Closed tjlundgren closed 3 years ago
fcyu
commented
3 years ago It is due to a bug in Philosopher that there are empay Prev AA or Next AA for decoy peptides (https://github.com/Nesvilab/FragPipe/issues/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
commented
3 years ago Thank you for the quick response!
anesvi
commented
3 years ago 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)
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It is due to a bug in Philosopher that there are empay Prev AA or Next AA for decoy peptides (Nesvilab/FragPipe#420https://github.com/Nesvilab/FragPipe/issues/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
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fcyu
commented
3 years ago 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< https://github.com/Nesvilab/FragPipe/issues/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
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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