structural variation calling through delly is stuck at Split-read assembly step

Question

[analyst]

Dear all,

I am performing structural variant calling on a grass data (close relative of Lolium perenne). Initially I performed variant calling analysis using Lolium perenne as a reference genome through delly and lumpy tools. But alignment rate was so low less than 40% that I decided to construct assembly of the reads for which reference genome is not yet available.

I have WGS short reads only i performed assembly through abyss tool followed by alignment through bwa that showed increased alignment rate of average 80%. Now when i performed structural variant analysis through lumpy and delly it is taking days to complete for a single sample that was run within minutes or a hour previously when using lolium perrene as a reference. Why is this happening where am i mistaken? Please guide.

This is delly command:

[2025-Mar-03 22:37:47] delly call -g Assembly/ABYSS/FA2_FT2/FA2_FT2-scaffolds.fa -o Alignment_assemb/abyss/FA2-FT2/delly/FA2_18_sv.bcf Alignment_assemb/abyss/FA2-FT2/bwa/FA2_18.bam 

I got this on terminal:

Warning: Sample has a non-default paired-end layout! File: Alignment_assemb/abyss/FA2-FT2/bwa/FA2_18.bam
The expected paired-end orientation is   ---Read1--->      <---Read2---  which is the default illumina paired-end layout.
[2025-Mar-03 22:38:19] Paired-end and split-read scanning
[2025-Mar-03 22:38:44] Split-read clustering
[2025-Mar-03 22:44:31] Paired-end clustering
[2025-Mar-03 22:44:31] Split-read assembly

[Pierre Lindenbaum]

Warning: Sample has a non-default paired-end layout

you should check this.

Warning: Sample has a non-default paired-end layout

for a human wgs, this part can takes more then 5 hours.

[analyst]

This is plant grass data.

It is paired end reads data.