philosopher

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`philosopher-v4.5.1-RC5 database --id UP000299084,UP000504605,UP000030684` does not work anymore

1

**Describe the bug** `philosopher-v4.5.1-RC5 database --id UP000299084,UP000504605,UP000030684` should download the FASTAs **To Reproduce** ``` #!/bin/bash set -euxo pipefail TMPDIR=$PWD TMP=$TMPDIR TEMP=$TMPDIR export TMPDIR TMP TEMP export JAVA_OPTS=-Djava.io.tmpdir=$PWD PHILOSOPHER=/usr/local/nesvilab/philosopher_v4.5.1/philosopher-v4.5.1-RC5 ${PHILOSOPHER} version...

cpanse

Philosopher: Cannot read file. Error parsing the file.

4

Hi, I have discovered a bug with Philosopher. Console Information: INFO[21:32:23] Executing Filter v5.1.0 INFO[21:32:23] Processing peptide identification files INFO[21:32:23] Parsing G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.mod.pep.xml ERRO[21:32:23] Cannot read file. Error parsing the file...

WenSheng-Ye

protein start and end positions not showing in combined peptides report.

1

Philosopher 5.0.0 release info: "Added the protein start and end positions to ions and peptides report." However, combined_peptides.tsv report does not contain the new and useful info. Please advise! Thank...

heuselm

I am trying to search my PAL dataset with the Mass offset workflow to precisely assign the sites of labeling. I encountered the PeptideProphet error message and don't know how...

chaudngo

- Describe the issue or question: In the combined_protein output file I'm missing the protein coverage column. - Upload your log file (If a log file hasn't been generated, go...

lyons89

PhilosopherAbacus exit code: 1 when using split database

8

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...

yannic-chen

Format error in combined_protein.tsv when MS1 quant is disabled

1

Dear developers, I've stumbled upon a small, but rather inconvenient bug when FragPipe is used without MS1 quant enabled. It appears that the combined_protein.tsv contains **more cells in the entry...

hollenstein

FDR ISSUE

2

Hi Fengchao, Hope you are well. I had an error see below, Do you suggest changing the fdr from 0.01 to 0.05 in the "fdr filter and report"section of the...

kwynne71

Dear FragPipe Team, **Is your feature request related to a problem?** The requested feature is only for convenience. Currently the psm.tsv, ion.tsv, and peptide.tsv tables (and the combined versions of...

hollenstein

Let Philosopher print errors when there are protein hits from PSMs that cannot be found in the fasta file.

1

This is a bug/feature I found by accident (https://github.com/Nesvilab/FragPipe/issues/537#issuecomment-995943414). Basically, when you search the data with FASTA file A, and run Philosopher to filter the result using FASTA file B,...

fcyu