specht/gpf

Genomic Peptide Finder

gpf's Issues

GPF segfault

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 
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-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)