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Published 20 hours ago • verified publisher icon gt1

bamsort crash at libmaus2::lz::BgzfDeflateParallel::flush

Open mmokrejs opened this issue 6 years ago • 4 comments

Hi, current git master checkout crashes for me (well even previous versions).

   repository:               https://github.com/gt1/libmaus2.git
   at the commit:            694c2180076cd5986fea0532b057065f905d49b5

   repository:               https://github.com/gt1/biobambam2.git
   at the commit:            5798e74558e001e33855cb93cc8bf149344b931d

LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE==1m

export LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE

bamsort SO=queryname inputthreads=10 outputthreads=40 level=9 index=1 O=HFYJ5AFXX.5kb.fragments-6.namesorted.bam I=HFYJ5AFXX.5kb.fragments-6.refsorted.bam
[V] Reading alignments from source.
[V] 1M
[V] 2M
[V] 3M
[V] 4M
[V] 5M
[V] 6M
[V] 7M
[V] 8M
[V] 9M
[V] 10M
[V] 11M
[V] 12M
[V] 13M
[V] 14M
[V] 15M
[V] 16M
[V] 17M
[V] 18M
[V] read 19175378 alignments
[V] producing sorted output
terminate called after throwing an instance of 'libmaus2::exception::LibMausException'
  what():  File is not sorted by coordinate.

/apps/gentoo/usr/lib64/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x68)[0x2aaaab59ef30]
bamsort(libmaus2::exception::LibMausException::LibMausException()+0x2b)[0x2aaaaab22dcb]
bamsort(+0xc37c5)[0x2aaaaab6e7c5]
bamsort(+0xc43e6)[0x2aaaaab6f3e6]
bamsort(+0x84479)[0x2aaaaab2f479]
bamsort(+0x8456b)[0x2aaaaab2f56b]
bamsort(+0x962ff)[0x2aaaaab412ff]
bamsort(libmaus2::parallel::PosixThread::dispatch(void*)+0x65)[0x2aaaaab2cac5]
/apps/gentoo/lib64/libpthread.so.0(+0x78b7)[0x2aaaac0ee8b7]
/apps/gentoo/lib64/libc.so.6(clone+0x3f)[0x2aaaad16644f]

Aborted                 (core dumped) bamsort SO=queryname inputthreads=10 outputthreads=40 level=9 index=1 O="$p".namesorted.bam I="$p".refsorted.bam

