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vice87 / gam-ngs

Genomic Assemblies Merger for NGS
GNU General Public License v3.0
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Issue with gam-merge: ***glibc detected*** #13

Closed skyvic234 closed 9 years ago

skyvic234 commented 10 years ago

My run of gam-merge terminated with errors of "* glibc detected * /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge: free(): invalid". Ran the test data set through and worked fine. I have no idea why it happens. Here is the debugging output. Can you give me some clues on how to fix the bug? Thank you.

[main] Loading blocks [main] Loaded blocks = 382 [main] Loading BAMs data [bam] Master PE-alignments file soap.txt successfully opened: /backup/Gene/ssun/MH/S2_block/merge/chr01/1/short.srt.bam inserts size = 273.199 +/- 36.545 coverage = 75.9661 [bam] Slave PE-alignments file masu.txt successfully opened: /backup/Gene/ssun/MH/S2_block/merge/chr01/1/masu.short.srt.bam inserts size = 273.432 +/- 36.5705 coverage = 78.0621 [main] Loading contigs data * glibc detected * /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge: free(): invalid next size (fast): 0x0000000000f4b1e0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3d9747174f] /lib64/libc.so.6(cfree+0x4b)[0x3d97475a4b] /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge(_Z18getNoBlocksContigsRKSt6vectorI11reference_tSaIS0_EES4_RKSt4listI5BlockSaIS6EERSt3setIiSt4lessIiESaIiEESG+0x625)[0x460a15] /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge(_ZN7modules5Merge7executeEv+0x1510)[0x4395b0] /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge(main+0x2f)[0x437e4f] /lib64/libc.so.6(libc_start_main+0xf4)[0x3d9741d9c4] /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge(gxx_personality_v0+0x199)[0x436bc9] ======= Memory map: ======== 00400000-00500000 r-xp 00000000 00:18 1124997048 /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge 00700000-00702000 rw-p 00100000 00:18 1124997048 /backup/Gene/wbjiao/usr/gam-ngs/bin/gam-merge 00702000-00703000 rw-p 00702000 00:00 0 00f0b000-00fc1000 rw-p 00f0b000 00:00 0 [heap] 3d97000000-3d9701c000 r-xp 00000000 08:03 49217862 /lib64/ld-2.5.so 3d9721c000-3d9721d000 r--p 0001c000 08:03 49217862 /lib64/ld-2.5.so 3d9721d000-3d9721e000 rw-p 0001d000 08:03 49217862 /lib64/ld-2.5.so 3d97400000-3d9754f000 r-xp 00000000 08:03 49217863 /lib64/libc-2.5.so 3d9754f000-3d9774f000 ---p 0014f000 08:03 49217863 /lib64/libc-2.5.so 3d9774f000-3d97753000 r--p 0014f000 08:03 49217863 /lib64/libc-2.5.so 3d97753000-3d97754000 rw-p 00153000 08:03 49217863 /lib64/libc-2.5.so 3d97754000-3d97759000 rw-p 3d97754000 00:00 0 3d97c00000-3d97c16000 r-xp 00000000 08:03 49217869 /lib64/libpthread-2.5.so 3d97c16000-3d97e16000 ---p 00016000 08:03 49217869 /lib64/libpthread-2.5.so 3d97e16000-3d97e17000 r--p 00016000 08:03 49217869 /lib64/libpthread-2.5.so 3d97e17000-3d97e18000 rw-p 00017000 08:03 49217869 /lib64/libpthread-2.5.so 3d97e18000-3d97e1c000 rw-p 3d97e18000 00:00 0 3d98000000-3d98082000 r-xp 00000000 08:03 49217868 /lib64/libm-2.5.so 3d98082000-3d98281000 ---p 00082000 08:03 49217868 /lib64/libm-2.5.so 3d98281000-3d98282000 r--p 00081000 08:03 49217868 /lib64/libm-2.5.so 3d98282000-3d98283000 rw-p 00082000 08:03 49217868 /lib64/libm-2.5.so 3d98400000-3d98414000 r-xp 00000000 08:03 49217875 /lib64/libz.so.1.2.3 3d98414000-3d98613000 ---p 00014000 08:03 49217875 /lib64/libz.so.1.2.3 3d98613000-3d98614000 