#399 Seg fault from make-pin

[William S Noble]

Kaipo,
Would you please take a look at this seg fault from make-pin? The command line is simply

crux make-pin search-for-xlinks.target.txt

The input files and the log file are attached. The backtrace from the seg fault looks like this:

(gdb) bt

0 0x00000000006ed51e in get_aa_mod_from_mass(float) ()

1 0x00000000006ed7d8 in get_aa_mod_from_mass(float) ()

2 0x00000000006eda93 in convert_to_mod_aa_seq(char const, unsigned short*, MASS_FORMAT_T) ()

3 0x00000000006d66e7 in MatchFileReader::parsePeptide() ()

4 0x00000000006d7598 in MatchFileReader::parseMatch() ()

5 0x00000000006d8a10 in MatchFileReader::parse() ()

6 0x00000000006d8cb3 in MatchFileReader::parse(std::basic_string<char, std::char_traits\<char="">, std::allocator\<char> > const&, Database, Database) ()</char></char,>

7 0x00000000006e1df3 in MatchCollectionParser::create(std::basic_string<char, std::char_traits\<char="">, std::allocator\<char> > const&, std::basic_string<char, std::char_traits\<char="">, std::allocator\<char> > const&) ()</char></char,></char></char,>

8 0x00000000006cd8d0 in MakePinApplication::main(std::vector<std::basic_string\<char, std::char_traits\<char="">, std::allocator\<char> >, std::allocator\<std::basic_string\<char, std::char_traits\<char="">, std::allocator\<char> > > > const&) ()</char></std::basic_string\<char,></char></std::basic_string\<char,>

9 0x00000000006ce961 in MakePinApplication::main(int, char**) ()

10 0x00000000006b036a in CruxApplicationList::main(int, char**) ()

11 0x00000000005a5de9 in main ()

(gdb)

[Kaipo]

I think this is happening because the parser is running into a PSM where the sequence is actually two sequences. I'm not sure what the correct behavior should be in this case, when we're trying to make a pin file?

[William S Noble]

I guess we should just copy the contents of the column (e.g., "KKVGLRK,
QQRKGR (1,4)") directly into the PIN file. If this turns out to confuse
Percolator, we may have to replace spaces with underscores.

On Wed, Jun 22, 2016 at 11:41 AM, Kaipo kaipot@users.sf.net wrote:

I think this is happening because the parser is running into a PSM where
the sequence is actually two sequences. I'm not sure what the correct
behavior should be in this case, when we're trying to make a pin file?

---

• [issues:#399] https://sourceforge.net/p/cruxtoolkit/issues/399/ Seg
  fault from make-pin*

Status: open
Milestone: Crux v2.0
Labels: High priority
Created: Tue Jun 21, 2016 11:52 PM UTC by William S Noble
Last Updated: Tue Jun 21, 2016 11:52 PM UTC
Owner: Kaipo
Attachments:

• make-pin.log.txt
  https://sourceforge.net/p/cruxtoolkit/issues/399/attachment/make-pin.log.txt
  (747 Bytes; text/plain)
• search-for-xlinks.decoy.txt
  https://sourceforge.net/p/cruxtoolkit/issues/399/attachment/search-for-xlinks.decoy.txt
  (1.1 MB; text/plain)
• search-for-xlinks.target.txt
  https://sourceforge.net/p/cruxtoolkit/issues/399/attachment/search-for-xlinks.target.txt
  (1.1 MB; text/plain)

Kaipo,
Would you please take a look at this seg fault from make-pin? The command
line is simply

crux make-pin search-for-xlinks.target.txt

The input files and the log file are attached. The backtrace from the seg
fault looks like this:

(gdb) bt
0 0x00000000006ed51e in get_aa_mod_from_mass(float) () 1
0x00000000006ed7d8 in get_aa_mod_from_mass(float) () 2 0x00000000006eda93
in convert_to_mod_aa_seq(char const, unsigned short, MASS_FORMAT_T) () 3
0x00000000006d66e7 in MatchFileReader::parsePeptide() () 4
0x00000000006d7598 in MatchFileReader::parseMatch() () 5
0x00000000006d8a10 in MatchFileReader::parse() () 6 0x00000000006d8cb3 in
MatchFileReader::parse(std::basic_string<char, std::char_traits\<char="">, std::allocator\<char> > const&, Database</char></char,>, Database) () 7
0x00000000006e1df3 in MatchCollectionParser::create(std::basic_string<char, std::char_traits\<char="">, std::allocator\<char> > const&,
std::basic_string<char, std::char_traits\<char="">, std::allocator\<char> >
const&) () 8 0x00000000006cd8d0 in
MakePinApplication::main(std::vector<std::basic_string\<char, std::char_traits\<char="">, std::allocator\<char> >, std::allocator\<std::basic_string\<char, std::char_traits\<char="">, std::allocator\<char> > > > const&) () 9 0x00000000006ce961 in
MakePinApplication::main(int, char</char></std::basic_string\<char,></char></std::basic_string\<char,></char></char,></char></char,>) () 10 0x00000000006b036a in
CruxApplicationList::main(int, char*) () 11 0x00000000005a5de9 in main ()

(gdb)

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