FragPipe

FragPipe copied to clipboard

Philosopher cannot create report files due to unknown reason. It also needs more than 2 TB memory with 280 GB interact.pep.xml files.

17

Hi FragPipe, I am trying to create a spectral library with DIA-Umpire_SpecLib workflow. While running Philosopher Report, an `Cannot write file` error occurred.  Here are some details: - Raw...

Wenhhao

ERRO[14:35:10] the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter

6

[log_2021-11-26_15-20-51.txt](https://github.com/Nesvilab/FragPipe/files/7609556/log_2021-11-26_15-20-51.txt)

DanielConole

PhilosopherFilter fails with `Cannot decode packed binary. expected element type <msms_pipeline_analysis> but have <msms_run_summary>`

18

**Describe the bug** I was running the `LFQ-phospho` workflow on a set of mzML files from Bruker data. After running the whole process during the `PhilosopherFilter` step one of the...

hguturu

New isobaric labels for FragPipe

1

There are only isobaric labels of TMT6, TMT10, TMT11, TMT16, iTRAQ4 and iTRAQ6 in FragPipe. If I use TMT2plex or TMT analogues, how can I add these custom labels by...

CNChomiX

Got a "FileNotFoundError" when using the split DB

3

**Describe the bug** Hi Fengchao, I got a "FileNotFoundError" when using the split DB. Attached is my log file. Can you please take a look and let me know if...

huiyinc

Accelerate single threaded jobs using multiple parallel processes

3

**Is your feature request related to a problem? Please describe.** Currently, FragPipe parallelizes jobs based on if the tool supports multiple threads. But, single threaded jobs like initializing philosopher, annotating...

hguturu

**Is your feature request related to a problem? Please describe.** My feature request would serve as additional value added to IonQuant outputs. This request was stimulated by discussions with @fcyu...

enonimos

Plant proteins not appearing in output files

8

**Describe the bug** I have used MSFragger to analyse proteomics data from Arabidopsis before, but when I tried with the latest version of MSFragger (in the FragPipe wrapper), it did...

ndtivendale

Spectral library generation part is using more threads that it is supposed to be

6

The EasyPQP `convert` command seems to be multithreading: each command is using all CPU cores. But the `gen_con_spec_lib.py` script also execute multiple `convert` commands in parallel, which makes the total...

fcyu

Report mass shift as a variable mod for pepxml import to Skyline

2

Hi Alexey, Fangchao, Daniel, I am using FragPipe to generate annotated spectra for import into Skyline and making raw spectral libraries for DIA. When using Open search and Mass offset...

dkueltz