When running SuMmOn with sample files (summon -c condition.xml SUMO2_conjugationA.mzXML), the program terminates after calculating candidate scores. The following error message is displayed:
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted
Can anyone offer help? The following is debug info:
---I found out where the program terminates. It is in SumoAnalysis.cpp----:
within function
void SumoAnalysis::scoreCandidate()
for( mScanReversePos = mScanReverse.begin() ; mScanReversePos !=
mScanReversePosEnd ; ++mScanReversePos) //the program terminates
after 2nd loop
{
m_Mod->generateCandidateMic( (vector< scanAnalysis
>::iterator) &mScanReversePos->second );
}
Target masses:
148.185
115.089
57.0519
128.131
97.1167
113.159
114.104
129.115
101.105
115.089
101.105
97.1167
71.0788
128.131
113.159
129.115
131.193
129.115
115.089
129.115
115.089
101.105
113.159
115.089
99.1326
147.177
128.131
128.131
128.131
101.105
57.0519
57.0519
0
endCharge: 5
Modified residue: K
notTerminal set to: 1
Adding variable modification of 16 to M
Digesting C terminal of: R not followed by: P
Digesting C terminal of: K not followed by: P
Inserting up to 1 missed cleavages, C terminal of: K
Forcing 1 missed cleavages, C terminal of: K not followed by P
Digestion step: 100000
Mass tolerance: 1
Digestion tolerance: 3
Normalization option: -2
Target MS level: 2
Calculating reverse modification scores.
Charge 3 average num of hits 43.4646 sd 33.6973
Charge 4 average num of hits 56.7121 sd 43.6837
Charge 5 average num of hits 66.6779 sd 52.049
Average peaks num: 252.759
Sorting scans
Calculating forward modification scores.
Loading DB subDB.fastaming charge: 5
Digesting C terminal of R
Digesting C terminal of K
Inserting 1 missed cleavages at K
Forcing 1 missed cleavages at K
Modifying M with 16
Calculating peptide masses
Calculating mass of fragments
I will remove 3552.72 from the precursorMH mass
Charge 3 average num of hits 44.7765 sd 34.3716
Charge 4 average num of hits 59.5689 sd 44.7922
Charge 5 average num of hits 68.2288 sd 52.5802
Average peaks num: 252.759
Sorting scans
Scoring candidates
| | | | |100%
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAM(16.000000)SGHHHHHHSGK
Rotated sequence 1 K(0)EDAM(16.000000)SGHHHHHHSGKP
Rotated sequence 2 EDAM(16.000000)SGHHHHHHSGKPK(0)
Rotated sequence 3 DAM(16.000000)SGHHHHHHSGKPK(0)E
Rotated sequence 4 AM(16.000000)SGHHHHHHSGKPK(0)ED
Rotated sequence 5 M(16.000000)SGHHHHHHSGKPK(0)EDA
Rotated sequence 6 &
Rotated sequence 7 &
Rotated sequence 8 &
Rotated sequence 9 &
Rotated sequence 10 &
Rotated sequence 11 &
Rotated sequence 12 &
Rotated sequence 13 &
Rotated sequence 14 &
Rotated sequence 15 &
Rotated sequence 16 &
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAMSGHHHHHHSGK
Rotated sequence 1 K(0)EDAMSGHHHHHHSGKP
