[mira_talk] GAP5 tg_index buffer overfow detected

  • From: Juan Daniel Montenegro Cabrera <jdmontenegroc@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sun, 30 Oct 2011 12:08:56 -0500

Dear all,

I have just installed the latest realease of the Staden Package which
includes GAP5.
However after filtering the caf file I try tg_index and found this problem:

g_index: Short Read Alignment Indexer, version 1.2.11

Author: James Bonfield (jkb@xxxxxxxxxxxx)
         2007-2011, Wellcome Trust Sanger Institute

Selecting output database filename 11A_50X_CJ_F.0
Processing CAF file 11A_50X_CJ_F.caf
Loading 11A_50X_CJ_F.caf...
Input summary
Reads 16076
Quality 16082
Contigs 6
Bases 16082
R + C 16082
Indexed in 0.169169 seconds
Loading ...
*** buffer overflow detected ***: tg_index.bin terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f9b83c881d7]
/lib/x86_64-linux-gnu/libc.so.6(+0xfd0f0)[0x7f9b83c870f0]
/usr/local/bin/../lib/staden/libtgap.so(contig_set_name+0x84)[0x7f9b8638b9c4]
/usr/local/bin/../lib/staden/libtgap.so(contig_new+0x89)[0x7f9b8638bb99]
/usr/local/bin/../lib/staden/libgap5.so(create_new_contig+0x7b)[0x7f9b85c4225b]
/usr/local/bin/../lib/staden/libgap5.so(parse_caf+0x417)[0x7f9b85c4d677]
tg_index.bin(main+0x6e5)[0x401c65]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7f9b83ba8eff]
tg_index.bin[0x4010a9]
======= Memory map: ========
00400000-00403000 r-xp 00000000 08:04 17401915
/usr/local/bin/tg_index.bin
00603000-00604000 r--p 00003000 08:04 17401915
/usr/local/bin/tg_index.bin
00604000-00605000 rw-p 00004000 08:04 17401915
/usr/local/bin/tg_index.bin
023bc000-02422000 rw-p 00000000 00:00 0
 [heap]
7f9b82a1c000-7f9b82a31000 r-xp 00000000 08:04 20725836
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9b82a31000-7f9b82c30000 ---p 00015000 08:04 20725836
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9b82c30000-7f9b82c31000 r--p 00014000 08:04 20725836
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9b82c31000-7f9b82c32000 rw-p 00015000 08:04 20725836
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9b82c56000-7f9b8311c000 rw-p 00000000 00:00 0
7f9b8311c000-7f9b83121000 r-xp 00000000 08:04 17203755
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f9b83121000-7f9b83320000 ---p 00005000 08:04 17203755
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f9b83320000-7f9b83321000 r--p 00004000 08:04 17203755
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f9b83321000-7f9b83322000 rw-p 00005000 08:04 17203755
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f9b83322000-7f9b83324000 r-xp 00000000 08:04 17203739
/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f9b83324000-7f9b83523000 ---p 00002000 08:04 17203739
/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f9b83523000-7f9b83524000 r--p 00001000 08:04 17203739
/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f9b83524000-7f9b83525000 rw-p 00002000 08:04 17203739
/usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f9b83525000-7f9b83540000 r-xp 00000000 08:04 17203763
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f9b83540000-7f9b8373f000 ---p 0001b000 08:04 17203763
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f9b8373f000-7f9b83740000 r--p 0001a000 08:04 17203763
