Issue with MSFragger interface with Koina Server

[BenSamy2020]

Greetings @fcyu,

I am experiancing the error of: {"error":"in ensemble 'Prosit_2020_intensity_HCD', Failed to process the request(s) for model instance 'Prosit_Preprocess_charge', message: IndexError: index 6 is out of bounds for axis 0 with size 6\n\nAt:\n /models/repo/Prosit_Preprocess_charge/1/model.py(14): indices_to_one_hot\n /models/repo/Prosit_Preprocess_charge/1/model.py(18): \n /models/repo/Prosit_Preprocess_charge/1/model.py(18): to_on_hot\n /models/repo/Prosit_Preprocess_charge/1/model.py(37): execute\n"}

Have attatched the log files here for your reference.
log_2024-09-09_08-42-57.txt

Please do advise me on how to troubleshoot, thank you.

I am not sure if I should post this issues here, if its need to be reported to Koina Server team, please do let me know.

[fcyu]

I will let Kevin @yangkl96 answer the Koina question.

Best,

Fengchao

[BenSamy2020]

Thank you @fcyu.

Regards,
Ben

[yangkl96]

Hi Ben,

This error is caused by peptides with charges higher than 6 not being properly filtered out during Prosit's NCE calibration. This error is fixed in the newest MSBooster here: https://www.dropbox.com/scl/fo/sioaysait4lkbdkvk5bn6/AKGomsKTlP6fSup8nnL43YE?rlkey=3k61o6l0o2wsg3m5ml2buv4f1&st=uo0bx12v&dl=0

Please let me know if this fixes the error.

Thanks for your bug reporting,
Kevin

[BenSamy2020]

Greetings @yangkl96,

I am still facing issues with MSBooster.

Error: Could not find or load main class Features.MainClass
Caused by: java.lang.ClassNotFoundException: Features.MainClass
Process 'MSBooster' finished, exit code: 1
Process returned non-zero exit code, stopping

log_2024-09-11_12-59-55.txt

[yangkl96]

My apologies, I forgot the newest MSBooster is only compatible with the newest FragPipe prerelease. I've added the new FragPipe to the Dropbox folder above. Just copy MSBooster-1.2.52.jar to the tools folder

[BenSamy2020]

Can I delete the older MSBooster version?

[yangkl96]

Yes

[BenSamy2020]

I am having issues with the3 step of:

2024-09-12 12:26:56 [ERROR] - {"error":"in ensemble 'Prosit_2019_intensity', Failed to process the request(s) for model instance 'Prosit_Preprocess_peptide', message: TypeError: object of type 'NoneType' has no len()\n\nAt:\n /models/repo/Prosit_Preprocess_peptide/1/sequence_conversion.py(72): character_to_array\n /models/repo/Prosit_Preprocess_peptide/1/model.py(25): \n /models/repo/Prosit_Preprocess_peptide/1/model.py(25): execute\n"}
2024-09-12 12:26:56 [ERROR] - D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_MOD_1\SLAS1_UNKNOWN_CANCER_FEMALE_272\best_model\Pr
log_2024-09-12_12-32-27.txt

[BenSamy2020]

Can the Koina serve models handle these modification:

[yangkl96]

Only AlphaPeptDeep will be able to support the modifications such as C-terminal PTMs and carbamidomethylation of noncysteine amino acids, since it attempts to predict all PTMs in UniMod. I have previously not tested MSBooster for C-terminal modifications, hence the errors. Do you mind sharing with me one mzml and its associated pin file? I can make the necessary changes and send you a working version.

[BenSamy2020]

Hi, please share dropbox link. thanks

[BenSamy2020]

Also, I suggest adding a warning or stop message upon clicking the start run button of the GUI to remind users that mods that are not trained on prosit cannot be utilised.

[fcyu]

It can. I think MSBooster will strip the PTMs that the model doesn't support and shift the peaks after getting the predicted spectra.

Best,

Fengchao

[yangkl96]

Here is the request link: https://www.dropbox.com/request/c9sgqiJOUG1EqZb0AYx0

Thanks for the suggestion, I can add a warning or documentation.

[BenSamy2020]

Hi @yangkl96,

Done thank you.

[BenSamy2020]

Hi can I get an update on this thank you.

[yangkl96]

I am making some final changes and should have a new version for you by tomorrow

[yangkl96]

Hi Ben,

Thanks for your patience. Can you try out the newest version 1.2.56 here?

