double free or corruption

[blahah]

Probably caused by my shoddy TPM hack...

You are using eXpress v1.5.0, which is the most recent release.

2013-Nov-25 18:12:50 - Attempting to read 'snapout.sam' in BAM format...
2013-Nov-25 18:12:50 - Input is not in BAM format. Trying SAM...
2013-Nov-25 18:12:50 - Loading target sequences and measuring bias background...

2013-Nov-25 18:13:11 - Processing input fragment alignments...
2013-Nov-25 18:13:13 - COMPLETED: Processed 25261 mapped fragments, targets are in 49061 bundles.
2013-Nov-25 18:13:13 - WARNING: Not enough fragments observed to accurately learn bias parameters. Either disable bias correction (--no-bias-correct) or provide a file containing auxiliary parameters (--aux-param-file).
2013-Nov-25 18:13:13 - Writing results to file...
2013-Nov-25 18:13:14 - Done.
*** Error in `/home/rds45/apps/express-1.5.0-linux_x86_64/express': double free or corruption (out): 0x0000000002f39b20 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x80a46)[0x7fee74f10a46]
/home/rds45/apps/express-1.5.0-linux_x86_64/express(_ZN13MismatchTableD1Ev+0x6a)[0x4e843a]
/home/rds45/apps/express-1.5.0-linux_x86_64/express(_ZN5boost6detail17sp_counted_impl_pI13MismatchTableE7disposeEv+0x12)[0x4e84d2]
/home/rds45/apps/express-1.5.0-linux_x86_64/express(_ZN7LibraryD1Ev+0x15a)[0x4e0bba]
/home/rds45/apps/express-1.5.0-linux_x86_64/express(_ZNSt6vectorI7LibrarySaIS0_EED1Ev+0x1b)[0x4e0eab]
/home/rds45/apps/express-1.5.0-linux_x86_64/express(_Z15estimation_mainv+0x10fc)[0x4de4cc]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7fee74eb1ea5]
/home/rds45/apps/express-1.5.0-linux_x86_64/express(_ZNSt15basic_streambufIcSt11char_traitsIcEE6xsputnEPKcl+0x61)[0x48e179]
======= Memory map: ========
00400000-00640000 r-xp 00000000 08:01 51643144                           /home/rds45/apps/express-1.5.0-linux_x86_64/express
00840000-00843000 rw-p 00240000 08:01 51643144                           /home/rds45/apps/express-1.5.0-linux_x86_64/express
00843000-00844000 rw-p 00000000 00:00 0
02831000-2d235000 rw-p 00000000 00:00 0                                  [heap]
7fee6c000000-7fee6c23c000 rw-p 00000000 00:00 0
7fee6c23c000-7fee70000000 ---p 00000000 00:00 0
7fee73c4f000-7fee73c50000 ---p 00000000 00:00 0
7fee73c50000-7fee74650000 rw-p 00000000 00:00 0
7fee74650000-7fee74666000 r-xp 00000000 08:01 13897435                   /lib/x86_64-linux-gnu/libresolv-2.17.so
7fee74666000-7fee74866000 ---p 00016000 08:01 13897435                   /lib/x86_64-linux-gnu/libresolv-2.17.so
7fee74866000-7fee74867000 r--p 00016000 08:01 13897435                   /lib/x86_64-linux-gnu/libresolv-2.17.so
7fee74867000-7fee74868000 rw-p 00017000 08:01 13897435                   /lib/x86_64-linux-gnu/libresolv-2.17.so
7fee74868000-7fee7486a000 rw-p 00000000 00:00 0
7fee74870000-7fee74876000 r-xp 00000000 08:01 13897388                   /lib/x86_64-linux-gnu/libnss_dns-2.17.so
7fee74876000-7fee74a75000 ---p 00006000 08:01 13897388                   /lib/x86_64-linux-gnu/libnss_dns-2.17.so
7fee74a75000-7fee74a76000 r--p 00005000 08:01 13897388                   /lib/x86_64-linux-gnu/libnss_dns-2.17.so
7fee74a76000-7fee74a77000 rw-p 00006000 08:01 13897388                   /lib/x86_64-linux-gnu/libnss_dns-2.17.so
7fee74a78000-7fee74a7a000 r-xp 00000000 08:01 13893671                   /lib/libnss_mdns4_minimal.so.2
7fee74a7a000-7fee74c79000 ---p 00002000 08:01 13893671                   /lib/libnss_mdns4_minimal.so.2
7fee74c79000-7fee74c7a000 r--p 00001000 08:01 13893671                   /lib/libnss_mdns4_minimal.so.2
7fee74c7a000-7fee74c7b000 rw-p 00002000 08:01 13893671                   /lib/libnss_mdns4_minimal.so.2
7fee74c80000-7fee74c8c000 r-xp 00000000 08:01 13897390                   /lib/x86_64-linux-gnu/libnss_files-2.17.so
7fee74c8c000-7fee74e8b000 ---p 0000c000 08:01 13897390                   /lib/x86_64-linux-gnu/libnss_files-2.17.so
