spechtm@vhip:~/gpf/projects/gpfquery (develop)$ gdb ../../gpfquery_debug
GNU gdb 6.8-debian
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
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This GDB was configured as "x86_64-linux-gnu"...
(gdb) run --searchIntronSplit yes --peptidesFile /data/tranche/shotgun_normal_28-peaks-results-peptides.txt --csvOutputPath /data/tranche/gpf-results.csv --peptidesOutputPath /data/tranche/gpf-results-peptides.txt /data/genomes/Mus_musculus.NCBIM37.50.dna.toplevel.fa.gpfindex
Starting program: /home/spechtm/gpf/gpfquery_debug --searchIntronSplit yes --peptidesFile /data/tranche/shotgun_normal_28-peaks-results-peptides.txt --csvOutputPath /data/tranche/gpf-results.csv --peptidesOutputPath /data/tranche/gpf-results-peptides.txt /data/genomes/Mus_musculus.NCBIM37.50.dna.toplevel.fa.gpfindex
[Thread debugging using libthread_db enabled]
[New Thread 0x7f25aac2e6f0 (LWP 29882)]
Processing query 915 of 166026 (AAGQRLNMDK)...
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7f25aac2e6f0 (LWP 29882)]
0x00007f25a9952ece in memcpy () from /lib/libc.so.6
(gdb) bt
#0 0x00007f25a9952ece in memcpy () from /lib/libc.so.6
#1 0x0000000000403f4d in k_GpfBase::readNucleotideTriplet (this=0x627d40,
auc_Buffer_=0x7f256be16010 "J�\005\200\204\001\003\002\001\200", aui_Gno=18446744073709551613) at ../../src/GpfBase.cpp:229
#2 0x0000000000412ea2 in k_GpfQuery::readFlankingAminoAcids (this=0x7fffb2c40b20, ai_Start=26, ai_Stop=0,
as_Left=@0x7fffb2c40030, as_Right=@0x7fffb2c40020, ai_BStep1=-1, ai_ScaffoldStart=0, ai_ScaffoldEnd=3993,
ac_TripletToAminoAcid_=0x2098610 "FLFLXXXXCWC*XXXXSSSSSSSSY*Y*", 'X' , "VVVVVVVVGGGGGGGGAAAAAAAADEDE", 'X' , "LLLLLLLLRRRRRRRRPPPPPPPPHQHQ", 'X' , "IMIIXXXX"...) at ../../src/GpfQuery.cpp:934
#3 0x0000000000414224 in k_GpfQuery::findAlignments (this=0x7fffb2c40b20, ak_GnoMap=@0x7fffb2c40840, ab_SearchImmediate=true,
ab_SearchIntronSplit=true, ak_FoundAssemblies=@0x7fffb2c40830) at ../../src/GpfQuery.cpp:465
#4 0x00000000004175bd in k_GpfQuery::execute (this=0x7fffb2c40b20, as_Peptide=@0x7fffb2c409c0, ai_PrecursorMass=11025548)
at ../../src/GpfQuery.cpp:264
#5 0x0000000000417803 in k_GpfQuery::execute (this=0x7fffb2c40b20, ak_Peptides=
{{p = {static shared_null = {ref = {_q_value = 53}, alloc = 0, begin = 0, end = 0, sharable = 1, array = {0x0}}, d = 0x7fffb2c41190}, d = 0x7fffb2c41190}}) at ../../src/GpfQuery.cpp:869
#6 0x000000000040efc5 in main (ai_ArgumentCount=10, ac_Arguments__=0x7fffb2c412e8) at ../../src/gpfquery_.cpp:316
(gdb)