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vice87 / gam-ngs

Genomic Assemblies Merger for NGS
GNU General Public License v3.0
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free(): invalid pointer error #10

Open NikiBe opened 10 years ago

NikiBe commented 10 years ago

Hi,

When running gam-create I get the error below. I have also copied the output of 'gdb backtrace' at the bottom of this issue. Does anyone have an idea how to solve this problem? It is a pretty large dataset (genome of ~3 Gbp) so memory limitations may play a role. However, the systems' memory use (>500 Gb RAM) was not at its limit (only ~20% was in use when the error occurred).

Thanks for your help!

* glibc detected * /gam-ngs/bin/gam-create: free(): invalid pointer: 0x00000000006ffce0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x33af276126] /usr/lib64/libstdc++.so.6(_ZNSs6assignERKSs+0x85)[0x33b929d565] /gam-ngs/bin/gam-create(ZN8BamTools12BamAlignmentaSERKS0+0x23)[0x462325] /gam-ngs/bin/gam-create(_ZN14MultiBamReader16GetNextAlignmentERN8BamTools12BamAlignmentEb+0x105)[0x4744e3] /gam-ngs/bin/gam-create(_ZN5Block10findBlocksERSt6vectorIS_SaIS_EER14MultiBamReaderiRN6google15sparse_hash_mapISs4ReadNSt3tr14hashISsEESt8equal_toISsENS6_27libc_allocator_with_reallocISt4pairIKSsS8_EEEEESK_RS0_IS0_IjSaIjEESaISM_EE+0x9c8)[0x46cc78] /gam-ngs/bin/gam-create(_ZN7modules12CreateBlocks7executeEv+0x61d)[0x452585] /gam-ngs/bin/gam-create(main+0x4e)[0x4510e2] /lib64/libc.so.6(__libc_start_main+0xfd)[0x33af21ecdd] /gam-ngs/bin/gam-create[0x450fd9] ======= Memory map: ======== 00400000-004d8000 r-xp 00000000 08:11 35652018 /gam-ngs/bin/gam-create 006d8000-006da000 rw-p 000d8000 08:11 35652018 /gam-ngs/bin/gam-create 006da000-24861f9000 rw-p 00000000 00:00 0 [heap] 33aea00000-33aea20000 r-xp 00000000 fd:00 1451235 /lib64/ld-2.12.so ... .... Program received signal SIGABRT, Aborted. 0x00000033af2328e5 in raise () from /lib64/libc.so.6

Running gdb backtrace resulted in the following:

(gdb) backtrace

0 0x00000033af2328e5 in raise () from /lib64/libc.so.6

1 0x00000033af2340c5 in abort () from /lib64/libc.so.6

2 0x00000033af2707f7 in __libc_message () from /lib64/libc.so.6

3 0x00000033af276126 in malloc_printerr () from /lib64/libc.so.6

4 0x00000033b929d565 in std::basic_string<char, std::char_traits, std::allocator >::assign(std::basic_string<char, std::char_traits, std::allocator > const&) () from /usr/lib64/libstdc++.so.6

5 0x0000000000462325 in BamTools::BamAlignment::operator= (this=0x7fffffffd8b0) at /gam-ngs/lib/bamtools-2.0.5/src/api/BamAlignment.h:32

6 0x00000000004744e3 in MultiBamReader::GetNextAlignment (this=0x7fffffffdc00, align=..., update_stats=true) at /gam-ngs/lib/src/bam/MultiBamReader.cc:323

7 0x000000000046cc78 in Block::findBlocks (outblocks=std::vector of length 3574546, capacity 4194304 = {...}, bamReader=..., minBlockSize=10, readsMap_1=..., readsMap_2=...,

coverage=std::vector of length 177072, capacity 177072 = {...}) at /gam-ngs/lib/src/assembly/Block.cc:495

8 0x0000000000452585 in modules::CreateBlocks::execute (this=0x7fffffffe1b0) at /gam-ngs/src/CreateBlocks.cc:141

9 0x00000000004510e2 in main (argc=9, argv=0x7fffffffe2c8) at /gam-ngs/src/gam-create.cc:49

vice87 commented 10 years ago

I'm sorry for replying so late. I've updated the source code with a recent version of the library used to handle BAMs. Hopefully, this fixed the problem.