rw-p 00013000 08:03 49217875 /lib64/libz.so.1.2.3 3d98800000-3d98807000 r-xp 00000000 08:03 49217870 /lib64/librt-2.5.so 3d98807000-3d98a07000 ---p 00007000 08:03 49217870 /lib64/librt-2.5.so 3d98a07000-3d98a08000 r--p 00007000 08:03 49217870 /lib64/librt-2.5.so 3d98a08000-3d98a09000 rw-p 00008000 08:03 49217870 /lib64/librt-2.5.so 3d99400000-3d9940d000 r-xp 00000000 08:03 49217866 /lib64/libgcc_s-4.1.2-20080825.so.1 3d9940d000-3d9960d000 ---p 0000d000 08:03 49217866 /lib64/libgcc_s-4.1.2-20080825.so.1 3d9960d000-3d9960e000 rw-p 0000d000 08:03 49217866 /lib64/libgcc_s-4.1.2-20080825.so.1 2ad91dac6000-2ad91dac9000 rw-p 2ad91dac6000 00:00 0 2ad91dac9000-2ad91db28000 r-xp 00000000 00:18 1126303879 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_graph.so.1.55.0 2ad91db28000-2ad91dd27000 ---p 0005f000 00:18 1126303879 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_graph.so.1.55.0 2ad91dd27000-2ad91dd2b000 rw-p 0005e000 00:18 1126303879 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_graph.so.1.55.0 2ad91dd2b000-2ad91dd92000 r-xp 00000000 00:18 1126304489 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_program_options.so.1.55.0 2ad91dd92000-2ad91df92000 ---p 00067000 00:18 1126304489 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_program_options.so.1.55.0 2ad91df92000-2ad91df96000 rw-p 00067000 00:18 1126304489 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_program_options.so.1.55.0 2ad91df96000-2ad91df97000 rw-p 2ad91df96000 00:00 0 2ad91df97000-2ad91df9a000 r-xp 00000000 00:18 1126303596 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_system.so.1.55.0 2ad91df9a000-2ad91e199000 ---p 00003000 00:18 1126303596 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_system.so.1.55.0 2ad91e199000-2ad91e19a000 rw-p 00002000 00:18 1126303596 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_system.so.1.55.0 2ad91e19a000-2ad91e1af000 r-xp 00000000 00:18 1126303796 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_filesystem.so.1.55.0 2ad91e1af000-2ad91e3af000 ---p 00015000 00:18 1126303796 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_filesystem.so.1.55.0 2ad91e3af000-2ad91e3b0000 rw-p 00015000 00:18 1126303796 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_filesystem.so.1.55.0 2ad91e3b0000-2ad91e49a000 r-xp 00000000 00:18 1232866104 /backup/Gene/local/gcc/lib64/libstdc++.so.6.0.17 2ad91e49a000-2ad91e699000 ---p 000ea000 00:18 1232866104 /backup/Gene/local/gcc/lib64/libstdc++.so.6.0.17 2ad91e699000-2ad91e6a1000 r--p 000e9000 00:18 1232866104 /backup/Gene/local/gcc/lib64/libstdc++.so.6.0.17 2ad91e6a1000-2ad91e6a3000 rw-p 000f1000 00:18 1232866104 /backup/Gene/local/gcc/lib64/libstdc++.so.6.0.17 2ad91e6a3000-2ad91e6ba000 rw-p 2ad91e6a3000 00:00 0 2ad91e6ba000-2ad91e7ab000 r-xp 00000000 00:18 1126303844 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_regex.so.1.55.0 2ad91e7ab000-2ad91e9aa000 ---p 000f1000 00:18 1126303844 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_regex.so.1.55.0 2ad91e9aa000-2ad91e9b0000 rw-p 000f0000 00:18 1126303844 /backup/Gene/wbjiao/usr/boost1.55/lib/libboost_regex.so.1.55.0 2ad91e9b0000-2ad91edb4000 rw-p 2ad91e9b0000 00:00 0 7fff85a12000-7fff85a28000 rw-p 7ffffffe8000 00:00 0 [stack] 7fff85b63000-7fff85b66000 r-xp 7fff85b63000 00:00 0 [vdso] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vsyscall] Aborted

vice87 commented 9 years ago

This issue should have been fixed in the last release.