SInC_simulate failure

[KosAL]

Hi,

I want to try the SInC simulator but it is aborting at the SInC step. In detail, I followed the steps below:

1. Quality profile generation

   ./genProfile -R 1 -l 100 SInC_input.txt
   ./genProfile -R 2 -l 100 SInC_input.txt

   The SInC_input.txt contains full paths of 2 fastq files
   /path/to/file/sample_1.fq
   /path/to/file/sample_2.fq

2. Simulation of SNPs, INDELs, CNVs

   ./SInC_simulate -S 0.002 -I 0.0001 -p 2 -l 1000 -u 150000 -t 2 /path/to/fasta_file/ref.fa

   Here is where I get the follwing error:

   SNP rate: 0.0020
   INDEL rate: 0.0001
   CNV rate: 2.0000
   CNV size upper limit: 150000
   CNV size lower limit: 1000
   CNV limit: 10
   ti/tv: 2.0000
   *** buffer overflow detected ***: ./SInC_simulate terminated
   ======= Backtrace: =========
   /lib64/libc.so.6(__fortify_fail+0x37)[0x39f1f02827]
   /lib64/libc.so.6[0x39f1f00710]
   /lib64/libc.so.6[0x39f1effb69]
   /lib64/libc.so.6(_IO_default_xsputn+0xc9)[0x39f1e74939]
   /lib64/libc.so.6(_IO_vfprintf+0x64f)[0x39f1e4491f]
   /lib64/libc.so.6(__vsprintf_chk+0x9d)[0x39f1effc0d]
   /lib64/libc.so.6(__sprintf_chk+0x7f)[0x39f1effb4f]
   ../SInC_simulate[0x405b71]
   ../SInC_simulate[0x401423]
   /lib64/libc.so.6(__libc_start_main+0xfd)[0x39f1e1ed1d]
   ../SInC_simulate[0x40180d]
   ======= Memory map: ========
   00400000-00409000 r-xp 00000000 00:15 28151973428 /home/kalexiou/local/SInC/SInC_simulate
   00608000-00609000 r--p 00008000 00:15 28151973428 /home/kalexiou/local/SInC/SInC_simulate
   00609000-0060a000 rw-p 00009000 00:15 28151973428 /home/kalexiou/local/SInC/SInC_simulate
   0060a000-0060d000 rw-p 00000000 00:00 0
   01c4f000-01c70000 rw-p 00000000 00:00 0 [heap]
   39f1600000-39f1620000 r-xp 00000000 fd:00 59506694 /lib64/ld-2.12.so
   39f181f000-39f1820000 r--p 0001f000 fd:00 59506694 /lib64/ld-2.12.so
   39f1820000-39f1821000 rw-p 00020000 fd:00 59506694 /lib64/ld-2.12.so
   39f1821000-39f1822000 rw-p 00000000 00:00 0
   39f1a00000-39f1a83000 r-xp 00000000 fd:00 59506763 /lib64/libm-2.12.so
   39f1a83000-39f1c82000 ---p 00083000 fd:00 59506763 /lib64/libm-2.12.so
   39f1c82000-39f1c83000 r--p 00082000 fd:00 59506763 /lib64/libm-2.12.so
   39f1c83000-39f1c84000 rw-p 00083000 fd:00 59506763 /lib64/libm-2.12.so
   39f1e00000-39f1f8b000 r-xp 00000000 fd:00 59506695 /lib64/libc-2.12.so
   39f1f8b000-39f218a000 ---p 0018b000 fd:00 59506695 /lib64/libc-2.12.so
   39f218a000-39f218e000 r--p 0018a000 fd:00 59506695 /lib64/libc-2.12.so
   39f218e000-39f218f000 rw-p 0018e000 fd:00 59506695 /lib64/libc-2.12.so
   39f218f000-39f2194000 rw-p 00000000 00:00 0
   39f2200000-39f23ea000 r-xp 00000000 fd:00 2099723 /usr/lib64/libgsl.so.0.14.0
   39f23ea000-39f25e9000 ---p 001ea000 fd:00 2099723 /usr/lib64/libgsl.so.0.14.0
   39f25e9000-39f25f7000 rw-p 001e9000 fd:00 2099723 /usr/lib64/libgsl.so.0.14.0
   39f2600000-39f2637000 r-xp 00000000 fd:00 2104771 /usr/lib64/libgslcblas.so.0.0.0
   39f2637000-39f2836000 ---p 00037000 fd:00 2104771 /usr/lib64/libgslcblas.so.0.0.0
   39f2836000-39f2837000 rw-p 00036000 fd:00 2104771 /usr/lib64/libgslcblas.so.0.0.0
   39f7200000-39f7216000 r-xp 00000000 fd:00 59507126 /lib64/libgcc_s-4.4.6-20120305.so.1
   39f7216000-39f7415000 ---p 00016000 fd:00 59507126 /lib64/libgcc_s-4.4.6-20120305.so.1
   39f7415000-39f7416000 rw-p 00015000 fd:00 59507126 /lib64/libgcc_s-4.4.6-20120305.so.1
   7f2cfde58000-7f2cfde5c000 rw-p 00000000 00:00 0
   7f2cfde66000-7f2cfde71000 rw-p 00000000 00:00 0
   7fff68d60000-7fff68d76000 rw-p 00000000 00:00 0 [stack]
   7fff68dd2000-7fff68dd3000 r-xp 00000000 00:00 0 [vdso]
   ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
   Abortado

Thanks,
KosAL

[KosAL]

[Saurabh Gupta]

Hi KosAL,

I believe the ref.fasta path that you are giving is very big, currently SInC only supports length filename(including path) as 100. Please softlink the ref.fasta in the folder from where you are running SInC and give absolute path. This should work. If any other issues let me know.