Problem with clone_filter

[Jon Puritz]

Hi,

Clone_filter is spitting out this error on some of our files, though it works fine for several others:

Reading data from:

  forward1 and

  reverse1

Writing data to:

  ./forward1.fil.fq_1 and

  ./reverse1.fil.fq_2

*** glibc detected *** clone_filter: malloc(): memory corruption (fast): 0x0000000000bec830 ***

======= Backtrace: =========

/lib64/libc.so.6(+0x76126)[0x7f9a54d29126]

/lib64/libc.so.6(+0x79edf)[0x7f9a54d2cedf]

/lib64/libc.so.6(__libc_malloc+0x71)[0x7f9a54d2d951]

/usr/lib64/libstdc++.so.6(_Znwm+0x1d)[0x37bdcbd0bd]

clone_filter[0x407793]

clone_filter[0x407b20]

clone_filter[0x407caa]

clone_filter[0x409388]

clone_filter[0x405e7f]

/lib64/libc.so.6(__libc_start_main+0xfd)[0x7f9a54cd1cdd]

clone_filter[0x402879]

======= Memory map: ========

00400000-00411000 r-xp 00000000 fd:00 2000299                            /usr/local/bin/clone_filter

00610000-00611000 rw-p 00010000 fd:00 2000299                            /usr/local/bin/clone_filter

00611000-00612000 rw-p 00000000 00:00 0 

00bdd000-00bfe000 rw-p 00000000 00:00 0                                  [heap]

3589400000-358940d000 r-xp 00000000 fd:00 2002316                        /usr/lib64/libgomp.so.1.0.0

358940d000-358960c000 ---p 0000d000 fd:00 2002316                        /usr/lib64/libgomp.so.1.0.0

358960c000-358960d000 rw-p 0000c000 fd:00 2002316                        /usr/lib64/libgomp.so.1.0.0

37b2000000-37b2015000 r-xp 00000000 fd:00 1180079                        /lib64/libz.so.1.2.3

37b2015000-37b2214000 ---p 00015000 fd:00 1180079                        /lib64/libz.so.1.2.3

37b2214000-37b2215000 r--p 00014000 fd:00 1180079                        /lib64/libz.so.1.2.3

37b2215000-37b2216000 rw-p 00015000 fd:00 1180079                        /lib64/libz.so.1.2.3

37bc000000-37bc016000 r-xp 00000000 fd:00 1180105                        /lib64/libgcc_s-4.4.6-20110824.so.1

37bc016000-37bc215000 ---p 00016000 fd:00 1180105                        /lib64/libgcc_s-4.4.6-20110824.so.1

37bc215000-37bc216000 rw-p 00015000 fd:00 1180105                        /lib64/libgcc_s-4.4.6-20110824.so.1

37bdc00000-37bdce8000 r-xp 00000000 fd:00 1996589                        /usr/lib64/libstdc++.so.6.0.13

37bdce8000-37bdee8000 ---p 000e8000 fd:00 1996589                        /usr/lib64/libstdc++.so.6.0.13

37bdee8000-37bdeef000 r--p 000e8000 fd:00 1996589                        /usr/lib64/libstdc++.so.6.0.13

37bdeef000-37bdef1000 rw-p 000ef000 fd:00 1996589                        /usr/lib64/libstdc++.so.6.0.13

37bdef1000-37bdf06000 rw-p 00000000 00:00 0 

7f9a5488e000-7f9a54895000 r-xp 00000000 fd:00 1179721                    /lib64/librt-2.12.so

7f9a54895000-7f9a54a94000 ---p 00007000 fd:00 1179721                    /lib64/librt-2.12.so

7f9a54a94000-7f9a54a95000 r--p 00006000 fd:00 1179721                    /lib64/librt-2.12.so

7f9a54a95000-7f9a54a96000 rw-p 00007000 fd:00 1179721                    /lib64/librt-2.12.so

7f9a54a96000-7f9a54aad000 r-xp 00000000 fd:00 1179684                    /lib64/libpthread-2.12.so

7f9a54aad000-7f9a54cad000 ---p 00017000 fd:00 1179684                    /lib64/libpthread-2.12.so

7f9a54cad000-7f9a54cae000 r--p 00017000 fd:00 1179684                    /lib64/libpthread-2.12.so

7f9a54cae000-7f9a54caf000 rw-p 00018000 fd:00 1179684                    /lib64/libpthread-2.12.so

7f9a54caf000-7f9a54cb3000 rw-p 00000000 00:00 0 

7f9a54cb3000-7f9a54e3d000 r-xp 00000000 fd:00 1179660                    /lib64/libc-2.12.so

7f9a54e3d000-7f9a5503c000 ---p 0018a000 fd:00 1179660                    /lib64/libc-2.12.so

7f9a5503c000-7f9a55040000 r--p 00189000 fd:00 1179660                    /lib64/libc-2.12.so

7f9a55040000-7f9a55041000 rw-p 0018d000 fd:00 1179660                    /lib64/libc-2.12.so

7f9a55041000-7f9a55046000 rw-p 00000000 00:00 0 

7f9a55046000-7f9a550c9000 r-xp 00000000 fd:00 1179712                    /lib64/libm-2.12.so

7f9a550c9000-7f9a552c8000 ---p 00083000 fd:00 1179712                    /lib64/libm-2.12.so

7f9a552c8000-7f9a552c9000 r--p 00082000 fd:00 1179712                    /lib64/libm-2.12.so

7f9a552c9000-7f9a552ca000 rw-p 00083000 fd:00 1179712                    /lib64/libm-2.12.so

7f9a552ca000-7f9a552ea000 r-xp 00000000 fd:00 1179783                    /lib64/ld-2.12.so

7f9a554c6000-7f9a554cd000 rw-p 00000000 00:00 0 

7f9a554e7000-7f9a554e9000 rw-p 00000000 00:00 0 

7f9a554e9000-7f9a554ea000 r--p 0001f000 fd:00 1179783                    /lib64/ld-2.12.so

7f9a554ea000-7f9a554eb000 rw-p 00020000 fd:00 1179783                    /lib64/ld-2.12.so

7f9a554eb000-7f9a554ec000 rw-p 00000000 00:00 0 

7fffd9f50000-7fffd9f65000 rw-p 00000000 00:00 0                          [stack]

7fffd9fff000-7fffda000000 r-xp 00000000 00:00 0                          [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Aborted (core dumped)

[Julian Catchen]

Hi Jon,

Can you create a set of test files that can reproduce the error (the smaller the
better) and make them available by email or by Dropbox? I'll debug it if you can.

julian