1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
<HTML>
<HEAD>
<TITLE>FAQ</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">FAQ </div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><h2 style="border-top:2px solid grey;">TOPP</h2>
<ul>
<li>
<p class="startli"><b>I'm getting the error message "Unexpected internal error (unable to allocate enough memory (size = 0 bytes)"</b><br/>
Call "OpenMSInfo" and look at "OS Information". <br/>
If you are using the 32bit version of <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a>, the data you are processing is probably too big (e.g. using RAW data files bigger than 1.5 GB as input, or many featureXML files etc). You can now either:<br/>
</p>
<ul>
<li>
switch to the 64bit Version of <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a>. Be aware though that your Operating System also needs to have 64bit. Furthermore your PC should have sufficient RAM, to hold the data. Otherwise your harddrive will be used extensively for swapping and processing will take longer. </li>
<li>
on 32bit Windows systems you can try the increase the allowed amount of memory from 2GB to 3GB by using the <em>"/3GB"</em> boot switch (boot.ini). This might already do the trick. However, if your data again gets bigger, this solution will only help temporarily. Google "3GB windows". This trick does not depend on the amount of memory installed on your system! You can use it even if you have only 1GB or 2GB of RAM, although you hard drive will be used for swapping then. </li>
<li>
on 32bit Linux systems: sorry, we cannot do anything. Use a 64bit system or reduce the amount of data. </li>
</ul>
<p>If you already have the 64bit version, you probably encountered a bug in our software. Please contact the mailing list (see OpenMS.de).</p>
<p class="endli"></p>
</li>
<li>
<p class="startli"><b>Calling msConvert (of ProteoWizard) results in small mzML files with no peak data.</b><br/>
The Thermo interface expects an english locale setting. Otherwise it will silently forget to return peak data. Set your locale to english and it should work.</p>
<p class="endli"></p>
</li>
<li>
<p class="startli"><b>Some TOPP tools always crashes when executed. Other TOPP tools work properly.</b><br/>
If a error message similar to </p>
<div class="fragment"><div class="line"><a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">OpenMS::File::find</a>(...) of File.C error message: the file 'CHEMISTRY/Elements.xml' could not be found </div>
</div><!-- fragment --><p> is shown, you have probably moved your OpenMS installation manually?! Then the TOPP tools cannot find some required data files anymore, e.g. XML schema files or chemical isotope data.</p>
<p>Either of the following actions should fix your problem:</p>
<ul>
<li>Set the environment variable <em>OPENMS_DATA_PATH</em> to your <OpenMS>/share/OpenMS/ folder.</li>
<li>[developers only] Use the cmake option <em>-D INSTALL_PREFIX=...</em> to set the installtion directory. Run '<em>make OpenMS TOPP UTILS</em>' again.</li>
<li>[developers only] Execute <em>cmake</em> in the new location and run '<em>make OpenMS TOPP UTILS</em>' again.</li>
</ul>
<p class="endli"></p>
</li>
<li>
<p class="startli"><b>A TOPP tool crashes when loading a certain input file. Other files work properly.</b><br/>
If an XML input file is used, please check if the file is valid.</p>
<p>For most XML data formats, this can be done using the <em>FileInfo</em> tool: </p>
<div class="fragment"><div class="line">FileInfo -v -in <file></div>
</div><!-- fragment --><p>You can also check for corrupt data in peak files: </p>
<div class="fragment"><div class="line">FileInfo -c -in <file></div>
</div><!-- fragment --><p class="endli"></p>
</li>
</ul>
</div></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
