Known Issues

General

• Java used memory size

  Ajust the memory usage by Java according to your needs. When using memory intensive tasks as mzIdentML conversion of large files, an adjustement of the Java Xmx values may be required. The default is the usage of 13 GB of your RAM. Please refer to the Java documentation for further information. http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/java.html In Ursgal the parameter java_-Xmx can be used to adjust the Java memory usage.

• MS-GF+ (or another Java based engine) crashes

  Please make sure that you have installed the current Java Runtime Environment Download (Java SE Development Kit 8u131):

  http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
  

Windows general

• Some modules can not be compiled/installed with python3.4+ using pip.

  E.g. pyahocorasick can not be installed. This has the consequence, that on Windows the old peptide mapper version is used. There are several workarounds to compile and install the modules manually, e.g.:

  http://haypo-notes.readthedocs.io/python.html#build-a-python-wheel-package-on-windows

Windows 10

• MS Amanda can not load .fasta files

• calculating the md5 can cause problems e.g. while executing test.

  This is due to different line endings on Unix and Windows systems. The test functions test for both md5, so this problem should be avoided.

MONO

• Mono is the .NET replacement under *nix systems, since .NET is not directly

  ported by Microsoft to other systems than windows. Unfortunately mono is not as stable as the official .NET build. Therefore:

  MS Amanda crashes randomly under *nix systems (e.g. Linux or OS X)