreak is using samtools and bwa and so on for running and it include these files.

The inputs are 'chr19.normal.bam', 'chr19.tumor.bam' and reference 'ucsc.hg19.fasta'. I sorted and indexed them using bwa and samtools.

However, there are the following errors

[main_samview] region "chr11:78901555-78902555" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr11:78901555-78902555" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr1:13432678-13433678" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr22:26206583-26207583" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr19:18835100-18836100" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr13:45670604-45671604" specifies an unknown reference name. Continue anyway.
....

I think it's samtools error but i am not familiar with samtools. So i can't find proper solution about it. Could you give me some advice about it? Thank you.

[colindaven]

Does your reference sequence have chromosome names like "11" and not chr11 ?

[seocd74]

My reference sequence have chromosome names like chr11