Updating Philosopher's Tables java.lang.NullPointerException

[tjlundgren]

Hello,
I'm attempting to run LFQ on a closed search of TIMSTOF DDA data, with the default IonQuant settings. I've run into an error at the Updating Philosopher's tables step, and unfortunately don't know what context or other information would be helpful. Any help would be appreciated, and please let me know what other information would be helpful in troubleshooting!

Full log--
log_2021-08-11_12-24-18.txt
Last bit of log --
2021-08-12 12:15:33 [INFO] - Estimating match-between-runs FDR...
2021-08-12 12:15:41 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.982800
2021-08-12 12:15:41 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100
2021-08-12 12:15:41 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100
2021-08-12 12:15:41 [INFO] - Updating Philosopher's tables...
java.lang.NullPointerException
at q.(Unknown Source)
at ionquant.IonQuant.main(Unknown Source)
2021-08-12 12:15:42 [ERROR] - null
Process 'IonQuant' finished, exit code: 1
Process returned non-zero exit code, stopping

[fcyu]

It is due to a bug in Philosopher that there are empay Prev AA or Next AA for decoy peptides (Nesvilab/FragPipe#420). Setting print-decoy to false can solve this problem. In most cases, there is no need to print decoys because the PSMs have been filtered with 1% FDR.

Best,

Fengchao

[tjlundgren]

Thank you for the quick response!

[anesvi]

Felipe can you release a fix to this issue? Fengchao: do we have a workflow where we checked ‘print decoys’ by default? Or the users change themselves? From: Fengchao ***@***.***> Sent: Friday, August 13, 2021 10:04 AM To: Nesvilab/IonQuant ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/IonQuant] Updating Philosopher's Tables java.lang.NullPointerException (#25) External Email - Use Caution It is due to a bug in Philosopher that there are empay Prev AA or Next AA for decoy peptides (Nesvilab/FragPipe#420<Nesvilab/FragPipe#420>). Setting print-decoy to false can solve this problem. In most cases, there is no need to print decoys because the PSMs have been filtered with 1% FDR. Best, Fengchao — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#25 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM6YP43YCHVSEYXPAANLT4UQ6BANCNFSM5CDUOXLQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[fcyu]

No, the "print decoys" in FragPipe is always false by default. Best, Fengchao

…

On Fri, Aug 13, 2021 at 10:08 AM Alexey Nesvizhskii < ***@***.***> wrote: Felipe can you release a fix to this issue? Fengchao: do we have a workflow where we checked ‘print decoys’ by default? Or the users change themselves? From: Fengchao ***@***.***> Sent: Friday, August 13, 2021 10:04 AM To: Nesvilab/IonQuant ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/IonQuant] Updating Philosopher's Tables java.lang.NullPointerException (#25) External Email - Use Caution It is due to a bug in Philosopher that there are empay Prev AA or Next AA for decoy peptides (Nesvilab/FragPipe#420< Nesvilab/FragPipe#420>). Setting print-decoy to false can solve this problem. In most cases, there is no need to print decoys because the PSMs have been filtered with 1% FDR. Best, Fengchao — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< #25 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AIIMM6YP43YCHVSEYXPAANLT4UQ6BANCNFSM5CDUOXLQ>. Triage notifications on the go with GitHub Mobile for iOS< https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android< https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABU27W23DKGRKZAPNCAD2M3T4URMDANCNFSM5CDUOXLQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

-- Dr. Fengchao Yu Research Investigator University of Michigan