v5.6.6

The MacOS M4 silicon executables are in the /ext directory with SyMAP added support - documentation.

Author: cariann09

docs/MUMmer.html

@@ -236,9 +236,12 @@ <h3>Limit CPUs and uncheck Concat</h3>
 size and complexity of the two genomes being compared. If you think memory may be tight,
 you can limit the amount used at one time by limiting the number of CPUs, as each
 CPU uses a considerable amount of memory (e.g. 4 CPUs could collectively use 20GB of memory at once).
-<p><a href="img/concat.png"><img src="img/concat.png" alt="concat" style="border: 1px solid black; width: 400px"></a>
-
-<p>See <a href="SystemHelp.html#concat" class="ext" target="_blank">Concat</a> for a description and timing results.
+<p>
+<table>
+<tr><td><a href="img/concat.png"><img src="img/concat.png" alt="concat" style="border: 1px solid black; width: 400px"></a>
+<td>See <a href="SystemHelp.html#concat" class="ext" target="_blank">CPU and Concat</a> for a description of these
+options and timing results.
+</table>
 
 <!----------------------------------------------------->
 <a id="mask"></a>

docs/Query.html

@@ -848,14 +848,17 @@ <h4>4.3 View 2D</h4>
 <table class="tx">
 <tr><td style="vertical-align: text-top;">
 	<td style="vertical-align: text-top;">
-	<p>The image on the right shows a Collinear set of 5.
+	The table below shows results from the <ttx>Collinear</ttx> search.
+	<p><a href="img/query_columns_mult.png"><img src="img/query_columns_mult.png" alt="query multi columns" style="border: 1px solid black; width: 280px"></a>
+
+	<p>The image on the right shows the <ttl>2D</ttl> for the set.
 	After the initial display, the <ttl>2D</ttl> view can be changed as described in the
 	<a href="UserGuide.html#control" class="ext" target="_blank">User Guide</a>.
 	<p>&nbsp;
 	<p>The table below shows results when the <ttx>Group</ttx> column has a value
 	(using <ttx>Gene#</ttx>, <ttx>Multi-gene</ttx> or <ttx>Cluster</ttx> search). The <ttl>Group</ttl> option
 	can be used with these rows.
-	<p><a href="img/query_columns_2D.png"><img src="img/query_columns_2D.png" alt="query 2D columns" style="border: 1px solid black; width: 280px"></a>
+	<p><a href="img/query_columns_mult.png"><img src="img/query_columns_mult.png" alt="query multi columns" style="border: 1px solid black; width: 280px"></a>
 
 	<td><a href="img/query_synteny.png"><img src="img/query_synteny.png" alt="query synteny" style="border: 1px solid black; width: 450px"></a>
 </table>

docs/Release.html

@@ -63,6 +63,26 @@ <h3>Summary of recent major releases</h3>
 <tr><td><a href="#v540">v5.4.0</a><td>(6-Apr-23)<td>Improved <ttx>Cluster Hit</ttx> algorithm <ttx>Algo1</ttx> for the detection of gene homology.
 </table>
 
+<a id="v565"></a>
+<h3>Release: v5.6.6 (6-May-25)</h3>
+The MacOS M4 silicon executables have been added to the <tt>/ext</tt> directory.
+The code has been updated to use them when running on MacOS M4.
+
+<ul>
+<li><tt>symap.config</tt>: There is a new setting called 'arch' that allows the user to specify
+a different machine architecture to use for the external executables; the user will need to provide
+the executables. See <a href="SystemGuide.html#ext" class="ext" target="_blank">External Executables</a>.
+<li><ttl>A&S</ttl>: MUMmer takes a while and can fail in one or more of the alignments. Its important to be clear
+what is happening, so the following was added:
+<ul>
+<li>If there is a ? in the Manager table cell for a pair, A&S will
+write to the terminal how many were finished and how many it has left to do.
+<li>The 'Alignments:' status now includes how many alignments had errors.
+</ul>
+<br>
+<li><small>Developers: Do not update numHits before A&S. Sort alignments to be processed.</small>
+</ul>
+
 <a id="v565"></a>
 <h3>Release: v5.6.5 (24-Apr-25)</h3>
 Updates for Queries: Support for non-annotated hit ends (pseudo genes) bug fixes

docs/SystemGuide.html

@@ -93,6 +93,7 @@
 3. <u>Install SyMAP</u>
 <ul>
 <li style="margin: 0.4em 0;"><a href="#installation">Installation</a>
+<li style="margin: 0.4em 0;"><a href="#ext">External executables</a>	<!-- in SyMAP -->
 <li style="margin: 0.4em 0;"><a href="#mysql">MySQL parameters for SyMAP</a>
 </ul>
 
