--razorbin (unknow flag) error when running LFQ of Bruker QTOF Data

[jjnbdal]

Dear Support,

I am having a difficulty in running LFQ workflow with Bruker QTOF data (not timsTOF Data). I have two cohorts: control and treated, with 3 technical replicates each. When I run them separately as a group of three files or an individual file, the run of peptideProphet and proteinProphet went to completion.
However, when I created a multi analysis run with Control_1, Control_2, Control_3 (experiment = Control, Bioreplicate = 1, 2, 3 and Experiment_1, Experiment_2, and Experiment_3, it failed at the peptideProphet of the second group (experiment). With the following error.

Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: C:\Data\SBC_results3\Control_2]
C:\MSPrograms\MSFragger\FragPipe-jre-19.1\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --prot 0.01 --picked --sequential --tag rev_ --pepxml C:\Data\SBC_results3\Control_2 --protxml C:\Data\SBC_results3\combined.prot.xml --razorbin C:\Data\SBC_results3\Control_1.meta\razor.bin
Error: unknown flag: --razorbin
Usage:
philosopher filter [flags]

Flags:
.
.
.
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: C:\Data\SBC_results3\Control_1]
C:\MSPrograms\MSFragger\FragPipe-jre-19.1\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[13:06:14] Executing Report v5.0.0
INFO[13:06:14] Creating reports
INFO[13:06:14] Done
Process 'PhilosopherReport' finished, exit code: 0
PhilosopherReport [Work dir: C:\Data\SBC_results3\Control_2]
C:\MSPrograms\MSFragger\FragPipe-jre-19.1\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
INFO[13:06:15] Executing Report v5.0.0
INFO[13:06:15] Creating reports
ERRO[13:06:15] Cannot read file. open .meta\pep.bin: The system cannot find the file specified.
Process 'PhilosopherReport' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 13 remaining tasks

I tried different experiment/bioreplicate setup but still getting the same error.
I attached the logfile for your consideration. Look forward to hearing from you.

Jaran
log_2023-08-03_13-06-15.txt

[fcyu]

The error was due to version incompatibility. Upgrading FragPipe to version 20.0 will solve it.

Best,

Fengchao

[jjnbdal]

Dear Fengchao, I am glad I asked. Thank you so much. Best regards, Jaran

…

On Thu, 3 Aug 2023 at 20:32 Fengchao ***@***.***> wrote: The error was due to version incompatibility. Upgrading FragPipe to version 20.0 will solve it. Best, Fengchao — Reply to this email directly, view it on GitHub <#453 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJN7TZUF7MBYOIUC7C5HEA3XTOK6JANCNFSM6AAAAAA3CWGH6I> . You are receiving this because you authored the thread.Message ID: ***@***.***>