Process 'DIA-NN: Propagate information' finished, exit code: 1

[Shinya-Watanabe]

Hi,
I have the same error with this #1684. It seems like it was fixed. Please let me know what I should do to avoid this error.

java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
	at com.dmtavt.fragpipe.tools.diann.LocalizedPeptide.getBestLocalization(LocalizedPeptide.java:89)
	at com.dmtavt.fragpipe.tools.diann.Propagation.editReport(Propagation.java:290)
	at com.dmtavt.fragpipe.tools.diann.Propagation.propagate(Propagation.java:190)
	at com.dmtavt.fragpipe.tools.diann.Propagation.main(Propagation.java:69)
Process 'DIA-NN: Propagate information' finished, exit code: 1
Process returned non-zero exit code, stopping

log_2024-10-04_07-20-30.txt

Best,
Shinya

[fcyu]

Hi Shinya,

It was actually due to a different reason. Could you share your .d folders with us?

Thanks,

Fengchao

[Shinya-Watanabe]

How do you want me to share .d file? I have 6 files, and each of them is about 5GB size.

[fcyu]

Yes, please. Here is the link to upload the .d: https://www.dropbox.com/request/TG1snTlVtJNHY1vuzReD

Thanks,

Fengchao

[Shinya-Watanabe]

Hi Fengchao,

I just finished uploading all the .d files.

Thanks,
Shinya

[fcyu]

Hi Shinya,

Thank you for sharing the files.

I think PTMProphet, which is used to perform PTM localization, has issues with C terminal modifications. For example, the localization probability of one peptide is like GFGFVTYATVE(0.0682)E(0.0748)VD(0.2317)AAMNTTPHKc. The summation of the probability does not equal to 1, which should.

There are also many weird errors printed by PTMProphet due to the C terminal modifications. Such as

[ERROR:] Cannot initialize for sequence: nEMNEAPSESGSWSSPEMc[61], unknown mods may exist in spectrum 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.174820.174820.3
[ERROR:] Cannot initialize for sequence: nIENLLQSLEMc[105], unknown mods may exist in spectrum 20240927_SW-KF_S1_sup_Slot2-37_1_8056_diatracer.183725.183725.2
...

After removing the C terminal modifications, it went well log_2024-10-05_13-21-57.txt

You could also disable the PTMProphet id you don't need the PTM localization prob.

Best,

Fengchao

[Shinya-Watanabe]

Thank you, Fengchao, for figuring this out.

Protein C-term modification is a positive control to check if we can detect the known modification site. I don't think PTM localization probabilities, but Do I still get PTM localization when PTMProphet is disabled?

Best,
Shinya

[fcyu]

If PTMProphet is disabled, you will still have the PTMs localized in the peptides, but there will be no probability to measure the confidence.

Best,

Fengchao

[Shinya-Watanabe]

Thanks. It seems like that is the only way to go for now. Is this a bug that PTMProphet would fix at some point?

Best,
Shinya

[fcyu]

We need to contact the PTMProphet developer to figure it out.

Best,

Fengchao

[Shinya-Watanabe]

Would you be able to report this issue to them? or Could you direct me how to contact them?

Best,
Shinya

[fcyu]

I will keep you updated.

Best,

Fengchao

[Shinya-Watanabe]

Thank you! I am looking forward to it!

Best,
Shinya