Segmentation fault (core dumped) delly cnv

dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

BSD 3-Clause "New" or "Revised" License

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Segmentation fault (core dumped) delly cnv #310

Open RochaLAJ opened 1 year ago

RochaLAJ commented 1 year ago

delly -v

Delly version: v1.1.6
 using Boost: v1.80.0
 using HTSlib: v1.15.1

uname -r 6.0.8-arch1-1

Map generated with dicey mappability2 S1.bam

Reference from: https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000001405.40/

Code $delly cnv -g GCF_000001405.40_GRCh38.p14_genomic.fna -m map.fa S1.bam

Hardware

Ram: 20GB
CPU: Ryzen 5 1600
SSD NVME 1TB

tobiasrausch commented 1 year ago

Is there any reason why you don't want to use the pre-computed GRCh38 mappability map? You can download it here.

The procedure to generate an indexed mappability map is described in the FAQ.

RochaLAJ commented 1 year ago

Hi Tobias! I'm trying to use my own map because name convensions are not the same as uploaded by your link. Mappability map chromosome naming disagrees with BAM file! Thank you for your time and effort.

shameem356 commented 1 year ago

Hello , I am also facing Segmentation fault for delly cnv. I am using plant genomes with the indexed mappability map file. Mappability file was created as per the institution mentioned in FAQ.

fabrimafe commented 1 year ago

Same problem. I had generated mappability files with a different strategies, and thought that the .map files were nothing but a hard-masked fasta. With these files, I was obtaining a segmentation fault. This was solved by replacing all retained bases with C. What is the difference between C and A in the .map files you suggest to use?

tobiasrausch commented 1 year ago

Hmm, sounds like a bug. I suspect this might be related to some small chromosomes where delly does not find enough mappable positions. Can you try removing small contigs <100,000bp from the mappability file? If that doesn't help I probably need to investigate the BAM and MAP files. Can you share those? Thanks!