PTM Prophet error crashes run

[Shinya-Watanabe]

I have the same issue with this #1310 unable to resolve. The error happens when searching specific PTM modifications search, like below. I used TMT11 plex. The monoisotopic mass of 156.1151 on CHK and 140.1201 on K are the PTM that I am looking for.

KEEPOLD STATIC EM=1 NIONS=b M:15.9949,n:42.0106,CHK:156.1151,K:140.1201 MINPROB=0.5 MAXTHREADS=1 interact-01MoTrPAC_PASS1B-06_T58_PR_BI_20200224_GY_f15.pep.xml interact-01MoTrPAC_PASS1B-06_T58_PR_BI_20200224_GY_f15.mod.pep.xml

Please wait. PTMProphet is running. It can take a long time.
[INFO:] Using statically set 15 PPM tolerance ... 
[INFO:] Writing file interact-01MoTrPAC_PASS1B-06_T58_PR_BI_20200224_GY_f14.pep.xml.tmp.a31788 ...

[INFO:] Creating 1 threads 
[INFO:] Wait for threads to finish ...
[INFO:] Reading file interact-01MoTrPAC_PASS1B-06_T58_PR_BI_20200224_GY_f14.pep.xml ...
​
[INFO:] processed 1000/12405 spectrum_queries		 ​
[INFO:] processed 2000/12405 spectrum_queries		 ​
[INFO:] processed 3000/12405 spectrum_queries		 ​
[INFO:] processed 4000/12405 spectrum_queries		 ​
[INFO:] processed 5000/12405 spectrum_queries		 ​
[INFO:] processed 6000/12405 spectrum_queries		 ​
[INFO:] processed 7000/12405 spectrum_queries		 ​
[INFO:] processed 8000/12405 spectrum_queries		 ​
[INFO:] processed 9000/12405 spectrum_queries		 [WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: n[230]ITDFGLC[160]K[653]EGISDGATMK[357]TFC[160]GTPEYLAPEVLEDNDYGR
	Neutral Mass (from pepXML) = 5352.71
	BAD (SpectraST::Peptide) = ITDFGLCK
	Neutral Computed Mass for Evaluation = 895.447
	PPM difference = 832711
[INFO:] please check your specified modification masses for precision or adjust MODPREC= parameter ...
[ERROR:] Scan 30559 ... number of mod combinations doesn't match the number of peptides ... 
[INFO:] Check the precision of specified PTM masses OR Adjust 'MODPREC=' parameter and rerun ... exiting ...
Process 'PTMProphet' finished, exit code: 1
Process returned non-zero exit code, stopping
Processing
 interrupted, stopping PTMProphet

log_2024-09-13_13-28-24.txt