Contents

• Hang
  • Hang on Load
  
  
• Memory
  • Not enough memory
  
  
• MySQL suggested settings
  • Slow to load sequence and annotation
  • Slow queries
  
  
• MySQL
  • Database connect errors ("Unable to connect","Error running SQL Command",...)
  • MariaDB cannot connect
  • The MySQL database does not support Innodb tables
  • Please read "Security" section of the manual to find out how to run mysqld as root
  • Can't create table (errno: 121)
  • MySQL indices
  
  
• Alignment
  • Status window disappeared
  • No anchors loaded
  
  
• MacOS
  • Running external programs
  • Fonts for MacOS Monterey

Hang

Hangs on Load

1. It occasionally hangs for no discernable reason (especially if I have been doing testing on MacOS, where I remove projects and reload over and over). If this happens, Cntl-C to stop the program (or kill it some other way), start up symap again, Remove project from database and try Load again.

2. If in the middle of a Load, any of the following actions: Cancel, or Cntl-C to stop the program, or killing it from the command line, can leave the database in a non-repairable state. Unfortunately, it has be removed and rebuilt.

3. Other apps may cause it to hang, e.g. on Mac, downloaded apps, such as Bartender may interfere with SyMAP, which causes it to hang. When Bartender was removed, SyMAP no longer hung on load.

Memory

Not enough memory

  #!/bin/sh
  mem="8192m";
  echo ">>>> SyMAP build, query and view ($mem)     `date` <<<<"
  java -Xmx$mem -classpath /Users/cari/Workspace/github/symap/java/jar/symap.jar symapCE.SyMAPmanager $@

If your machine does not have much memory, you can reduce the amount of memory requested, but beware, you probably will not have enough memory to process large genomes.

For memory issues related to running MUMmer, see MUMmer.

Slow to load sequence and annotation

To check the values, start mysql and type:

show variables like "innodb_buffer_pool_size";
show variables like "innodb_flush_log_at_trx_commit";

set global innodb_buffer_pool_size=1073741824;
set global innodb_flush_log_at_trx_commit=0;

Different machines and MySQL installations can produce different results with these variables. If the SyMAP demo-seq to demo-seq2 load and synteny computations seem slow, try different combinations of these two variables to see what performs the fastest inserts.

Slow queries

To check the value, start mysql and type:

show variables like "max_allowed_packet"; 

set global max_allowed_packet=1073741824;

Database connect errors

com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception:

** BEGIN NEXTED EXCEPTION **

On startup, 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. First, make sure your db_adminuser and db_adminpasswd are correct.

These days, the best way to find the MySQL problems is to search the internet. However, the 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 running the read/write symap, then the relevant user is db_adminuser. If you are running a read-only session using viewSymap, it will use the read-only db_clientuser or read-write db-adminuser. 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

Unable to connect to the mysql database on localhost; are username and password correct?

[mysqld]
character-set-server=utf8mb4

Thanks to Lori for this solution!

The database does not support Innodb tables

• 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.

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

Can't create table (errno: 121)

MySQL indices

No anchors loaded This message indicates that SyMAP could not parse the MUMmer or BLAT output files to load the anchors. For MUMmer, see MUMmer.

• Using the Finder, go to the symap_5/ext/mummer/mac/aux_bin directory.
• Select prepro and "Open With" → "Terminal" (see lower right image).
• You will get a pop-up, select "Open".
• A terminal window will popup, you can close it.

  mummer
  mgaps
  show-coords
  aux_bin/prepro
  aux_bin/postpro
  aux_bin/prenuc
  aux_bin/postnuc

After that, you should be able to run these via SyMAP, even if you move the symap_5 directory.

This worked with my previous Catalina, Monterey, and current Sonoma but if it does not work for you, see Apple Help, section "If you want to open an app that has not been notarized or is from an unidentified developer".

MacOS Monterey

Warning: the fonts "Times" and "Lucida Bright" are not available for the Java logical font "Serif",
 which may have unexpected appearance or behavior. Re-enable the "Times" font to remove this warning.

• Download Lucida Bright.zip and Times.zip from LengionFonts.
• Double click to unzip into Times.tff. Double click Times.tff, which brings up the FontBook, then install.
• Do the same for Lucida Bright.zip.
• Note: after OS updates, you may have to install again.

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