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wtsi-proteomics / MascotPercolator

MascotPercolator is a software package that interfaces the database search algorithm Mascot with Percolator, a well-performing machine learning algorithm for re-scoring database search results.
MIT License
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Cannot run MascotPercolator on Linux #2

Open lhuangjs opened 5 years ago

lhuangjs commented 5 years ago

I install MaxcotPercolator following https://www.sanger.ac.uk/science/tools/mascotpercolator. I try to run MascotPercolator on my Linux computer. However, it cannot work well and warn No modifiactions loaded. But the mod_file file is in the correct path.

Config File Location:/home/huangjs/Documents/MascotPercolator/MascotPercolator.2.16/config.properties

Mascot Percolator v2.11
Created by Markus Brosch and James Wright at the Wellcome Trust Sanger Institute
Documentation: http://www.sanger.ac.uk/Software/analysis/MascotPercolator/

Please cite:
- K�ll, L., Canterbury, J. D., Weston, J., Noble, W. S., and MacCoss, M. J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods, 4(11), 923-925.
- Brosch, M., Yu, L., Hubbard, T., and Choudhary, J. (2009) Accurate and Sensitive Peptide Identification with Mascot Percolator. J Proteome Res, 8(6), 3176-3181.
- Wright, J. C., Collins, M. O., Yu, L., Kall L., Brosch, M., and Choudhary, J. (2012) Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator. Mol Cell Proteomics, 11(8), 478-491.

/home/huangjs/Documents/MascotPercolator/demo/F001618.dat
MascotPercolator/INPUT/
features file created: /tmp/percolator_features17531594468736670226.tmp.txt

reading file: /home/huangjs/Documents/MascotPercolator/demo/F001618.dat
setup target processing ...
/home/huangjs/Documents/MascotPercolator/MascotPercolator.2.16/mod_file
No modifiactions loaded.
/home/huangjs/Documents/MascotPercolator/MascotPercolator.2.16/mod_file
false

How to solve the problem?

By the way, I found the source code is old on github. Can you provide the latest version of the code? Thanks!

lhuangjs commented 5 years ago

The problem may be caused by mascot msparser. mascot msparser requiresglibc-2.3.4 or later and libstdc++-6.0.3 or later. mascot msparser installation installation

The 64-bit version of Mascot Parser Java toolkit requires glibc-2.3.4 or later and libstdc++-6.0.3 or later. The 32-bit version requires glibc-2.3.4 or later.

wtsi-proteomics commented 5 years ago

Hi, I will try and help,

Can you tell me:

  1. Which version of Mascot Server are you using / have the .dat file be created with?
  2. can you verify the contents of the mod_file please?

The error relates to msparser not thinking that the mod_file is valid, this file is only required for quite old versions of MascotServer, from I think version 2.3 onwards modification information in contained within the dat file itself.

I no longer work at the Sanger Institute hence there have been no updated releases of the code or software.

cheers

James