core dump with simuReads

[ThomasGro]

Hi, thank you for providing this tool to simulate variation reference data.

I get a segmentation fault (core dump) when I run:

simuscop-master/bin/simuReads ./config_WES_TN.txt

Details of the aberrations loaded from file variations_HCC1395_hg38.txt are as follows:
CNV: 331
SNV: 3178
Insert: 108
Deletion: 236

1711 SNPs to simulate were loaded from file 
snp_variants_mutect_HCC1395_hg38.txt

Reference sequence was loaded from file 
GRCh38.d1.vd1.fa

total 295480 targets were loaded from file 
S07604624_Covered_human_all_v6_plus_UTR.liftover.to.hg38.bed

total 4 population combinations were loaded from file ./abundance.txt

number of available threads: 576
number of used threads: 5

profile was loaded from file ./WES_FD_1_N.model

Number of reads to sample: 170524513

Average copy number of populations:
normal: 2
tumor: 2.82521

*****Generating samples*****

current mixed proportions:
1       0
file name:
tumor_1.000+normal_0.000
Segmentation fault (core dumped)

But when I search for the core dump file to analyse it further, I cannot find it in the output or working directory or in the bin directory of simuscop.

[ThomasGro]

I investigated further: With the minimal parameters it runs without segmentation fault:

simuscop-master/bin/simuReads ./config_WES_TN.txt
Warning: SNP file not specified!
No SNPs will be inserted into the genome.
Warning: variation file not specified!
No variations will be inserted into the genome.

Reference sequence was loaded from file GRCh38.d1.vd1.fa

number of available threads: 576
number of used threads: 5

profile was loaded from file ./WES_FD_1_N.model

Number of reads to sample: 4407909958

Average copy number:
tumor: 2

*****Generating samples*****

But when including variation information if crashes:

simuscop-master/bin/simuReads ./config_WES_TN.txt
Warning: SNP file not specified!
No SNPs will be inserted into the genome.

Details of the aberrations loaded from file 
variations_HCC1395_hg38.txt are as follows:
CNV: 331
SNV: 3178
Insert: 108
Deletion: 236

Reference sequence was loaded from file 
GRCh38.d1.vd1.fa

number of available threads: 576
number of used threads: 5

profile was loaded from file ./WES_FD_1_N.model

Number of reads to sample: 4407909958

Average copy number:
tumor: 2.82028

*****Generating samples*****
Segmentation fault (core dumped)

[ThomasGro]

Again, investigated further: when adding CNV variations the program crashes. The other variation types seem not to cause a core dump.

simuscop-master/bin/simuReads ./config_WES_TN.txt
Warning: SNP file not specified!
No SNPs will be inserted into the genome.

Details of the aberrations loaded from file 
cnv_variant_HCC1395_hg38.txt are as follows:
CNV: 331
SNV: 0
Insert: 0
Deletion: 0

Reference sequence was loaded from file 
GRCh38.d1.vd1.fa

number of available threads: 576
number of used threads: 5

profile was loaded from file ./WES_FD_1_N.model

Number of reads to sample: 4407909958

Average copy number:
tumor: 2.82028

*****Generating samples*****
Segmentation fault (core dumped)

[ivan-balashov]

+1 I have same issue

[ivan-balashov]

@ThomasGro Maybe you have some CNV records with 0 CN or MajorAllele? I exclude them and now it works.

[ThomasGro]

@ivan-balashov Yes, I do have those cases in. But of course I would want to model also loss of chromosomal parts. So I think CN 0 cases need to handled, if they cause the issue.