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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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assemble-complexSVs "Called 0 connected assemblies" #30

Open DittmanC opened 2 years ago

DittmanC commented 2 years ago

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 commented 2 years ago

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.