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Nesvilab / IonQuant

A label free quantification tool.
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Java NumberFormatException on MS1 Quant #16

Closed BrendonSeale closed 3 years ago

BrendonSeale commented 3 years ago

Hello,

I am running into an issue with IonQuant & MBR where IonQuant fails due to a Number Format Exception while assigning razor peptides (I think). I've run this twice now (a dataset containing 10 different timsTOF datafiles) and it fails on the same peptide: TVKPSEC[57.0215]S. It succeeds on another modified peptide so I'm not sure what the issue is.

I have attached my logfile. Let me know if you need anything else, I can provide the data if necessary (though very large). I am running a custom database so I can try a standard one from UniProt if you think that would be helpful as well.

Thanks, Brendon Seale

log_2021-03-31_12-23-09.txt

fcyu commented 3 years ago

Your logs shows that something unexpected was happened before IonQuant:

2021-03-31 10:44:24 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\10to1_1/protein.tsv. Will not update it.
2021-03-31 10:44:36 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\10to1_2/protein.tsv. Will not update it.
2021-03-31 10:44:49 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\1to1_1/protein.tsv. Will not update it.
2021-03-31 10:45:01 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\1to1_2/protein.tsv. Will not update it.
2021-03-31 10:45:16 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\2to1_1/protein.tsv. Will not update it.
2021-03-31 10:45:28 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\2to1_2/protein.tsv. Will not update it.
2021-03-31 10:45:44 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\3to1_1/protein.tsv. Will not update it.
2021-03-31 10:45:59 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\3to1_2/protein.tsv. Will not update it.
2021-03-31 10:46:11 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\5to1_1/protein.tsv. Will not update it.
2021-03-31 10:46:23 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\5to1_2/protein.tsv. Will not update it.
2021-03-31 11:35:47 [WARNING] - Ion SAGLGPK@2 was assigned to different razor proteins: NP_001139698.1|gn|KRT72:140807| and Q14CN4-1. Skip this in MSstats.tsv.
2021-03-31 11:35:47 [WARNING] - Ion PPLPPPPPR@2 was assigned to different razor proteins: NP_001258580.1|gn|FBXL19:54620| and NP_001093254.2|gn|FBXL19:54620|. Skip this in MSstats.tsv.
2021-03-31 11:35:47 [WARNING] - Ion ELGELIK@1 was assigned to different razor proteins: NP_000274.2|gn|PDE6B:5158| and NP_001138763.1|gn|PDE6B:5158|. Skip this in MSstats.tsv.
2021-03-31 11:35:47 [WARNING] - Ion AAAAAAAAAAK@2 was assigned to different razor proteins: NP_001075222.1|gn|ELN:2006| and NP_003964.3|gn|RPL14:9045|. Skip this in MSstats.tsv.
...

Can you send us all of the result files except for .d?

Best,

Fengchao

BrendonSeale commented 3 years ago

Can you access this link:

https://1drv.ms/u/s!AqAzfSxL_4mUgq9eu1lExOCJMN5d4Q?e=BBcKMW

Thanks

From: Fengchao @. Sent: March 31, 2021 1:00 PM To: Nesvilab/IonQuant @.> Cc: Brendon Seale @.>; Author @.> Subject: Re: [Nesvilab/IonQuant] Java NumberFormatException on MS1 Quant (#16)

Your logs shows that something unexpected was happened before IonQuant:

2021-03-31 10:44:24 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\10to1_1/protein.tsv. Will not update it.

2021-03-31 10:44:36 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\10to1_2/protein.tsv. Will not update it.

2021-03-31 10:44:49 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\1to1_1/protein.tsv. Will not update it.

2021-03-31 10:45:01 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\1to1_2/protein.tsv. Will not update it.

2021-03-31 10:45:16 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\2to1_1/protein.tsv. Will not update it.

2021-03-31 10:45:28 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\2to1_2/protein.tsv. Will not update it.

2021-03-31 10:45:44 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\3to1_1/protein.tsv. Will not update it.

2021-03-31 10:45:59 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\3to1_2/protein.tsv. Will not update it.

2021-03-31 10:46:11 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\5to1_1/protein.tsv. Will not update it.

2021-03-31 10:46:23 [WARNING] - There is no usable protein table: D:\Tims_out\Species_Quant_2\5to1_2/protein.tsv. Will not update it.

2021-03-31 11:35:47 [WARNING] - Ion @.*** was assigned to different razor proteins: NP_001139698.1|gn|KRT72:140807| and Q14CN4-1. Skip this in MSstats.tsv.

2021-03-31 11:35:47 [WARNING] - Ion @.*** was assigned to different razor proteins: NP_001258580.1|gn|FBXL19:54620| and NP_001093254.2|gn|FBXL19:54620|. Skip this in MSstats.tsv.

2021-03-31 11:35:47 [WARNING] - Ion @.*** was assigned to different razor proteins: NP_000274.2|gn|PDE6B:5158| and NP_001138763.1|gn|PDE6B:5158|. Skip this in MSstats.tsv.

2021-03-31 11:35:47 [WARNING] - Ion @.*** was assigned to different razor proteins: NP_001075222.1|gn|ELN:2006| and NP_003964.3|gn|RPL14:9045|. Skip this in MSstats.tsv.

...

Can you send us all of the result files except for .d?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/IonQuant/issues/16#issuecomment-811253060, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASD2G3ZXL4L2LUOUTWVYDWTTGNII3ANCNFSM42FATTIA.

fcyu commented 3 years ago

There is no protein.tsv in your folders. All spectral count, ion count, and intensity columns in your combined_protein.tsv are zero. Can you delete all files and rerun everything again?

Best,

Fengchao

BrendonSeale commented 3 years ago

That seemed to get it. Something must have gone wrong running again in the same folder. Thanks for the help!

From: Fengchao @. Sent: March 31, 2021 2:43 PM To: Nesvilab/IonQuant @.> Cc: Brendon Seale @.>; Author @.> Subject: Re: [Nesvilab/IonQuant] Java NumberFormatException on MS1 Quant (#16)

There is no protein.tsv in your folders. All spectral count, ion count, and intensity columns in your combined_protein.tsv are zero. Can you delete all files and rerun everything again?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/IonQuant/issues/16#issuecomment-811334074, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASD2G375BIR7P7W5CCPXYWTTGNUMPANCNFSM42FATTIA.

fcyu commented 3 years ago

You are welcome.