CNVnator output file error

Question

[jinxinhao1988]

Hi，

I am using CNVnator to detect CNV. After the first step, I've got the error info as follows:

Parsing file tumor_sorted.bam ... 
Assuming BAM file for tumor_sorted.bam
Allocating memory ...
Done.
Writing histograms ...
Total of 0 reads were placed.

My command line is:

/share/biosoft/apps/CNVnator_v0.2.7/src/cnvnator -genome /share/biosoft/Database/HG_19/hg19.fasta -root tumor_output.root -chrom chr1 chr19 -tree tumor_sorted.bam

I just want to see the CNV in Chr1 and Chr19 region, and I didn't use the whole hg19 as a reference to align the reads. I just use part of the genome to make our own reference sequence. So I wonder if this is the reason, since the software has indicated that the genome file had to be hg19,hg38,etc. So if this means that I must use hg19 as the reference sequence to align my reads to generate the bam file. I can't use the other reference generated by myself.

If anyone had come across this situation before, and how to fix this problem.

Thank you in advance.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[jinxinhao1988]

Thank you very much. I will pay attention next time.