Segmentation fault

[Bennett Henzeler]

Kia Ora, 

I have attached the source code, output, and error file for the corset run. After running for 1 sample, the code throws an error. I would appreciate any advice you can provide

Script:

#!/bin/bash -e

#SBATCH --cpus-per-task 18
#SBATCH --job-name Corset
#SBATCH --mem 100G  
#SBATCH --time 120:00:00
#SBATCH --account uoo03567
#SBATCH --output %x_%j.out  
#SBATCH --error %x_%j.err  
#SBATCH --mail-type ALL  
#SBATCH --mail-user bennett....@postgrad.otago.ac.nz

module purge
module load Corset/1.09-GCC-9.2.0
cd /nesi/nobackup/uoo03619/BH/Mapping/Second

corset -g 1,1,1,2,2,2 -n A1,A2,A3,B1,B2,B3 -f true *_sorted.bam

Output:

Running Corset Version 1.09
Setting sample groups:1,1,1,2,2,2, 2 groups in total
Setting sample names to:A1,A2,A3,B1,B2,B3
Setting output files to be overridden
Reading bam file : Huhu-L1_sorted.bam
0 million alignments read
0.2 million alignments read
0.4 million alignments read
0.6 million alignments read
0.8 million alignments read
1 million alignments read
1.2 million alignments read
1.4 million alignments read
1.6 million alignments read
1.8 million alignments read
2 million alignments read
2.2 million alignments read
2.4 million alignments read
2.6 million alignments read
2.8 million alignments read
3 million alignments read
3.2 million alignments read
3.4 million alignments read
3.6 million alignments read
3.8 million alignments read
4 million alignments read
4.2 million alignments read
4.4 million alignments read
4.6 million alignments read
4.8 million alignments read
5 million alignments read
5.2 million alignments read
5.4 million alignments read
5.6 million alignments read
5.8 million alignments read
6 million alignments read
6.2 million alignments read
6.4 million alignments read
6.6 million alignments read
6.8 million alignments read
7 million alignments read
7.2 million alignments read
7.4 million alignments read
7.6 million alignments read
7.8 million alignments read
8 million alignments read
8.2 million alignments read
8.4 million alignments read
8.6 million alignments read
8.8 million alignments read
9 million alignments read
9.2 million alignments read
9.4 million alignments read
9.6 million alignments read
9.8 million alignments read
10 million alignments read
10.2 million alignments read
10.4 million alignments read
10.6 million alignments read
10.8 million alignments read
11 million alignments read
11.2 million alignments read
11.4 million alignments read
11.6 million alignments read
11.8 million alignments read
12 million alignments read
12.2 million alignments read
12.4 million alignments read
12.6 million alignments read
12.8 million alignments read
13 million alignments read
13.2 million alignments read
13.4 million alignments read
13.6 million alignments read
13.8 million alignments read
14 million alignments read
14.2 million alignments read
14.4 million alignments read
14.6 million alignments read
14.8 million alignments read
15 million alignments read
15.2 million alignments read
15.4 million alignments read
15.6 million alignments read
15.8 million alignments read
16 million alignments read
16.2 million alignments read
16.4 million alignments read
16.6 million alignments read
16.8 million alignments read
17 million alignments read
17.2 million alignments read
17.4 million alignments read
17.6 million alignments read
17.8 million alignments read
18 million alignments read
18.2 million alignments read
18.4 million alignments read
18.6 million alignments read
18.8 million alignments read
19 million alignments read
19.2 million alignments read
19.4 million alignments read
19.6 million alignments read
19.8 million alignments read
20 million alignments read
20.2 million alignments read
20.4 million alignments read
20.6 million alignments read
20.8 million alignments read
21 million alignments read
21.2 million alignments read
21.4 million alignments read
21.6 million alignments read
21.8 million alignments read
22 million alignments read
22.2 million alignments read
22.4 million alignments read
22.6 million alignments read
22.8 million alignments read
23 million alignments read
23.2 million alignments read
23.4 million alignments read
23.6 million alignments read
23.8 million alignments read
24 million alignments read
24.2 million alignments read
24.4 million alignments read
24.6 million alignments read
24.8 million alignments read
25 million alignments read
25.2 million alignments read
25.4 million alignments read
25.6 million alignments read
25.8 million alignments read
26 million alignments read
26.2 million alignments read
26.4 million alignments read
26.6 million alignments read
26.8 million alignments read
27 million alignments read
27.2 million alignments read
27.4 million alignments read
27.6 million alignments read
27.8 million alignments read
28 million alignments read
28.2 million alignments read
28.4 million alignments read
28.6 million alignments read
28.8 million alignments read
29 million alignments read
29.2 million alignments read
29.4 million alignments read
29.6 million alignments read
29.8 million alignments read
30 million alignments read
30.2 million alignments read
30.4 million alignments read
30.6 million alignments read
30.8 million alignments read
31 million alignments read
31.2 million alignments read
31.4 million alignments read
31.6 million alignments read
31.8 million alignments read
32 million alignments read
32.2 million alignments read
32.4 million alignments read