Rotated sequence 2 EDAMSGHHHHHHSGKPK(0)
Rotated sequence 3 DAMSGHHHHHHSGKPK(0)E
Rotated sequence 4 AMSGHHHHHHSGKPK(0)ED
Rotated sequence 5 MSGHHHHHHSGKPK(0)EDA
Rotated sequence 6 SGHHHHHHSGKPK(0)EDAM
Rotated sequence 7 GHHHHHHSGKPK(0)EDAMS
Rotated sequence 8 HHHHHHSGKPK(0)EDAMSG
Rotated sequence 9 HHHHHSGKPK(0)EDAMSGH
Rotated sequence 10 HHHHSGKPK(0)EDAMSGHH
Rotated sequence 11 HHHSGKPK(0)EDAMSGHHH
Rotated sequence 12 HHSGKPK(0)EDAMSGHHHH
Rotated sequence 13 HSGKPK(0)EDAMSGHHHHH
Rotated sequence 14 SGKPK(0)EDAMSGHHHHHH
Rotated sequence 15 GKPK(0)EDAMSGHHHHHHS
Rotated sequence 16 KPK(0)EDAMSGHHHHHHSG
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAMSGHHHHHHSGK
Rotated sequence 1 K(0)EDAMSGHHHHHHSGKP
Rotated sequence 2 EDAMSGHHHHHHSGKPK(0)
Rotated sequence 3 DAMSGHHHHHHSGKPK(0)E
Rotated sequence 4 AMSGHHHHHHSGKPK(0)ED
Rotated sequence 5 MSGHHHHHHSGKPK(0)EDA
Rotated sequence 6 SGHHHHHHSGKPK(0)EDAM
Rotated sequence 7 GHHHHHHSGKPK(0)EDAMS
Rotated sequence 8 HHHHHHSGKPK(0)EDAMSG
Rotated sequence 9 HHHHHSGKPK(0)EDAMSGH
Rotated sequence 10 HHHHSGKPK(0)EDAMSGHH
Rotated sequence 11 HHHSGKPK(0)EDAMSGHHH
Rotated sequence 12 HHSGKPK(0)EDAMSGHHHH
Rotated sequence 13 HSGKPK(0)EDAMSGHHHHH
Rotated sequence 14 SGKPK(0)EDAMSGHHHHHH
Rotated sequence 15 GKPK(0)EDAMSGHHHHHHS
Rotated sequence 16 KPK(0)EDAMSGHHHHHHSG
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAMSGHHHHHHSGK
Rotated sequence 1 K(0)EDAMSGHHHHHHSGKP
Rotated sequence 2 EDAMSGHHHHHHSGKPK(0)
Rotated sequence 3 DAMSGHHHHHHSGKPK(0)E
Rotated sequence 4 AMSGHHHHHHSGKPK(0)ED
Rotated sequence 5 MSGHHHHHHSGKPK(0)EDA
Rotated sequence 6 SGHHHHHHSGKPK(0)EDAM
Rotated sequence 7 GHHHHHHSGKPK(0)EDAMS
Rotated sequence 8 HHHHHHSGKPK(0)EDAMSG
Rotated sequence 9 HHHHHSGKPK(0)EDAMSGH
Rotated sequence 10 HHHHSGKPK(0)EDAMSGHH
Rotated sequence 11 HHHSGKPK(0)EDAMSGHHH
Rotated sequence 12 HHSGKPK(0)EDAMSGHHHH
Rotated sequence 13 HSGKPK(0)EDAMSGHHHHH
Rotated sequence 14 SGKPK(0)EDAMSGHHHHHH
Rotated sequence 15 GKPK(0)EDAMSGHHHHHHS
Rotated sequence 16 KPK(0)EDAMSGHHHHHHSG
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 MLK(0)SLPTHK
Rotated sequence 1 LK(0)SLPTHKM
Rotated sequence 2 K(0)SLPTHKML
Rotated sequence 3 SLPTHKMLK(0)
Rotated sequence 4 LPTHKMLK(0)S
Rotated sequence 5 PTHKMLK(0)SL
Rotated sequence 6 THKMLK(0)SLP
Rotated sequence 7 HKMLK(0)SLPT
Rotated sequence 8 KMLK(0)SLPTH
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 FVEK(0)M(16.000000)NGGR
Rotated sequence 1 VEK(0)M(16.000000)NGGRF
Rotated sequence 2 EK(0)M(16.000000)NGGRFV
Rotated sequence 3 K(0)M(16.000000)NGGRFVE
Rotated sequence 4 M(16.000000)NGGRFVEK(0)
Rotated sequence 5
Rotated sequence 6
Rotated sequence 7
Rotated sequence 8
deleted array pointer
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted
