Open ThomasGro opened 1 year ago
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)
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)
+1 I have same issue
@ThomasGro Maybe you have some CNV records with 0 CN or MajorAllele? I exclude them and now it works.
@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.
Hi, thank you for providing this tool to simulate variation reference data.
I get a segmentation fault (core dump) when I run:
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.