assemble-complexSVs "Called 0 connected assemblies"

[DittmanC]

I have no idea why I got all zero in assemble-complexSVs....
Inside my breaks.sv.txt file would be like this..
chr15 chr2 -+ 35700000 216100000 translocation
chr1 chr15 +- 109750000 101140000 translocation
chr1 chr15 -- 109750000 101410000 translocation
chr3 chrX -- 146910000 150740000 translocation
chr3 chrX -+ 145730000 154240000 translocation

I have been running at 50kb and 100kb resolution, and got the same result
assemble-complexSVs -O $sample -B $sample_merge.breaks.sv.txt -H $sample_50000_adjustedCNV.cool
root INFO @ 01/11/22 16:24:41:

ARGUMENT LIST:

Output Prefix = $sample

Break Points = $sample_merge.breaks.sv.txt

Minimum fragment size = 500000bp

Cooler URI = $sample_50000_adjustedCNV.cool

Extended Genomic Span = 5000000bp

Balance Type = CNV

Experimental protocol = insitu

Number of Processes = 1

Log file name = assembleSVs.log

......
[Parallel(n_jobs=1)]: Done 58 out of 58 | elapsed: 6.0s finished
root INFO @ 01/11/22 16:24:48: 0 SVs left
root INFO @ 01/11/22 16:24:48: Building SV connecting graph ...
root INFO @ 01/11/22 16:24:48: Discovering and re-ordering complex SVs ...
neoloop.assembly INFO @ 01/11/22 16:24:48: Filtering 0 redundant candidates ...
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done 0 out of 0 | elapsed: 0.0s finished
root INFO @ 01/11/22 16:24:48: Called 0 connected assemblies
root INFO @ 01/11/22 16:24:48: Output ...
root INFO @ 01/11/22 16:24:48: Done

[XiaoTaoWang]

Hi, sorry for the confusion. Currently both assemble-complexSVs and neoloop-caller have such limitations: 1. for --protocol dilution, they can only be run at 10kb, 20kb, 25kb, 40kb, or 50kb; 2. for --protocol insitu, they can only be run at 5kb, 10kb, 20kb, or 25kb.