ERRO:Cannot read file. open .meta\psm.bin: The system cannot find the file specified.

[yuewang-wy]

• Describe the issue or question: I'm submitting a:

[ X] problem running the software ✔ bug report feature request question My MSFragger use case:

[ X] ✔Closed search (standard small precursor mass tolerance) Open search (large precursor mass tolerance) put your general problem description here

System info System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_201, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 18.0 MSFragger version 3.8 Philosopher version 5.0.0 IonQuant version 1.9.8

Genral proteomics experiment description e.g. "TMT, Mouse, full cell lysate with Trypsin，multi-sets of TMT"

Sequence database mouse uniprot

• Upload your log file

(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.) Process 'PhilosopherFilter' finished, exit code: 0 FreeQuant [Work dir: I:\Data\dataIndividual\SCP\20230704\test\set4] D:\FragPipe-18.0\philosopher_v5.0.0_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir I:\Data\dataIndividual\SCP\20230704\test INFO[10:07:37] Executing Label-free quantification v5.0.0
INFO[10:07:38] Indexing PSM information
INFO[10:07:38] Reading spectra and tracing peaks
INFO[10:07:38] Processing TMT18_Set4_20230704 INFO[10:08:24] Assigning intensities to data layers
INFO[10:08:24] Done
Process 'FreeQuant' finished, exit code: 0 FreeQuant [Work dir: I:\Data\dataIndividual\SCP\20230704\test\set5] D:\FragPipe-18.0\philosopher_v5.0.0_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir I:\Data\dataIndividual\SCP\20230704\test INFO[10:08:24] Executing Label-free quantification v5.0.0
ERRO[10:08:24] Cannot read file. open .meta\psm.bin: The system cannot find the file specified. Process 'FreeQuant' finished, exit code: 1 Process returned non-zero exit code, stopping

Cancelling 13 remaining tasks

[yuewang-wy]

I have no idea what's wrong with my procedure，please help me~

[fcyu]

Could you upgrade FragPipe to version 20.0, and try again?

Thanks,

Fengchao

[yuewang-wy]

Thank you very much，I have solved！

[Ale-ksa-ndra]

hello it was working FP v22.0 now i got this message level=error msg="Cannot read file. open .meta\psm.bin: The system cannot find the file specified can you please help?

[danielgeiszler]

Please open a new issue and follow the instructions for uploading your log file.

[Ale-ksa-ndra]

thank you for your reply it does not help

i have followed this: Select workflow and add spectral files In the ‘Workflow’ tab:

1. Choose the workflow you want to use from the dropdown menu and press ‘Load’. Use the Default workflow for simple conventional (closed) searches. A number of common workflows (including glyco and DIA) are provided. We always recommend starting with one of the provided workflows and customizing it as needed. Customized workflows can be saved (with a unique name) for future use or sharing with other users (all workflows are stored in the FragPipe ‘workflows’ folder).
2. Set the amount of memory & number of logical cores to use. A RAM setting of 0 will allow FragPipe to automatically detect available memory and allocate a safe amount. Notes about HPC: On some high performance computing configurations, RAM=0 may be interpreted literally, so users should manually specify an appropriate amount of memory.
3. Select ‘IM-MS’ for Bruker timsTOF PASEF data or ‘Regular MS’ for all other data types (including FAIMS). Drag & drop LC/MS files into the window or use ‘Add files’ or ‘Add Folder Recursively’ to add all files in a folder, including those in subfolders.

Notes about timsTOF data: We recommend using raw ddaPASEF files (.d files), where the .d folder is the raw file. If you have already run MSFragger on the .d files, having the .mzBIN files from that analysis in the same directory as the .d files will speed up the analysis. If you don’t need to perform quantification, you can use .mgf files (which can be generated by Bruker’s instrument software immediately after data acquisition is completed) instead of .d. Once you’ve loaded your spectral files, set the data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-Lib; hover over ‘Data type’ in FragPipe to view the tooltip with more information) and annotate your data to specify Experiment and Bioreplicates, which determines how your PSM/peptide/protein etc. reports will be generated (the ‘Save as manifest’ button stores file locations and annotations for future use):

[fcyu]

@Ale-ksa-ndra can you upload the log file?

Thanks,

Fengchao

[Ale-ksa-ndra]

log_2024-06-25_13-13-27.txt

[Ale-ksa-ndra]

this is the one thank you

[fcyu]

You skipped many steps between MSFragger and quant

Cmd: [START], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [CheckCentroid], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [MSFragger], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [FreeQuant], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [PhilosopherReport], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [PTMShepherd], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [WorkspaceClean], Work dir: [C:\Users\achojna1\Documents\results]

Please read the tutorials, load the LFQ-MBR workflow, and try again.

Best,

Fengchao

[Ale-ksa-ndra]

ok, thank you. log_2024-06-06_11-30-19.txt it was working before thank you i will

[fcyu]

This one has a different but good configuration

Execution order:

Cmd: [START], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [CheckCentroid], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [MSFragger], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [Percolator], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [ProteinProphet], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [PhilosopherFilter], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [PhilosopherReport], Work dir: [C:\Users\achojna1\Documents\results]
Cmd: [WorkspaceClean], Work dir: [C:\Users\achojna1\Documents\results]

Best,

Fengchao

[Ale-ksa-ndra]

thank you

[Ale-ksa-ndra]

hi i have other problem today which i do not understand pleasee see below

[Ale-ksa-ndra]

ionquant is there, also the newest version

[fcyu]

@Ale-ksa-ndra I think you have created a new issue about it https://github.com/Nesvilab/FragPipe/issues/1650