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vpc-ccg / svict

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA
BSD 3-Clause "New" or "Revised" License
25 stars 6 forks source link

double free or corruption (!prev) #14

Open sungkyu-kyung opened 5 years ago

sungkyu-kyung commented 5 years ago

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 commented 2 years ago

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 commented 2 years ago

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