$ gdb /apps/gentoo/usr/bin/bamsort /ramdisk/7948775.isrv5/core.95405 
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-92.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /apps/gentoo/usr/bin/bamsort...done.
[New Thread 95405]
[New Thread 96708]
[New Thread 96732]
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Reading symbols from /apps/gentoo/usr/lib64/libmaus2.so.2...done.
Loaded symbols for /apps/gentoo/usr/lib64/libmaus2.so.2
Reading symbols from /apps/gentoo/usr/lib64/libmaus2_simd_align_128.so.2...done.
Loaded symbols for /apps/gentoo/usr/lib64/libmaus2_simd_align_128.so.2
Reading symbols from /apps/gentoo/usr/lib64/libmaus2_simd_align_256.so.2...done.
Loaded symbols for /apps/gentoo/usr/lib64/libmaus2_simd_align_256.so.2
Reading symbols from /apps/gentoo/lib64/libpthread.so.0...(no debugging symbols found)...done.
[Thread debugging using libthread_db enabled]
Loaded symbols for /apps/gentoo/lib64/libpthread.so.0
Reading symbols from /apps/gentoo/lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/lib64/libdl.so.2
Reading symbols from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libstdc++.so.6...done.
Loaded symbols for /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libstdc++.so.6
Reading symbols from /apps/gentoo/lib64/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/lib64/libm.so.6
Reading symbols from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgomp.so.1...done.
Loaded symbols for /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgomp.so.1
Reading symbols from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1...done.
Loaded symbols for /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1
Reading symbols from /apps/gentoo/lib64/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/lib64/libc.so.6
Reading symbols from /apps/gentoo/usr/lib64/libsnappy.so.1...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libsnappy.so.1
Reading symbols from /apps/gentoo/usr/lib64/libgnutls.so.30...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libgnutls.so.30
Reading symbols from /apps/gentoo/usr/lib64/libnettle.so.6...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libnettle.so.6
Reading symbols from /apps/gentoo/usr/lib64/libgmp.so.10...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libgmp.so.10
Reading symbols from /apps/gentoo/usr/lib64/liblzma.so.5...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/liblzma.so.5
Reading symbols from /apps/gentoo/lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/lib64/ld-linux-x86-64.so.2
Reading symbols from /apps/gentoo/usr/lib64/libz.so.1...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libz.so.1
Reading symbols from /apps/gentoo/usr/lib64/libunistring.so.2...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libunistring.so.2
Reading symbols from /apps/gentoo/usr/lib64/libtasn1.so.6...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libtasn1.so.6
Reading symbols from /apps/gentoo/usr/lib64/libhogweed.so.4...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libhogweed.so.4
Reading symbols from /apps/gentoo/usr/lib64/libidn2.so.0...(no debugging symbols found)...done.
Loaded symbols for /apps/gentoo/usr/lib64/libidn2.so.0
Core was generated by `bamsort SO=queryname inputthreads=10 outputthreads=40 level=9 index=1 O=HFYJ5AF'.
Program terminated with signal 6, Aborted.
#0  0x00002aaaad0a0f90 in raise () from /apps/gentoo/lib64/libc.so.6
(gdb) where
#0  0x00002aaaad0a0f90 in raise () from /apps/gentoo/lib64/libc.so.6
#1  0x00002aaaad0a2bb0 in abort () from /apps/gentoo/lib64/libc.so.6
#2  0x00002aaaac5c0075 in __gnu_cxx::__verbose_terminate_handler() () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc:95
#3  0x00002aaaac5bdc36 in __cxxabiv1::__terminate(void (*)()) () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc:47
#4  0x00002aaaac5bcb29 in __cxa_call_terminate () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/eh_call.cc:54
#5  0x00002aaaac5bd518 in __gxx_personality_v0 () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/eh_personality.cc:676
#6  0x00002aaaace62cd3 in _Unwind_RaiseException_Phase2 () from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1
#7  0x00002aaaace6352d in _Unwind_Resume () from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1
#8  0x00002aaaaab42ad1 in libmaus2::lz::BgzfDeflateParallel::flush() () at /apps/gentoo/usr/include/libmaus2/lz/BgzfDeflateParallel.hpp:255
#9  0x00002aaaaab439a8 in libmaus2::bambam::BamWriterParallelStreamBase::~BamWriterParallelStreamBase() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:159
#10 0x00002aaaaab43b92 in libmaus2::bambam::BamWriterParallelStreamBaseWrapper::~BamWriterParallelStreamBaseWrapper() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:217
#11 0x00002aaaaac7236c in libmaus2::bambam::BamParallelWriter::~BamParallelWriter() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:528
#12 0x00002aaaaac72388 in libmaus2::bambam::BamParallelWriter::~BamParallelWriter() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:528
#13 0x00002aaaaabac77c in std::default_delete<libmaus2::bambam::BamBlockWriterBase>::operator()(libmaus2::bambam::BamBlockWriterBase*) const () at /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/include/g++-v7/bits/unique_ptr.h:78
#14 0x00002aaaaab7eadd in std::unique_ptr<libmaus2::bambam::BamBlockWriterBase, std::default_delete<libmaus2::bambam::BamBlockWriterBase> >::~unique_ptr() () at /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/include/g++-v7/bits/unique_ptr.h:268
#15 0x00002aaaaab1ea3d in bamsort(libmaus2::util::ArgInfo const&) () at programs/bamsort.cpp:362
#16 0x00002aaaaab204fa in main () at programs/bamsort.cpp:1098
(gdb)  bt full
#0  0x00002aaaad0a0f90 in raise () from /apps/gentoo/lib64/libc.so.6
No symbol table info available.
#1  0x00002aaaad0a2bb0 in abort () from /apps/gentoo/lib64/libc.so.6
No symbol table info available.
#2  0x00002aaaac5c0075 in __gnu_cxx::__verbose_terminate_handler() () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc:95
No locals.
#3  0x00002aaaac5bdc36 in __cxxabiv1::__terminate(void (*)()) () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc:47
No locals.
#4  0x00002aaaac5bcb29 in __cxa_call_terminate () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/eh_call.cc:54
No locals.
#5  0x00002aaaac5bd518 in __gxx_personality_v0 () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-7.3.0-r1/work/gcc-7.3.0/libstdc++-v3/libsupc++/eh_personality.cc:676
No locals.
#6  0x00002aaaace62cd3 in _Unwind_RaiseException_Phase2 () from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1
No symbol table info available.
#7  0x00002aaaace6352d in _Unwind_Resume () from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1
No symbol table info available.
#8  0x00002aaaaab42ad1 in libmaus2::lz::BgzfDeflateParallel::flush() () at /apps/gentoo/usr/include/libmaus2/lz/BgzfDeflateParallel.hpp:255
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#9  0x00002aaaaab439a8 in libmaus2::bambam::BamWriterParallelStreamBase::~BamWriterParallelStreamBase() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:159
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#10 0x00002aaaaab43b92 in libmaus2::bambam::BamWriterParallelStreamBaseWrapper::~BamWriterParallelStreamBaseWrapper() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:217
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#11 0x00002aaaaac7236c in libmaus2::bambam::BamParallelWriter::~BamParallelWriter() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:528
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#12 0x00002aaaaac72388 in libmaus2::bambam::BamParallelWriter::~BamParallelWriter() () at /apps/gentoo/usr/include/libmaus2/bambam/BamWriter.hpp:528
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#13 0x00002aaaaabac77c in std::default_delete<libmaus2::bambam::BamBlockWriterBase>::operator()(libmaus2::bambam::BamBlockWriterBase*) const () at /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/include/g++-v7/bits/unique_ptr.h:78
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#14 0x00002aaaaab7eadd in std::unique_ptr<libmaus2::bambam::BamBlockWriterBase, std::default_delete<libmaus2::bambam::BamBlockWriterBase> >::~unique_ptr() () at /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/include/g++-v7/bits/unique_ptr.h:268
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#15 0x00002aaaaab1ea3d in bamsort(libmaus2::util::ArgInfo const&) () at programs/bamsort.cpp:362
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
#16 0x00002aaaaab204fa in main () at programs/bamsort.cpp:1098
        std::__ioinit = {static _S_refcount = 158, static _S_synced_with_stdio = true}
(gdb)

mmokrejs avatar Apr 12 '18 17:04 mmokrejs