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Hello,
I've been trying to apply the Philosopher pipeline to a recently published [CPTAC proteomics dataset](https://www.sciencedirect.com/science/article/pii/S0092867420314513). The workflow appear…
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Hi,
I am running the pipeline mode, and I want to optimise the computational resources used. I have tried assigning different amount of RAM and number of threads to analyse the same set of files, b…
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Hi,
I am trying to use philosopher in order to perform quantification. I first performed MSFragger and got to the point where I generated interact.prot.xml.
Now when I run the following code:
$…
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with philosopher version 3.2.9. An error message is as following, I am not sure it is due to improperly configuration of our local clustering or any configuration I can set in philosopher_329.yml..
I…
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I'm still running that TMT pipeline on some CPTAC datasets and am getting a strange error with PeptideProphet where it claims it can't find a protein database. There are two odd quirks to this. First …
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**Describe the bug**
I am following the instructions on "Running a FragPipe-equivalent workflow on Linux", here: https://msfragger.nesvilab.org/tutorial_linux.html
I've run my analyses on the exac…
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Hello!
I'm working on running CPTAC data through the Philosopher pipeline. Everything seems to be coming out all right except for the TMT-Integrator step; it runs with no errors, although the files i…
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apparently the FileConverter right now does not convert mzML to csv, however it converts to DTA / DTA2D which is basically csv. This is confusing for users
```
Executing the previous command results…
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Hi, further to [another issue](https://github.com/Nesvilab/philosopher/issues/139) I was discussing which I now believe to be resolved, I am using the TMT pipeline to analyse databases that I am downl…
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Hi,
I have interact.pep.xml and interact.prot.xml and when I wanted to perform label quantification, it gives me an error.
INFO[09:13:07] Executing Isobaric-label quantification v2.1.1
FATA[09…