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When running SuMmOn with sample files (summon -c condition.xml SUMO2_conjugationA.mzXML), the program terminates after calculating candidate scores. The following error message is displayed:
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted
Can anyone offer help? The following is debug info:
---I found out where the program terminates. It is in SumoAnalysis.cpp----:
within function
void SumoAnalysis::scoreCandidate()
for( mScanReversePos = mScanReverse.begin() ; mScanReversePos !=
mScanReversePosEnd ; ++mScanReversePos) //the program terminates
after 2nd loop
{
m_Mod->generateCandidateMic( (vector< scanAnalysis
>::iterator) &mScanReversePos->second );
}
Target masses:
148.185
115.089
57.0519
128.131
97.1167
113.159
114.104
129.115
101.105
115.089
101.105
97.1167
71.0788
128.131
113.159
129.115
131.193
129.115
115.089
129.115
115.089
101.105
113.159
115.089
99.1326
147.177
128.131
128.131
128.131
101.105
57.0519
57.0519
0
endCharge: 5
Modified residue: K
notTerminal set to: 1
Adding variable modification of 16 to M
Digesting C terminal of: R not followed by: P
Digesting C terminal of: K not followed by: P
Inserting up to 1 missed cleavages, C terminal of: K
Forcing 1 missed cleavages, C terminal of: K not followed by P
Digestion step: 100000
Mass tolerance: 1
Digestion tolerance: 3
Normalization option: -2
Target MS level: 2
Calculating reverse modification scores.
Charge 3 average num of hits 43.4646 sd 33.6973
Charge 4 average num of hits 56.7121 sd 43.6837
Charge 5 average num of hits 66.6779 sd 52.049
Average peaks num: 252.759
Sorting scans
Calculating forward modification scores.
Loading DB subDB.fastaming charge: 5
Digesting C terminal of R
Digesting C terminal of K
Inserting 1 missed cleavages at K
Forcing 1 missed cleavages at K
Modifying M with 16
Calculating peptide masses
Calculating mass of fragments
I will remove 3552.72 from the precursorMH mass
Charge 3 average num of hits 44.7765 sd 34.3716
Charge 4 average num of hits 59.5689 sd 44.7922
Charge 5 average num of hits 68.2288 sd 52.5802
Average peaks num: 252.759
Sorting scans
Scoring candidates
| | | | |100%
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAM(16.000000)SGHHHHHHSGK
Rotated sequence 1 K(0)EDAM(16.000000)SGHHHHHHSGKP
Rotated sequence 2 EDAM(16.000000)SGHHHHHHSGKPK(0)
Rotated sequence 3 DAM(16.000000)SGHHHHHHSGKPK(0)E
Rotated sequence 4 AM(16.000000)SGHHHHHHSGKPK(0)ED
Rotated sequence 5 M(16.000000)SGHHHHHHSGKPK(0)EDA
Rotated sequence 6 &
Rotated sequence 7 &
Rotated sequence 8 &
Rotated sequence 9 &
Rotated sequence 10 &
Rotated sequence 11 &
Rotated sequence 12 &
Rotated sequence 13 &
Rotated sequence 14 &
Rotated sequence 15 &
Rotated sequence 16 &
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAMSGHHHHHHSGK
Rotated sequence 1 K(0)EDAMSGHHHHHHSGKP