32.6 million alignments read
32.8 million alignments read
33 million alignments read
33.2 million alignments read
33.4 million alignments read
33.6 million alignments read
33.8 million alignments read
34 million alignments read
34.2 million alignments read
34.4 million alignments read
34.6 million alignments read
34.8 million alignments read
35 million alignments read
35.2 million alignments read
35.4 million alignments read
35.6 million alignments read
35.8 million alignments read
36 million alignments read
36.2 million alignments read
36.4 million alignments read
36.6 million alignments read
36.8 million alignments read
37 million alignments read
37.2 million alignments read
37.4 million alignments read
37.6 million alignments read
37.8 million alignments read
38 million alignments read
38.2 million alignments read
38.4 million alignments read
38.6 million alignments read
38.8 million alignments read
39 million alignments read
39.2 million alignments read
39.4 million alignments read
39.6 million alignments read
39.8 million alignments read
40 million alignments read
40.2 million alignments read
40.4 million alignments read
40.6 million alignments read
40.8 million alignments read
41 million alignments read
41.2 million alignments read
41.4 million alignments read
41.6 million alignments read
41.8 million alignments read
42 million alignments read
42.2 million alignments read
42.4 million alignments read
42.6 million alignments read
42.8 million alignments read
43 million alignments read
43.2 million alignments read
43.4 million alignments read
43.6 million alignments read
43.8 million alignments read
44 million alignments read
44.2 million alignments read
44.4 million alignments read
44.6 million alignments read
44.8 million alignments read
45 million alignments read
45.2 million alignments read
45.4 million alignments read
45.6 million alignments read
45.8 million alignments read
46 million alignments read
46.2 million alignments read
46.4 million alignments read
46.6 million alignments read
46.8 million alignments read
47 million alignments read
47.2 million alignments read
47.4 million alignments read
47.6 million alignments read
47.8 million alignments read
48 million alignments read
48.2 million alignments read
48.4 million alignments read
48.6 million alignments read
48.8 million alignments read
49 million alignments read
49.2 million alignments read
49.4 million alignments read
49.6 million alignments read
49.8 million alignments read
50 million alignments read
50.2 million alignments read
50.4 million alignments read
50.6 million alignments read
50.8 million alignments read
51 million alignments read
51.2 million alignments read
51.4 million alignments read
51.6 million alignments read
51.8 million alignments read
52 million alignments read
52.2 million alignments read
52.4 million alignments read
52.6 million alignments read
52.8 million alignments read
53 million alignments read
53.2 million alignments read
53.4 million alignments read
53.6 million alignments read
53.8 million alignments read
54 million alignments read
54.2 million alignments read
54.4 million alignments read
54.6 million alignments read
54.8 million alignments read
55 million alignments read
55.2 million alignments read
55.4 million alignments read
55.6 million alignments read
55.8 million alignments read
56 million alignments read
56.2 million alignments read
56.4 million alignments read
56.6 million alignments read
56.8 million alignments read
57 million alignments read
57.2 million alignments read
57.4 million alignments read
57.6 million alignments read
57.8 million alignments read
58 million alignments read
58.2 million alignments read
58.4 million alignments read
58.6 million alignments read
58.8 million alignments read
59 million alignments read
59.2 million alignments read
59.4 million alignments read
59.6 million alignments read
59.8 million alignments read
60 million alignments read
60.2 million alignments read
60.4 million alignments read
60.6 million alignments read
60.8 million alignments read
61 million alignments read
61.2 million alignments read
61.4 million alignments read
61.6 million alignments read
61.8 million alignments read
62 million alignments read
62.2 million alignments read
62.4 million alignments read
62.6 million alignments read
62.8 million alignments read
63 million alignments read
63.2 million alignments read
63.4 million alignments read
63.6 million alignments read
63.8 million alignments read
64 million alignments read
64.2 million alignments read
64.4 million alignments read
64.6 million alignments read
64.8 million alignments read
65 million alignments read
65.2 million alignments read
65.4 million alignments read
65.6 million alignments read
65.8 million alignments read
66 million alignments read
66.2 million alignments read
66.4 million alignments read
66.6 million alignments read
66.8 million alignments read
67 million alignments read
67.2 million alignments read
67.4 million alignments read
67.6 million alignments read
67.8 million alignments read
68 million alignments read
68.2 million alignments read
68.4 million alignments read
68.6 million alignments read
Done reading Huhu-L1_sorted.bam

Error:

The following modules were not unloaded:
   (Use "module --force purge" to unload all):

  1) XALT/minimal   2) slurm   3) NeSI
/var/spool/slurm/job31151099/slurm_script: line 17: 108712 Segmentation fault      corset -g 1,1,1,2,2,2 -n A1,A2,A3,B1,B2,B3 -f true *_sorted.bam

Cheers

Bennett Henzeler