SVDSS
SVDSS copied to clipboard
Seg default
When I used LRA to align the HG002 ONT data and ran the following code, I did not get any results. However, other alignment software worked fine.
/home/xxx/00.Software/SVDSS/SVDSS_linux_x86-64 index
/home/xxx/00.Software/SVDSS/SVDSS_linux_x86-64 smooth --reference /home/xxx/01.Reference/Human_GRCh37/GCF_000001405.25_GRCh37.p13_genomic.fa --bam ${sample} --threads 20 > ${path}/${name}.smoothed.bam
samtools index -@ 20 ${path}/${name}.smoothed.bam
/home/xxx/00.Software/SVDSS/SVDSS_linux_x86-64 search --index /home/xxx/01.Reference/Human_GRCh37/GCF_000001405.25_GRCh37.p13_genomic.fmd --bam ${path}/${name}.smoothed.bam --threads 20 >${path}/${name}.txt
/home/xxx/00.Software/SVDSS/SVDSS_linux_x86-64 call --reference
(svdss) [xxx@hpc01 08.lra]$ /home/xxx/00.Software/SVDSS/SVDSS_linux_x86-64 call --reference /home/xxx/01.Reference/Human_GRCh37/GCF_000001405.25_GRCh37.p13_genomic.fa --bam HG002.ONT_lra.smoothed.bam --sfs ./HG002.ONT_lra.txt --threads 20 --min-cluster-weight 2 --clipped >calls.vcf
[2024-08-18 17:58:25.669] [stderr] [info] Loading reference genome from /home/jiaoh/01.Reference/Human_GRCh37/GCF_000001405.25_GRCh37.p13_genomic.fa..
[2024-08-18 17:58:47.035] [stderr] [info] Loading SFSs from ./HG002.ONT_lra.txt..
[2024-08-18 17:59:02.036] [stderr] [info] Loaded 15907313 SFSs from 1768750 reads.
[2024-08-18 17:59:02.099] [stderr] [info] Placing SFSs on reference genome
[2024-08-18 18:01:11.676] [stderr] [info] 107/0/0 unplaced SFSs. 0 erroneus SFSs. 3500774 clipped SFSs.
[2024-08-18 18:01:11.676] [stderr] [info] Clustering 1054888 SFSs..
[2024-08-18 18:01:12.731] [stderr] [info] Maximum extended SFS length: 49162bp. Using separation distance: 54078bp.
[2024-08-18 18:01:13.337] [stderr] [info] Extending 314027 clusters..
[2024-08-18 18:03:18.167] [stderr] [info] Filtered 1247 SFSs. Filtered 214848 clusters. Filtered 39 global clusters.
[2024-08-18 18:03:18.167] [stderr] [info] Calling SVs from 314027 clusters..
Segmentation fault (core dumped)
I would greatly appreciate it if you could help me identify the error!!!!