7fee74e8b000-7fee74e8c000 r--p 0000b000 08:01 13897390                   /lib/x86_64-linux-gnu/libnss_files-2.17.so
7fee74e8c000-7fee74e8d000 rw-p 0000c000 08:01 13897390                   /lib/x86_64-linux-gnu/libnss_files-2.17.so
7fee74e90000-7fee7504e000 r-xp 00000000 08:01 13897317                   /lib/x86_64-linux-gnu/libc-2.17.so
7fee7504e000-7fee7524d000 ---p 001be000 08:01 13897317                   /lib/x86_64-linux-gnu/libc-2.17.so
7fee7524d000-7fee75251000 r--p 001bd000 08:01 13897317                   /lib/x86_64-linux-gnu/libc-2.17.so
7fee75251000-7fee75253000 rw-p 001c1000 08:01 13897317                   /lib/x86_64-linux-gnu/libc-2.17.so
7fee75253000-7fee75258000 rw-p 00000000 00:00 0
7fee75258000-7fee7526c000 r-xp 00000000 08:01 13897342                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee7526c000-7fee7546c000 ---p 00014000 08:01 13897342                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee7546c000-7fee7546d000 r--p 00014000 08:01 13897342                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee7546d000-7fee7546e000 rw-p 00015000 08:01 13897342                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee75470000-7fee75573000 r-xp 00000000 08:01 13897365                   /lib/x86_64-linux-gnu/libm-2.17.so
7fee75573000-7fee75773000 ---p 00103000 08:01 13897365                   /lib/x86_64-linux-gnu/libm-2.17.so
7fee75773000-7fee75774000 r--p 00103000 08:01 13897365                   /lib/x86_64-linux-gnu/libm-2.17.so
7fee75774000-7fee75775000 rw-p 00104000 08:01 13897365                   /lib/x86_64-linux-gnu/libm-2.17.so
7fee75778000-7fee7585d000 r-xp 00000000 08:01 8396585                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7fee7585d000-7fee75a5c000 ---p 000e5000 08:01 8396585                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7fee75a5c000-7fee75a64000 r--p 000e4000 08:01 8396585                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7fee75a64000-7fee75a66000 rw-p 000ec000 08:01 8396585                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7fee75a66000-7fee75a7b000 rw-p 00000000 00:00 0
7fee75a80000-7fee75a98000 r-xp 00000000 08:01 13897429                   /lib/x86_64-linux-gnu/libpthread-2.17.so
7fee75a98000-7fee75c97000 ---p 00018000 08:01 13897429                   /lib/x86_64-linux-gnu/libpthread-2.17.so
7fee75c97000-7fee75c98000 r--p 00017000 08:01 13897429                   /lib/x86_64-linux-gnu/libpthread-2.17.so
7fee75c98000-7fee75c99000 rw-p 00018000 08:01 13897429                   /lib/x86_64-linux-gnu/libpthread-2.17.so
7fee75c99000-7fee75c9d000 rw-p 00000000 00:00 0
7fee75ca0000-7fee75cb6000 r-xp 00000000 08:01 13897470                   /lib/x86_64-linux-gnu/libz.so.1.2.7
7fee75cb6000-7fee75eb5000 ---p 00016000 08:01 13897470                   /lib/x86_64-linux-gnu/libz.so.1.2.7
7fee75eb5000-7fee75eb6000 r--p 00015000 08:01 13897470                   /lib/x86_64-linux-gnu/libz.so.1.2.7
7fee75eb6000-7fee75eb7000 rw-p 00016000 08:01 13897470                   /lib/x86_64-linux-gnu/libz.so.1.2.7
7fee75eb8000-7fee75edb000 r-xp 00000000 08:01 13897293                   /lib/x86_64-linux-gnu/ld-2.17.so
7fee760b7000-7fee760b8000 rw-p 00000000 00:00 0
7fee760d4000-7fee760da000 rw-p 00000000 00:00 0
7fee760da000-7fee760db000 r--p 00022000 08:01 13897293                   /lib/x86_64-linux-gnu/ld-2.17.so
7fee760db000-7fee760dd000 rw-p 00023000 08:01 13897293                   /lib/x86_64-linux-gnu/ld-2.17.so
7fee760dd000-7fee760e0000 rw-p 00000000 00:00 0
7fffe9b3e000-7fffe9f01000 rw-p 00000000 00:00 0                          [stack]
7fffe9f58000-7fffe9f5a000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Command terminated by signal 6

[blahah]

@adarob is this what you were fixing in c81799d2cca62378342b134fd4277f65c0fe4d25?

[blahah]

I take it back - it wasn't my TPM implementation :). I get the same error with v1.4.1.

[adarob]

Could you send me the input files that are producing this?