I am trying to use Squid for calling SVs in my datasets. I have 87 samples and all are processed in the same way. I ran Squid as follows:
$ squid-v1.5_linux_x86_64/squid --bwa -b Sample_X.readgroup.sorted.bam -o Sample_X
Squid ran perfectly on 85 of them. But for the two remaining samples, I face segmentation fault as follows:
Reference name chr1 --> 0
Reference name chr10 --> 9
Reference name chr11 --> 10
Reference name chr12 --> 11
Reference name chr13 --> 12
Reference name chr14 --> 13
Reference name chr15 --> 14
Reference name chr16 --> 15
Reference name chr17 --> 16
Reference name chr18 --> 17
Reference name chr19 --> 18
Reference name chr2 --> 1
Reference name chr20 --> 19
Reference name chr21 --> 20
Reference name chr22 --> 21
Reference name chr3 --> 2
Reference name chr4 --> 3
Reference name chr5 --> 4
Reference name chr6 --> 5
Reference name chr7 --> 6
Reference name chr8 --> 7
Reference name chr9 --> 8
Reference name chrM --> 22
Reference name chrX --> 23
Reference name chrY --> 24
[Thu Feb 23 10:57:43 2023] Starting reading bam file.
[Thu Feb 23 11:06:06 2023] Building nodes, finish seeding.
[Thu Feb 23 11:06:06 2023] Building nodes, finish expanding to whole genome.
[Thu Feb 23 11:06:08 2023] Finish calculating reads per node.
[Thu Feb 23 11:06:08 2023] Starting building edges.
[Thu Feb 23 12:01:03 2023] Finish raw edges.
[Thu Feb 23 12:01:05 2023] Finish filtering edges from multi-aligned reads.
[Thu Feb 23 14:11:18 2023] Finish adding partial aligned reads.
[Thu Feb 23 14:11:32 2023] Finish building edges.
Maximum connected component size=2275
64636 30528
line 13: 142068 Segmentation fault (core dumped) squid-v1.5_linux_x86_64/squid --bwa -b Sample_X.readgroup.sorted.bam -o Sample_X
I am using 200GB of memory. What may be the problem? Could you please help?
Hi,
I am trying to use Squid for calling SVs in my datasets. I have 87 samples and all are processed in the same way. I ran Squid as follows:
$ squid-v1.5_linux_x86_64/squid --bwa -b Sample_X.readgroup.sorted.bam -o Sample_X
Squid ran perfectly on 85 of them. But for the two remaining samples, I face segmentation fault as follows:I am using 200GB of memory. What may be the problem? Could you please help?