SyMAP 4.2 Troubleshooting  
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This guide is intended to aid in the installation and configuration of SyMAP.
Please send questions and suggestions to symap@agcol.arizona.edu.

Problems



Circle view (web version) won't display, error "No font drivers..."

The website version of the circle view, created by circmap.cgi, needs the unix library freetype-devel. The full error message shown in the web browser is
"No font drivers enabled that can support this file, rebuild Imager with any of ft2 (FreeType 2.x), tt (FreeType 1.x) to use this font file at circmap.cgi line 162."

To resolve this, first install freetype-devel using

yum install freetype-devel
Then, the perl Imager module must be installed or reinstalled using
cpan -f -i Imager
After this, circmap.cgi should work.

Slow to load sequence and annotation

Two MySQL settings are especially important for SyMAP performance (and generally for InnoDB table performance). You can set these in the MySQL configuration file "my.cnf" and restart MySQL. Note that my.cnf is located at /etc/my.cnf, on both Linux and Mac.

innodb_buffer_pool_size The default is too low for most purposes. You should set this to around 1Gb if possible (note that the units are bytes).
innodb_flush_log_at_trx_commit=0 The default setting is 1, which results in very slow uploading of data.

Chromosome Explorer won't run on Macintosh

Typically this means there is a conflict with 3D Java libraries already on the Mac system. Note, the libraries supplied by Apple are out of date and not necessary to the system.

Before trying to fix the libraries the first thing to try is to run it without 3D:

./symap -no3d

Now if you want to use the 3D views, you need to remove the Mac libraries. They are in /System/Library/Java/Extensions. Just make a "3D" directory and move them all in there, where the system can't find them. Move all the ones called "j3d", plus "vecmath", and try symap again.

Not Enough Memory

This problem can occur when running from a web page (see (1) below) or as a standalone application (see (2) below).

(1) Adjusting Web Applet Memory Use
When running SyMAP from a web page (i.e., as an applet): The default Java applet memory limit is very low, and memory may run out for large displays or for the 2D Base View. Increase the Java memory limit for your system using the instructions below:

On Windows:

  1. From the Start menu button, select Settings, then Control Panel to open the Control Panel. Or right click on the Java icon in the lower right of the task bar.
  2. Double click the Java icon to open the Java Control Panel.
  3. Select the Java tab.
  4. Click the View button under Java Applet Runtime Settings.
  5. For each row, click the Java Runtime Parameters column and type -Xmx512m and press enter.
  6. Click the OK button to close the Control Panel.
  7. Restart your browser.
On Mac:
  1. In the Finder, select Go then select Applications.
  2. In the new window select Utilities, then double-click Java Preferences to open the Java Control Panel.
  3. Select the top-most Java version in the list under Java Applet Plugin and click Options.
  4. Under Java Runtime Parameters enter -Xmx512m.
  5. Click the OK button and close the Control Panel.
  6. Restart your browser.
On Unix:
  1. First locate the Java plugin file, under your home directory in either ~/.mozilla/plugins or ~/.mozilla/firefox/plugins
  2. Use ls -l to find where the plugin is linked from. This is the Java install directory.
  3. Change to ths install directory and execute bin/ControlPanel to open the Java Control Panel.
  4. Select the Java tab.
  5. Click the View button under Java Applet Runtime Settings.
  6. For each row, click the Java Runtime Parameters column and enter -Xmx512m.
  7. Click the OK button to close the Control Panel.
  8. Restart your browser.

(2) Adjusting Standalone Memory Use
When running SyMAP as a standlone application: For very large projects, or queries involving multiple genomes (e.g., 5 or more), the Project Manager may run out of memory. To fix this problem, run symap with the -m parameter to increase the maximum memory used from the default 2048 MB to 4096 MB.:

     > ./symap -m 4096
You will also need to be using a 64-bit processor. It should not be necessary to go any higher than this.

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Database connect errors

Error messages mentioning the database or SQL probably mean that the database connection could not be established or was lost. A message at startup means SyMAP was not able to connect to the database using the provided information in symap.config; see below for steps to debug this.

After startup, if the program is left idle for some time then its database connection will close and it will show a complicated-looking error on next usage. In this case the solution is to restart the program.

Following are some things to check for connection problems on SyMAP startup:

Check the database privileges

The database users specified in symap.config may not have necessary access to the database. If you are running the standalone version, then the relevant user is 'db_adminuser' (unless you are running a read-only session using 'symap -r' parameter). If you are running through the web applet, then is is 'db_clientuser'. In either case the user needs to have database access privileges from the machine where you are working. Note that MySQL privileges are granted specifically to certain users on certain machines. You can test the user access by using the MySQL command line client mysql, if it is installed on your machine, or by looking at the privilege table using an administration interface such as PHPMyAdmin. The mysqlaccess tool is also useful, if it is installed on your machine.

Check the MySQL configuration

The MySQL configuration file (/etc/my.cnf) should not contain any of the following lines that prevent remote access to the database.
     bind_address=127.0.0.1
     skip_networking 

Make sure the port is visible

If the database is on a different computer, test that its port 3306 is visible from your computer:
     telnet <server address> 3306
If it doesn't make a connection then either the server isn't running, or it is set to run on a non-standard port, or the port is blocked by a firewall. Contact a system administrator. (Note, to get out of telnet type "^]".)

Perl error on Web Install: "Can't locate ..."