[BenSamy2020]

Greeting @yangkl96 ,

Please share the file again, thank you.

Regards,
Ben

[yangkl96]

https://www.dropbox.com/scl/fo/sioaysait4lkbdkvk5bn6/AKGomsKTlP6fSup8nnL43YE?rlkey=3k61o6l0o2wsg3m5ml2buv4f1&st=uqvbom7j&dl=0

You can use the most recent upload, MSBooster-1.2.59.jar

[BenSamy2020]

log_2024-10-22_00-29-18.txt

Greetings @yangkl96,

I am still facing issue with MSBooster.

Operating on slice 10 of 10:
Fragment index slice generated in 77.54 s
001. SLAS2_1845_DIABETES-MELLITUS.mzBIN_calibrated 0.2 s
[progress: 31545/31669 (100%) - 3140 spectra/s]​
[progress: 31669/31669 (100%) - 2988 spectra/s] 10.6s
Building spectral index for the mzBIN_calibrated file 34.3 s
Rescoring with peak tracing 7.4 s
Picking top PSMs for each precursor 0.1 s
Rescoring 1.2 s
Writing results 0.6 s
MAIN SEARCH DONE IN 16.080 MIN

TOTAL TIME 17.322 MIN*
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
D:\FragPipe-jre-22.0\jre\bin\java.exe -cp D:\FragPipe-jre-22.0\lib\fragpipe-22.0.jar;/D:/FragPipe-jre-22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\SLAS2_1845_DIABETES-MELLITUS_rank1.pepXML D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\SLAS2_NON_CANCER_282\SLAS2_1845_DIABETES-MELLITUS_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
D:\FragPipe-jre-22.0\jre\bin\java.exe -cp D:\FragPipe-jre-22.0\lib\fragpipe-22.0.jar;/D:/FragPipe-jre-22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\SLAS2_1845_DIABETES-MELLITUS_rank2.pepXML D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\SLAS2_NON_CANCER_282\SLAS2_1845_DIABETES-MELLITUS_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
D:\FragPipe-jre-22.0\jre\bin\java.exe -cp D:\FragPipe-jre-22.0\lib\fragpipe-22.0.jar;/D:/FragPipe-jre-22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\SLAS2_1845_DIABETES-MELLITUS_rank3.pepXML D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\SLAS2_NON_CANCER_282\SLAS2_1845_DIABETES-MELLITUS_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
D:\FragPipe-jre-22.0\jre\bin\java.exe -cp D:\FragPipe-jre-22.0\lib\fragpipe-22.0.jar;/D:/FragPipe-jre-22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\SLAS2_1845_DIABETES-MELLITUS_rank4.pepXML D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\SLAS2_NON_CANCER_282\SLAS2_1845_DIABETES-MELLITUS_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
D:\FragPipe-jre-22.0\jre\bin\java.exe -cp D:\FragPipe-jre-22.0\lib\fragpipe-22.0.jar;/D:/FragPipe-jre-22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\SLAS2_1845_DIABETES-MELLITUS_rank5.pepXML D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\SLAS2_NON_CANCER_282\SLAS2_1845_DIABETES-MELLITUS_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
D:\FragPipe-jre-22.0\jre\bin\java.exe -cp D:\FragPipe-jre-22.0\lib\fragpipe-22.0.jar;/D:/FragPipe-jre-22.0/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\SLAS2_1845_DIABETES-MELLITUS.pin D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\SLAS2_NON_CANCER_282\SLAS2_1845_DIABETES-MELLITUS.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2]
D:\FragPipe-jre-22.0\jre\bin\java.exe -Xmx120G -cp D:\FragPipe-jre-22.0\tools\MSBooster-1.2.59.jar;D:\FragPipe-jre-22.0\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList D:\MSFragger_Temp\Healthy_Pre_Post_Exercise\Output_LFQ-MBR_OpenProt_2\msbooster_params.txt
Error: Could not find or load main class Features.MainClass
Caused by: java.lang.ClassNotFoundException: Features.MainClass
Process 'MSBooster' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 2063 remaining tasks

[yangkl96]

You have to run it with FragPipe 22.1: https://www.dropbox.com/scl/fi/af1f06z39790c7bz0utwv/FragPipe-22.1-build06.zip?rlkey=ph04c6on0edy8grmimx55589c&st=y8vo725z&dl=0