Rotated sequence 2 EDAMSGHHHHHHSGKPK(0)
Rotated sequence 3 DAMSGHHHHHHSGKPK(0)E
Rotated sequence 4 AMSGHHHHHHSGKPK(0)ED
Rotated sequence 5 MSGHHHHHHSGKPK(0)EDA
Rotated sequence 6 SGHHHHHHSGKPK(0)EDAM
Rotated sequence 7 GHHHHHHSGKPK(0)EDAMS
Rotated sequence 8 HHHHHHSGKPK(0)EDAMSG
Rotated sequence 9 HHHHHSGKPK(0)EDAMSGH
Rotated sequence 10 HHHHSGKPK(0)EDAMSGHH
Rotated sequence 11 HHHSGKPK(0)EDAMSGHHH
Rotated sequence 12 HHSGKPK(0)EDAMSGHHHH
Rotated sequence 13 HSGKPK(0)EDAMSGHHHHH
Rotated sequence 14 SGKPK(0)EDAMSGHHHHHH
Rotated sequence 15 GKPK(0)EDAMSGHHHHHHS
Rotated sequence 16 KPK(0)EDAMSGHHHHHHSG
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAMSGHHHHHHSGK
Rotated sequence 1 K(0)EDAMSGHHHHHHSGKP
Rotated sequence 2 EDAMSGHHHHHHSGKPK(0)
Rotated sequence 3 DAMSGHHHHHHSGKPK(0)E
Rotated sequence 4 AMSGHHHHHHSGKPK(0)ED
Rotated sequence 5 MSGHHHHHHSGKPK(0)EDA
Rotated sequence 6 SGHHHHHHSGKPK(0)EDAM
Rotated sequence 7 GHHHHHHSGKPK(0)EDAMS
Rotated sequence 8 HHHHHHSGKPK(0)EDAMSG
Rotated sequence 9 HHHHHSGKPK(0)EDAMSGH
Rotated sequence 10 HHHHSGKPK(0)EDAMSGHH
Rotated sequence 11 HHHSGKPK(0)EDAMSGHHH
Rotated sequence 12 HHSGKPK(0)EDAMSGHHHH
Rotated sequence 13 HSGKPK(0)EDAMSGHHHHH
Rotated sequence 14 SGKPK(0)EDAMSGHHHHHH
Rotated sequence 15 GKPK(0)EDAMSGHHHHHHS
Rotated sequence 16 KPK(0)EDAMSGHHHHHHSG
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 PK(0)EDAMSGHHHHHHSGK
Rotated sequence 1 K(0)EDAMSGHHHHHHSGKP
Rotated sequence 2 EDAMSGHHHHHHSGKPK(0)
Rotated sequence 3 DAMSGHHHHHHSGKPK(0)E
Rotated sequence 4 AMSGHHHHHHSGKPK(0)ED
Rotated sequence 5 MSGHHHHHHSGKPK(0)EDA
Rotated sequence 6 SGHHHHHHSGKPK(0)EDAM
Rotated sequence 7 GHHHHHHSGKPK(0)EDAMS
Rotated sequence 8 HHHHHHSGKPK(0)EDAMSG
Rotated sequence 9 HHHHHSGKPK(0)EDAMSGH
Rotated sequence 10 HHHHSGKPK(0)EDAMSGHH
Rotated sequence 11 HHHSGKPK(0)EDAMSGHHH
Rotated sequence 12 HHSGKPK(0)EDAMSGHHHH
Rotated sequence 13 HSGKPK(0)EDAMSGHHHHH
Rotated sequence 14 SGKPK(0)EDAMSGHHHHHH
Rotated sequence 15 GKPK(0)EDAMSGHHHHHHS
Rotated sequence 16 KPK(0)EDAMSGHHHHHHSG
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 MLK(0)SLPTHK
Rotated sequence 1 LK(0)SLPTHKM
Rotated sequence 2 K(0)SLPTHKML
Rotated sequence 3 SLPTHKMLK(0)
Rotated sequence 4 LPTHKMLK(0)S
Rotated sequence 5 PTHKMLK(0)SL
Rotated sequence 6 THKMLK(0)SLP
Rotated sequence 7 HKMLK(0)SLPT
Rotated sequence 8 KMLK(0)SLPTH
deleted array pointer
Starting to create reverse sequence
Rotated sequence 0 FVEK(0)M(16.000000)NGGR
Rotated sequence 1 VEK(0)M(16.000000)NGGRF
Rotated sequence 2 EK(0)M(16.000000)NGGRFV
Rotated sequence 3 K(0)M(16.000000)NGGRFVE
Rotated sequence 4 M(16.000000)NGGRFVEK(0)
Rotated sequence 5
Rotated sequence 6
Rotated sequence 7
Rotated sequence 8
deleted array pointer
terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted