PhilosopherAbacus exit code: 1 when using split database

[yannic-chen]

Hello Fragpipe Team,

I am running samples through multiple databases and two of those would need to be split as they would produce more than 2 billion peptides. However, this resulted in the following error:

C:\Programme\FragPipe_v20.0\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe abacus --razor --reprint --tag rev_ --protein --peptide exp_1 exp_10 exp_11 exp_12 exp_2 exp_3 exp_4 exp_5 exp_6 exp_7 exp_8 exp_9 INFO[10:28:48] Executing Abacus v5.0.0 INFO[10:28:48] Restoring PSM results INFO[10:28:58] Processing combined file INFO[10:28:58] Parsing combined.pep.xml ERRO[10:28:58] Cannot read file. Error parsing the file Process 'PhilosopherAbacus' finished, exit code: 1 Process returned non-zero exit code, stopping

Fragpipe runs flawlessly with the smaller databases which do not require splitting on these samples.

I have attached the complete log. log_2023-12-13_14-59-19.txt

[hdesai17]

Hi team

I'm also running into this issue in both FP v20 & v21 -- experiment group searches w/ database splitting results in this exact Abacus error; however, without database splitting it finishes. No experiment groups' w/ database splitting also finishes. So errors occur when both are used

Appreciate any help, thank you!! -Heta

[fcyu]

Thanks for reporting the bug. Please find the fixed FragPipe in https://www.dropbox.com/t/z9IDmxRdXYF0zUdO

Best,

Fengchao

[hdesai17]

Thanks! Anyway to get version with JRE?

[fcyu]

Sure, here it is https://www.dropbox.com/t/HurKqYXY3sqXbVEl

Best,

Fengchao

[djnesbitt]

Sure, here it is https://www.dropbox.com/t/HurKqYXY3sqXbVEl

Best,

Fengchao

I've also been having this issue - would you be able to re-share the DropBox link?

Thanks, Daniel

[fcyu]

@djnesbitt , sure. Here it is https://www.dropbox.com/t/rLtfTwzJeIVXZMzx

Best,

Fengchao

[djnesbitt]

@djnesbitt , sure. Here it is https://www.dropbox.com/t/rLtfTwzJeIVXZMzx

Best,

Fengchao

Is this the version with the JRE?

Thanks, Daniel

[fcyu]

@djnesbitt , no. Here is the one with jre https://www.dropbox.com/t/gOzPKWM7QqCwz3Av

Best,

Fengchao