empty call CNV .tsv files

[wbsimey]

Hello, I am learning to use CNVpyter. I have a non model species with a reference genome. In your Getting Started page, you state we should use a reference genome and mask for GC correction and strict mask filtering. I have not created these files yet. For the following list of commands, things seem to be running well, until I run the Call CNV regions step. This is creating empty .tsv files without error messages.

cnvpytor -root "$root_name.pytor" -rd "$bam_file" -chrom Chr1_nf Chr2_nf ... ChrY_nf

cnvpytor -root "$root_name.pytor" -his 10000 100000

cnvpytor -root "$root_name.pytor" -partition 10000 100000

cnvpytor -root "$root_name.pytor" -call 10000 > "${root_name}_all_calls.10k.tsv"

An -ls of my root file shows:

Filename 'Nfusc_GG29.pytor'
---------------------------
File created: 2023-09-26 21:46 using CNVpytor ver 1.3.1

Chromosomes with RD signal: Chr1_nf, Chr2_nf, Chr3_nf, Chr4_nf, Chr5_nf, Chr6_nf, Chr7_nf, Chr8_nf, Chr9_nf, Chr10_nf, Chr11_nf, Chr12_nf, Chr13_nf, Chr14_nf, Chr15_nf, Chr16_nf, Chr17_nf, Chr18_nf, Chr19_nf, Chr20_nf, Chr21_nf, Chr22_nf, Chr23_nf, Chr24_nf, Chr25_nf, Chr26_nf, Chr27_nf, ChrX_nf, ChrY_nf

Chromosomes with SNP signal:

Reference genome is not set.

Chromosomes with RD histograms [bin sizes]:  []

Chromosomes with SNP histograms [bin sizes]:  []

Chromosome lengths: {'Chr1_nf': '102568024', 'Chr2_nf': '155800727', 'Chr3_nf': '145145283', 'Chr4_nf': '105276828', 'Chr5_nf': '59708665', 'Chr6_nf': '184469985', 'Chr7_nf': '65483321', 'Chr8_nf': '153402896', 'Chr9_nf': '122435622', 'Chr10_nf': '53912713', 'Chr11_nf': '116729924', 'Chr12_nf': '97637404', 'Chr13_nf': '86517301', 'Chr14_nf': '113902124', 'Chr15_nf': '86948236', 'Chr16_nf': '92831008', 'Chr17_nf': '80864831', 'Chr18_nf': '80079930', 'Chr19_nf': '124178961', 'Chr20_nf': '110326479', 'Chr21_nf': '81067044', 'Chr22_nf': '74506876', 'Chr23_nf': '80157658', 'Chr24_nf': '71941365', 'Chr25_nf': '71491146', 'Chr26_nf': '67672728', 'Chr27_nf': '85665422', 'ChrX_nf': '160218175', 'ChrY_nf': '118176462'}

Can you see where I am messing this up?

[arpanda]

The reference genome needs to be set and its showing empty.

Reference genome is not set.

-Arijit

[wbsimey]

I think I got the non model ref genome created. I have a bed file with soft masking (upper and lower case format) for our genome. Is it possible to use this to create a mask file?

[arpanda]

The mask file is optional. If you would like to create mask file, please visit the examples/AddReferenceGenome.md page for input details.

-Arijit