The SyMAP web displays need some non-standard Perl modules. If any of these modules are missing, the install script will fail:
     Can't locate Data/Page.pm in @INC (...)
     Can't locate DBI.pm in @INC (...)
     Can't locate GD.pm in @INC (...)
	 Can't location Imager in @INC (...)
To install these modules on your server, execute the following commands (you will need admin privileges):
     > cpan Data::Page
     > cpan DBI
     > cpan GD
	 > cpan Imager
Note: CPAN is the Comprehensive Perl Archive Network.

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Unable to view Java applets on MacOS

A. Safari is currently not supported; please try Firefox or Google Chrome.

B. Support for Java within MacOS seems to be problematic. However, as of 8/2012, if you have Mac OSX 10.6.8, and have installed all updates, it should work through either Firefox or Chrome. On Firefox, it is also possible that Java is dis abled by the browser. You can check this in "tools->add-ons".

Unable to view Java applets using Firefox

It is also possible that Java is disabled by the browser. You can check this in "tools->add-ons".

Unable to view Java applets over the Web

First, make sure you have Java 1.6 (or later) installed and that its plugin is enabled. On MacOSX, this is done through the Preferences manager which is in Applications/Utilities. On Windows, it is a Java icon on the Control Panel. On Unix, the plugin must be installed into a subdirectory of .mozilla in your home directory,

If it still doesn't work (after restarting computer), then check the platform and browser-specific troubleshooting sections as follows:

"No projects found" on the web display

If there are no projects to select in the main projects web page (projects.cgi), then either the demo was not run, or the demo projects were not properly loaded into the database. Re-run the
demo and try again.

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"The built-in MySQL server cannot run..."

SyMAP comes with a MySQL server built in, but it does not run right if there is another MySQL server already running on the computer. There are two solutions: either stop the other server temporarily, or edit the parameters file to point SyMAP at that server (or another server) so it doesn't use the built-in MySQL.

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"Status window disappeared"

Occassionally the status window disappears when running an alignment. Clicking the top of the project manager sometimes brings it back. Otherwise, just check the output to the terminal, which tells you when it is done. You may have to restart the project manager to see the results.

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"No anchors loaded"

This message indicates that SyMAP could not parse the MUMmer or BLAT output files to load the anchors.

The most likely reason is that MUMmer or BLAT failed to run. Usually this is because the platform (linux 32/64 bit, or mac) was not detected properly. First try re-starting symap using the '-32, -64, -linux, -mac' parameters to specify your platform (run 'symap -h' for list of parameters).

The next likely cause is trying to run a whole-chromosome MUMmer alignment on a 32-bit machine. MUMmer usually uses more than 2Gb per thread, which is not possible on a 32-bit machine. If you suspect this is the problem, try running on a 64-bit machine. If you compiled MUMmer yourself, check here.

If that does not resolve the problem, The next step is to look in symap.log for more detailed error messages. Then, you should look at the MUMmer log files (extension .mum.log) in the appropriate anchors directory

data/pseudo_pseudo/<proj1_to_proj2>/anchors/pseudo_pseudo
These contain the messages printed by MUMmer, and should show why it failed to run.

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BES not loaded, or BES hits not loading

Generally, this is caused by a name formatting error. Make sure the BES names are formatted as clone names with extension "r" or "f". The clone names should exactly match those in FPC, and there should be no other prefix or suffix. Do not use ".r" or ".f".

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InnoDB tables not supported

This can happen in a couple of ways ways. Look in the mysql log for clues.
  • MySQL started with the "skip-innodb" flag. Solution is to remove this.
  • InnoDB log file problems. This can happen if you change the log file size, without deleting the log file. Solution: shut down mysql, remove the innodb log file, and restart mysql.
  • prior to v3.5, this message would also be shown if InnoDB was set as the default engine, however this has been fixed in v3.5.

    Did you compile MUMmer yourself?

    If so you may not have built a correct 64-bit version, in which case it will fail to process large sequences. See the next section.

    MUMmer/PROmer can't handle large sequences

    If the alignment doesn't produce results and you see errors indicating that promer cannot produce the .aaqry file, then the mummer binary may not be 64-bit. You can tell for sure by looking at the output lines like
    # (maximum reference length is 536870908)
    # (maximum query length is 4294967295)
    
    If you see small numbers like this, it is not 64-bit. For 64-bit, the numbers are extremely large, much larger than any possible genome. To build a 64-bit mummer, you must set
    #define SIXTYFOURBITS 
    
    in src/kurtz/libbasedir/types.h (and, of course, compile on a 64-bit machine). We fixed this problem in the 3.4 version of SyMAP, for lintel64, but if you're building for a different platform you'll have to make this fix.

    Please read "Security" section of the manual to find out how to run mysqld as root!

    You are launching SyMAP as the unix root user, which is blocked by MySQL as a security hazard. Solution is simply to use a regular non-root user account.

    The 3D display will not show

    It is possible that your computer doesn't support 3D Java graphics. In this case, when you try to open the Chromosome Explorer, it will fail and you'll see a message to the console starting something like
    Canvas 3D: null graphics configuration
    Solution is to run in 2D mode,
    ./symap -no3d

    /lib64/libc.so.6: version `GLIBC_2.7' not found

    If this occurs while you are doing an alignment, it means that some libraries on your system are not compatible with those required by the version of MUMmer which is included with SyMAP. To solve this you will need to obtain the MUMmer source code distribution and compile it on your own system, which is not hard to do (however, note this important detail). Then, copy the binary named "mummer" to the appropriate ext/mummer/<platform> directory and re-run SyMAP.

    Can't create table (errno: 121)

    This can occur if you try to create a SyMAP database whose name differs only by case from an existing database, e.g. "symapTest" when "symaptest" already exists.

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  • Email Comments To: symap@agcol.arizona.edu