Got warning big karyograph > 50000 nodes and too many structure variations in the report

[yelingqun]

Hi, I recently upgraded JaBbA to the latest version and rerun some of our samples. I found too many junctions in all samples in the latest version. espetially on chromosome 2. Here I attached the parameters, log, and gGnome figures of one sample. Any suggestions? Like which parameters I should change, or which part of script I should look into. Thanks!

THe parameters of the 2 runs are just the same:

--geno FALSE --indel exclude --tfield tier --iterate 0 --rescue.window 1000 --rescue.all TRUE --nudgebalanced TRUE
--edgenudge 0.1
--strict FALSE --allin FALSE --field ratio --maxna 0.5 --ploidy 3.64230306687785 --purity 0.72
--ppmethod sequenza --cnsignif 1e-05
--slack 100 --linear FALSE --tilim 100000 --epgap 1e-05
--outdir $HOME/jba_result --name tumor --cores 10
--mem 16 --fix.thres -1 --lp TRUE --ism FALSE --filter_loose FALSE --gurobi FALSE --verbose FALSE --help FALSE
--junctions svaba_unfilteredd.sv.vcf
--coverage cov_ratio.rds

Here is the log output of the old version (2022):

JaBbA 2022-12-28 15:26:30: Number of gaps with nonzero width: 1115
JaBbA 2022-12-28 15:26:30: Number of segments before gap filtering: 1696
JaBbA 2022-12-28 15:26:30: 835 segments produced after gap filtering
JaBbA 2022-12-28 15:26:49: Definining coverage good quality nodes as >=50% bases covered by non-NA and non-Inf values in +/-100KB region
JaBbA 2022-12-28 15:26:49: Hard setting 231.790753 Mb of the genome to NA that didn't pass our quality threshold
JaBbA 2022-12-28 15:26:49: Using loess to fit mean to variance relationship in segments with greater than 1 bins
JaBbA 2022-12-28 15:26:50: Built gGraph with 1734 nodes, 1378 edges, purity 0.8, and ploidy 1.91

Here is the log output of the new version:

JaBbA 2024-11-26 17:48:10: Number of gaps with nonzero width: 1115
JaBbA 2024-11-26 17:48:10: Number of segments before gap filtering: 1696
JaBbA 2024-11-26 17:48:10: 835 segments produced after gap filtering
JaBbA 2024-11-26 17:48:10: creating karyograph
JaBbA 2024-11-26 17:48:19: WARNING: big karyograph > 50000 nodes, may take longer to finish.
JaBbA 2024-11-26 17:48:34: Definining coverage good quality nodes as >=50% bases covered by non-NA and non-Inf values in +/-100KB region
JaBbA 2024-11-26 17:48:34: Hard setting 185.706818 Mb of the genome to NA that didn't pass our quality threshold
JaBbA 2024-11-26 17:48:34: Using loess to fit mean to variance relationship in segments with greater than 1 bins
JaBbA 2024-11-26 17:48:55: Built gGraph with 142774 nodes, 223662 edges, purity 0.8, and ploidy 1.91

Based on the log, the segments numbers are the same, but way more nodes and edges are identified in the new version.

Figures: