cole-trapnell-lab / cufflinks

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A bug in cuffdiff in the version 2.2.2 #49

Closed sethbrin closed 8 years ago

sethbrin commented 8 years ago

cuffdiff -o diff/ -L input1,input2 -u merged.gtf a.sam b.sam, A eror occured.

 terminate called after throwing an instance of 'std::bad_alloc'
 what():  std::bad_alloc
 Aborted (core dumped)

backtrace info

(gdb) backtrace 
#0  0x00000037332328a5 in raise () from /lib64/libc.so.6
#1  0x0000003733234085 in abort () from /lib64/libc.so.6
#2  0x00007ffff7724a7d in __gnu_cxx::__verbose_terminate_handler() () from     /usr/lib64/libstdc++.so.6
#3  0x00007ffff7722bd6 in ?? () from /usr/lib64/libstdc++.so.6 
#4  0x00007ffff7722c03 in std::terminate() () from /usr/lib64/libstdc++.so.6
#5  0x00007ffff7722d22 in __cxa_throw () from /usr/lib64/libstdc++.so.6
#6  0x00007ffff772311d in operator new(unsigned long) () from /usr/lib64/libstdc++.so.6
#7  0x00007ffff77023c9 in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) () from /usr/lib64/libstdc++.so.6
#8  0x00007ffff770319b in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_M_clone(std::allocator<char> const&, unsigned long) () from /usr/lib64/libstdc++.so.6
#9  0x00007ffff77035ec in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long) () from /usr/lib64/libstdc++.so.6
#10 0x00007ffff7703771 in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(unsigned long, char) () from /usr/lib64/libstdc++.so.6
#11 0x00007ffff79a9642 in boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits<char> >::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) () from boost/lib/libboost_serialization.so.1.59.0
#12 0x00007ffff79a97da in boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::init() () from boost/lib/libboost_serialization.so.1.59.0
#13 0x00000000004322b7 in boost::archive::binary_iarchive_impl<boost::archive::binary_iarchive, char, std::char_traits<char> >::init (this=0x9705e0, flags=0) at boost/include/boost/archive/binary_iarchive_impl.hpp:64
#14 0x000000000042876c in boost::archive::binary_iarchive_impl<boost::archive::binary_iarchive, char, std::char_traits<char> >::binary_iarchive_impl (this=0x9705e0, is=..., flags=0) at boost/include/boost/archive/binary_iarchive_impl.hpp:93
#15 0x000000000041eec7 in boost::archive::binary_iarchive::binary_iarchive (this=0x9705e0, is=..., flags=0) at boost/include/boost/archive/binary_iarchive.hpp:44
#16 0x0000000000421c3b in PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory (this=0x973ba0, 
expression_file_name="a.sam", insert_table=..., reference_table=...) at hits.h:818
#17 0x00000000004174df in driver (ref_gtf=0x9702b0, mask_gtf=0x0, contrast_file=0x0, norm_standards_file=0x0, sam_hit_filename_lists=std::vector of length 2, capacity 2 = {...}, outfiles=...) at cuffdiff.cpp:1580
#18 0x000000000041e259 in main (argc=9, argv=0x7fffffffd068) at cuffdiff.cpp:2684