FragPipe
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Nesvilab
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
The modified file is a tutorial on how to run **FragPipe** using **Docker** and **Apptainer** (formerly Singularity). It explains how to pull and run the `fcyucn/fragpipe:` container in Docker, convert...
Greetings @fcyu, I am experiancing the error of: **{"error":"in ensemble 'Prosit_2020_intensity_HCD', Failed to process the request(s) for model instance 'Prosit_Preprocess_charge', message: IndexError: index 6 is out of bounds for axis...
Hi We ran DIA_spec_diaPASEF workflow and DIA NN output protein group files does not have protein name. However, if i run DIA NN without using FragP [PG_output.xlsx](https://github.com/user-attachments/files/17395333/PG_output.xlsx) ipe then protein...
This is PR revised the SDRF module based on Yasset's suggestion and feedback. No need for others to review. I will merge after thorough testing. Best, Fengchao
Hi, I have the same error with this #1684. It seems like it was fixed. Please let me know what I should do to avoid this error. ``` java.lang.ArrayIndexOutOfBoundsException: Index...
Hi all, I had a quick question regarding how the calculation of protein coverage is performed in the `protein.tsv` report. I was trying to compute protein coverage by using the...
Dear Fragpipe team, while revising the output of MSFragger (combined.proteins.tsv) I´ve just observed the lack of a "Combined.Unique.Peptides" column, why this absence? I am asking you this because there is...
I have the same issue with this #1310 unable to resolve. The error happens when searching specific PTM modifications search, like below. I used TMT11 plex. The monoisotopic mass of...
Dear fragpipe team, Although I'm running the DIA_DIA-Umpire_SpecLib_Quant workflow, I get an error about incompatibility with database splitting. `Please set the split database to 1. For DIA and DIA-Lib data...
['F:\\Sara\\fragpipe\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx20G', WindowsPath('F:/Sara/fragpipe/tools/MSFragger-4.1/MSFragger-4.1.jar'), '--generate_expect_functions', 'DQB2-notrypsin-DDA_scores_histogram.tsv'] Traceback (most recent call last): File "F:\Sara\fragpipe\tools\msfragger_pep_split.py", line 631, in main() File "F:\Sara\fragpipe\tools\msfragger_pep_split.py", line 623, in main combine_results() File "F:\Sara\fragpipe\tools\msfragger_pep_split.py", line 477, in...