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f9b83740000-7f9b83741000 rw-p 0001b000 08:04 17203763
/usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f9b83741000-7f9b83767000 r-xp 00000000 08:04 20725826
/lib/x86_64-linux-gnu/libpng12.so.0.44.0
7f9b83767000-7f9b83966000 ---p 00026000 08:04 20725826
/lib/x86_64-linux-gnu/libpng12.so.0.44.0
7f9b83966000-7f9b83967000 r--p 00025000 08:04 20725826
/lib/x86_64-linux-gnu/libpng12.so.0.44.0
7f9b83967000-7f9b83968000 rw-p 00026000 08:04 20725826
/lib/x86_64-linux-gnu/libpng12.so.0.44.0
7f9b83968000-7f9b83989000 r-xp 00000000 08:04 17091021
/usr/lib/liblzma.so.2.0.0
7f9b83989000-7f9b83b88000 ---p 00021000 08:04 17091021
/usr/lib/liblzma.so.2.0.0
7f9b83b88000-7f9b83b89000 r--p 00020000 08:04 17091021
/usr/lib/liblzma.so.2.0.0
7f9b83b89000-7f9b83b8a000 rw-p 00021000 08:04 17091021
/usr/lib/liblzma.so.2.0.0
7f9b83b8a000-7f9b83d14000 r-xp 00000000 08:04 20725835
/lib/x86_64-linux-gnu/libc-2.13.so
7f9b83d14000-7f9b83f13000 ---p 0018a000 08:04 20725835
/lib/x86_64-linux-gnu/libc-2.13.so
7f9b83f13000-7f9b83f17000 r--p 00189000 08:04 20725835
/lib/x86_64-linux-gnu/libc-2.13.so
7f9b83f17000-7f9b83f18000 rw-p 0018d000 08:04 20725835
/lib/x86_64-linux-gnu/libc-2.13.so
7f9b83f18000-7f9b83f1e000 rw-p 00000000 00:00 0
7f9b83f1e000-7f9b83f51000 r-xp 00000000 08:04 17401326
/usr/local/lib/libstaden-read.so.1.1.3
7f9b83f51000-7f9b84150000 ---p 00033000 08:04 17401326
/usr/local/lib/libstaden-read.so.1.1.3
7f9b84150000-7f9b84151000 r--p 00032000 08:04 17401326
/usr/local/lib/libstaden-read.so.1.1.3
7f9b84151000-7f9b84155000 rw-p 00033000 08:04 17401326
/usr/local/lib/libstaden-read.so.1.1.3
7f9b84155000-7f9b84198000 rw-p 00000000 00:00 0
7f9b84198000-7f9b841a1000 r-xp 00000000 08:04 18106572
/usr/local/lib/staden/libmisc.so
7f9b841a1000-7f9b843a0000 ---p 00009000 08:04 18106572
/usr/local/lib/staden/libmisc.so
7f9b843a0000-7f9b843a1000 r--p 00008000 08:04 18106572
/usr/local/lib/staden/libmisc.so
7f9b843a1000-7f9b843a2000 rw-p 00009000 08:04 18106572
/usr/local/lib/staden/libmisc.so
7f9b843a2000-7f9b843a4000 rw-p 00000000 00:00 0
7f9b843a4000-7f9b84428000 r-xp 00000000 08:04 20725860
/lib/x86_64-linux-gnu/libm-2.13.so
7f9b84428000-7f9b84627000 ---p 00084000 08:04 20725860
/lib/x86_64-linux-gnu/libm-2.13.so
7f9b84627000-7f9b84628000 r--p 00083000 08:04 20725860
/lib/x86_64-linux-gnu/libm-2.13.so
7f9b84628000-7f9b84629000 rw-p 00084000 08:04 20725860
/lib/x86_64-linux-gnu/libm-2.13.so
7f9b84629000-7f9b84641000 r-xp 00000000 08:04 20725897
/lib/x86_64-linux-gnu/libpthread-2.13.so
7f9b84641000-7f9b84841000 ---p 00018000 08:04 20725897
/lib/x86_64-linux-gnu/libpthread-2.13.so
7f9b84841000-7f9b84842000 r--p 00018000 08:04 20725897
/lib/x86_64-linux-gnu/libpthread-2.13.so
7f9b84842000-7f9b84843000 rw-p 00019000 08:04 20725897
/lib/x86_64-linux-gnu/libpthread-2.13.so
7f9b84843000-7f9b84847000 rw-p 00000000 00:00 0
7f9b84847000-7f9b84849000 r-xp 00000000 08:04 20725854
/lib/x86_64-linux-gnu/libdl-2.13.so
7f9b84849000-7f9b84a49000 ---p 00002000 08:04 20725854
/lib/x86_64-linux-gnu/libdl-2.13.sozsh: abort      tg_index -C
11A_50X_CJ_F.caf

Do you have any idea how to solve this?

What is going on? Sorrry for such a long mail.

Regards,

Juan Montenegro

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