compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
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Search hangs on "Converting Spectrum file xxxxx.mgf to peak list" even using most up to date Java #357

Closed nCeon closed 1 year ago

nCeon commented 1 year ago

I am attempting to follow the mass-spec analysis tutorial at https://www.compomics.com/bioinformatics-for-proteomics/ and even when I use the resource files provided by the tutorial itself ("qExactive01819.mgf" and "uniprot-human-reviewed-trypsin-june-2021.fasta"), the search is hanging indefinitely on

Thu Jul 27 17:50:59 EDT 2023 Importing spectrum files. Thu Jul 27 17:50:59 EDT 2023 Importing spectrum file qExactive01819.mgf Thu Jul 27 17:50:59 EDT 2023 Importing spectrum files completed (15.0 milliseconds).

Thu Jul 27 17:50:59 EDT 2023 Converting spectrum file qExactive01819.mgf to peak list.

I am using the most up to date version of Java 1.8.0_38, which does show as red text in the "Java settings" of SearchGUI, so maybe there is some issue with the most recent java update?

Thank you all for making this tool available to the community and I would greatly appreciate any help getting it to work in my hands.

Operating System: Windows 10 Home 64-bit Java Version: Java 1.8.0_38 Search type being attempted: X! Tandem and OMSSA

Edit: I also attempted this on an Ubuntu workstation and it hangs at the same point. It also has the most up to date version of Java though.

**Edit2: Uninstalling Java and reinstalling version 20.0.2 fixed this issue, so it seems that maybe one of the more recent java updates broke the converting to peak list function?