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#374 Seg fault from spectral-counts

post v2.0
open
Kaipo
crux-users (14) High priority (56)
2016-02-18
2016-02-18
William S Noble
No

A Crux user (Brittney Mets, brittney.mets@uky.edu) provided this sample command line:

crux spectral-counts --verbosity 50 --protein-database human_Streptavidin.fasta --overwrite T --threshold-type none --measure SIN --input-ms2 Spielmann_011116_01122016_hv.mgf ./Spielmann_011116_01122016_hv.pep.xml

It yields a seg fault (see below).

Here is the location of the seg fault, according to the debugger:

(gdb) bt

0 0x000000000089f60e in copy_mod_aa_seq (source=0x1ef72c0) at /net/noble/vol1/home/noble/proj/crux/trunk/src/util/modifications.cpp:530

1 0x00000000008e2988 in Crux::Peptide::setModifiedAASequence (this=0x1ef7040, mod_seq=0x1ef72c0, decoy=true) at /net/noble/vol1/home/noble/proj/crux/trunk/src/model/Peptide.cpp:719

2 0x00000000008ec1b4 in PepXMLReader::modAminoAcidMassOpen (this=0x1d58890, attr=0x1d58ef0) at /net/noble/vol1/home/noble/proj/crux/trunk/src/io/PepXMLReader.cpp:428

3 0x00000000008eaad9 in open_handler (data=0x1d58890, el=0x1d5cf5c "mod_aminoacid_mass", attr=0x1d58ef0) at /net/noble/vol1/home/noble/proj/crux/trunk/src/io/PepXMLReader.cpp:44

4 0x0000000000ad6560 in doContent ()

5 0x0000000000ad7231 in contentProcessor ()

6 0x0000000000ad99b2 in XML_ParseBuffer ()

7 0x00000000008eb130 in PepXMLReader::parse (this=0x1d58890) at /net/noble/vol1/home/noble/proj/crux/trunk/src/io/PepXMLReader.cpp:161

8 0x00000000008ecc7c in PepXMLReader::parse (file_path="./Spielmann_011116_01122016_hv.pep.xml", database=0x1bc5d00, decoy_database=0x1d58770) at /net/noble/vol1/home/noble/proj/crux/trunk/src/io/PepXMLReader.cpp:608

9 0x000000000089e52f in MatchCollectionParser::create (this=0x1bc83b8, match_path="./Spielmann_011116_01122016_hv.pep.xml", fasta_path="human_Streptavidin.fasta") at /net/noble/vol1/home/noble/proj/crux/trunk/src/io/MatchCollectionParser.cpp:191

10 0x0000000000921fe1 in SpectralCounts::filterMatches (this=0x1bc8330) at /net/noble/vol1/home/noble/proj/crux/trunk/src/app/SpectralCounts.cpp:566

11 0x000000000091f86e in SpectralCounts::main (this=0x1bc8330, argc=12, argv=0x7fffffffb390) at /net/noble/vol1/home/noble/proj/crux/trunk/src/app/SpectralCounts.cpp:63

12 0x0000000000876844 in CruxApplicationList::main (this=0x7fffffffb1e0, argc=13, argv=0x7fffffffb388) at /net/noble/vol1/home/noble/proj/crux/trunk/src/app/CruxApplicationList.cpp:222

13 0x000000000078686d in main (argc=13, argv=0x7fffffffb388) at /net/noble/vol1/home/noble/proj/crux/trunk/src/crux-main.cpp:103

  • /net/noble/vol1/home/noble/proj/crux/trunk/debug/src/crux spectral-counts --verbosity 50 --protein-database human_Streptavidin.fasta --overwrite T --threshold-type none --measure SIN --input-ms2 Spielmann_011116_01122016_hv.mgf ./Spielmann_011116_01122016_hv.pep.xml
    INFO: Beginning spectral-counts.
    WARNING: The output directory 'crux-output' already exists.
    Existing files will be overwritten.
    WARNING: The file 'crux-output/spectral-counts.log.txt' already exists and will be overwritten.
    INFO: CPU: pyrrolysine.gs.washington.edu
    INFO: Crux version: 2.1
    INFO: Thu Feb 18 12:18:05 PST 2016
    DEBUG: OutputFiles is opening 1 files (1 decoys) in 'crux-output' with root ''. Overwrite: 1.
    DEBUG: match path:./Spielmann_011116_01122016_hv.pep.xml
    DEBUG: fasta path:human_Streptavidin.fasta
    DEBUG: Creating new database from 'human_Streptavidin.fasta'
    DEBUG: Generate name given filename 'human_Streptavidin.fasta', old suffix '.fasta', new suffix '-binary-fasta', new path '.'
    DEBUG: Final name is './human_Streptavidin-binary-fasta'
    DEBUG: Transforming text file 'human_Streptavidin.fasta' to binary file './human_Streptavidin-binary-fasta'
    INFO: Reached protein 1000
    INFO: Reached protein 2000
    INFO: Reached protein 3000
    INFO: Reached protein 4000
    INFO: Reached protein 5000
    INFO: Reached protein 6000
    INFO: Reached protein 7000
    INFO: Reached protein 8000
    INFO: Reached protein 9000
    INFO: Reached protein 10000
    INFO: Reached protein 20000
    INFO: Total proteins found: 20194
    DEBUG: Parsing binary fasta file './human_Streptavidin-binary-fasta'
    DEBUG: Parsing binary fasta file './human_Streptavidin-binary-fasta'
    total matches: 0
    DEBUG: Unsupported open tag:msms_pipeline_analysis
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    WARNING: No modification identifier found for mass shift 15.99.
    Warning Suppressed, others may exist
    INFO: Creating modification for 15.994915
    DEBUG: Creating new protein for P61264
    DEBUG: adding to target database
    DEBUG: Creating new protein for P63048
    DEBUG: adding to target database
    DEBUG: Creating new protein for P62992
    DEBUG: adding to target database
    DEBUG: Creating new protein for P0CG67
    DEBUG: adding to target database
    INFO: Creating modification for 57.021465
    ./runall: line 32: 12339 Segmentation fault (core dumped) ~/proj/crux/trunk/debug/src/crux spectral-counts --verbosity 50 --protein-database human_Streptavidin.fasta --overwrite T --threshold-type none --measure SIN --input-ms2 Spielmann_011116_01122016_hv.mgf ./Spielmann_011116_01122016_hv.pep.xml
    bash-4.1$ ulimit
    unlimited
    bash-4.1$

The files are too large to attach, but can be found in

~wnoble/proj/crux-projects/2010tinkering/results/2016-02-18brittney/

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