double free or corruption (!prev)

[sungkyu-kyung]

Hi, I have read paper of SViCT and tried to use this tool for my analysis.

The compilation was successful and ran this tool using cfDNA sample and the core dump has raised.

Command line I have used is shown below.

svict -i /path/to/my/sample.bam -r hg19.fa -o /path/to/my/sample

The error is shown below.

chrM
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
Assembling contigs...
chrchrM done
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
chrchr16 done
chrchr17 done
chrchr18 done
chrchr19 done
chrchr20 done
chrchr21 done
chrchr22 done
chrchrX done
chrchrY done
Processing 1 supplementary clusters...
Indexing contigs...
Generating intervals...
chrchrM done
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
*** Error in `/usr/bin/svict': double free or corruption (!prev): 0x000000005d109200 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7f437cc2a489]
/usr/bin/svict[0x42bd89]
/usr/bin/svict[0x433a18]
/usr/bin/svict[0x408b35]
/usr/bin/svict[0x4049f3]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f437cbcb3d5]
/usr/bin/svict[0x40505f]
======= Memory map: ========
00400000-0047c000 r-xp 00000000 fd:02 310083803 /usr/bin/svict
0067b000-0067c000 r--p 0007b000 fd:02 310083803 /usr/bin/svict
0067c000-0067d000 rw-p 0007c000 fd:02 310083803 /usr/bin/svict
0067d000-0067e000 rw-p 00000000 00:00 0
00a3c000-71c92000 rw-p 00000000 00:00 0 [heap]
7f4318000000-7f4318021000 rw-p 00000000 00:00 0
7f4318021000-7f431c000000 ---p 00000000 00:00 0
7f431dd97000-7f43233c3000 rw-p 00000000 00:00 0
7f432958c000-7f437cba9000 rw-p 00000000 00:00 0
7f437cba9000-7f437cd6b000 r-xp 00000000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cd6b000-7f437cf6b000 ---p 001c2000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cf6b000-7f437cf6f000 r--p 001c2000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cf6f000-7f437cf71000 rw-p 001c6000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cf71000-7f437cf76000 rw-p 00000000 00:00 0
7f437cf76000-7f437cf8b000 r-xp 00000000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437cf8b000-7f437d18a000 ---p 00015000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437d18a000-7f437d18b000 r--p 00014000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437d18b000-7f437d18c000 rw-p 00015000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437d18c000-7f437d28d000 r-xp 00000000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d28d000-7f437d48c000 ---p 00101000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d48c000-7f437d48d000 r--p 00100000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d48d000-7f437d48e000 rw-p 00101000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d48e000-7f437d577000 r-xp 00000000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d577000-7f437d776000 ---p 000e9000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d776000-7f437d77e000 r--p 000e8000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d77e000-7f437d780000 rw-p 000f0000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d780000-7f437d795000 rw-p 00000000 00:00 0
7f437d795000-7f437d7ac000 r-xp 00000000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d7ac000-7f437d9ab000 ---p 00017000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d9ab000-7f437d9ac000 r--p 00016000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d9ac000-7f437d9ad000 rw-p 00017000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d9ad000-7f437d9b1000 rw-p 00000000 00:00 0
7f437d9b1000-7f437d9c6000 r-xp 00000000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437d9c6000-7f437dbc5000 ---p 00015000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437dbc5000-7f437dbc6000 r--p 00014000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437dbc6000-7f437dbc7000 rw-p 00015000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437dbc7000-7f437dbe9000 r-xp 00000000 fd:00 1616418 /usr/lib64/ld-2.17.so
7f437ddc7000-7f437ddcd000 rw-p 00000000 00:00 0
7f437dde5000-7f437dde8000 rw-p 00000000 00:00 0
7f437dde8000-7f437dde9000 r--p 00021000 fd:00 1616418 /usr/lib64/ld-2.17.so
7f437dde9000-7f437ddea000 rw-p 00022000 fd:00 1616418 /usr/lib64/ld-2.17.so
7f437ddea000-7f437ddeb000 rw-p 00000000 00:00 0
7fffb071b000-7fffb073c000 rw-p 00000000 00:00 0 [stack]
7fffb07ed000-7fffb07ef000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

Thanks

[esamorodnitsky]

Hi, I have a question. Did you ever solve this issue? I got the same issue myself. I ran 68 samples and got this error on one of them. I am scratching my head here. Any help would be much appreciated.

[esamorodnitsky]

I got around this by changing the -s flag from 2 to 3.