segmentation fault error

[kuangzhuoran]

My command is : "valor -i Klg2.bam -s peregrine.chr11.sonic -o Klg2.manual -f INV --contig_count 1"

Here are my logs:
Loading SONIC file..

SONIC Info:
Built in Thu Sep 12 02:55:39 2024

Number of chromosomes: 1
Loading gap intervals.
Loading duplication intervals.
Loading repeats.
SONIC file loaded. Memory usage: 1.18 MB.

VALOR: Variation with LOng Range
Version: 2.1.5
Build Date: Mon Sep 9 10:58:00 CST 2024
Output: Klg2.manual-predicted_svs.bedpe
Logfile: Klg2.manual-valor.log
Loading SONIC file..

SONIC Info:
Built in Thu Sep 12 02:55:39 2024

Number of chromosomes: 1
Loading gap intervals.
Loading duplication intervals.
Loading repeats.
SONIC file loaded. Memory usage: 1.18 MB.
Reading BAM file: Klg2.bam

Finding structural variants in chromosome chr11
Recovering split molecules..
Sorting the DNA Intervals
Recovering molecules
Global molecule depth mean: 20.260342
Global molecule depth standard deviation: 5.335327
[1] 19300 segmentation fault valor -i Klg2.bam -s peregrine.chr11.sonic -o Klg2.manual -f INV 1

[f0t1h]

Hi, is there a small reproducing dataset you can send me so I can debug this problem?

[kuangzhuoran]

Thanks for your help
please run "gunzip test.fa.gz && mv test.sonic.gz test.sonic"
test.fa.gz
test.sonic.gz

[kuangzhuoran]

Please run "mv test.bam.zip test.bam"
test.bam.zip

[f0t1h]

Hi,

Please make sure that bam header and the sonic file is consistent. You can either provide a sonic file with all chromosomes in the bam header or remove those chromosomes from the bam and pass -c 1 to valor to avoid this problem.