@@ -262,6 +263,12 @@ <h3>System Requirements</h3>
 SyMAP has been tested on the following:
 <table class="ty" style="font-family: Verdana, Arial, Helvetica, sans-serif; font-size:9pt">
 <tr><td><i>Machine</i><td><i>MySQL</i><td><i>Java</i><td><i>Core</i><td><i>Memory</i><td><i>Purchased</i>
+<tr><td colspan=2><ttl>v5.6.6 and later</ttl>:
+<tr><td>MacOS M4 (Sequoia)
+	<td>MySQL v8.0.42
+	<td>24 from <a href="https://www.oracle.com/java/" class="ext" target="_blank">Oracle</a>
+	<td>M4 12-Core<td>&nbsp;48 GB<td>2025
+
 <tr><td colspan=2><ttl>v5.4.1 and later</ttl>:
 
 <tr><td>MacOS x86_64 (Sonoma 14.4.1)<sup>1</sup>
@@ -384,7 +391,10 @@ <h3>Installation</h3>
 <u>Data</u>: The <ttx>data/</ttx> directory contains a <ttx>/seq</ttx> sub-directory,
 which contains the demo files, and is the default location for all input sequence files.
 
-<p><u>Externals</u>: The <ttx>ext/</ttx> directory contains the external programs
+<a id="ext"></a><!-- in SyMAP -->
+<h3>External executables</h3>
+
+The <ttx>ext/</ttx> directory contains the external programs
 MUMmer<sup>1,2</sup> for sequence alignment,
 and MAFFT<sup>6</sup> and MUSCLE<sup>7</sup> for
 interactive MSA alignment (for <a href="./Query.html#msaAlign" class="ext" target="_blank">Queries</a>).
@@ -393,7 +403,27 @@ <h3>Installation</h3>
 <pre>
 	README		mummer/		mummer4/	muscle/		mafft/
 </pre>
-For MUMmer, see <a href="MUMmer.html#ext" class="ext" target="_blank">Executables</a>
+
+Each has subdirectories:
+<table class="ty">
+<tr><td><i>Subdirectory</i><td><i>OS (Architecture)</i><td><i>Note</i>
+<tr><td>lintel64<td>Linux<td>
+<tr><td>mac<td>Mac OS X (x86_64)<td>
+<tr><td>macM4<td>Mac OS X (M4 silicon)<td>No muscle executable
+</table>
+SyMAP will determine which subdirectory to use.
+
+<p>If you compile your own executables for a different architecture, do the following:
+<ol>
+<li>Under mummer and mafft, make a directory with your architecture name (e.g. <tt>mine</tt>).
+<li>Put the executables under this directory in the exact same way as shown for linux64.
+<li>In the symap configuration file (default <tt>symap.config</tt>), add a line <tt>arch={your architecture name}</tt>
+(e.g. <tt>arch=mine</tt>).
+</ol>
+Note that I do not have an alternative machine to try this on, but it should work. Email me
+at symap@agcol.arizona.edu if it does not.
+
+<p>For MUMmer, see <a href="MUMmer.html#ext" class="ext" target="_blank">Executables</a>
 and <a href="MUMmer.html#mum4" class="ext" target="_blank">Using MUMmer4</a>.
 On MacOS, you may also need <a href="TroubleShoot.html#macos" class="ext" target="_blank">MacOS externals</a>.
 
@@ -736,8 +766,11 @@ <h3>Alignment&amp;Synteny</h3>
 <td style="text-align: right"><a href="#top">Go to top</a></table>
 
 <table class="tx">
-<tr><td>See <a href="./SystemHelp.html#pairParams" class="ext" target="_blank">pair parameters</a>
+<tr><td>See <a href="./SystemHelp.html#pairParams" class="ext" target="_blank">Pair Parameters</a>
 on setting the pair parameters for the this step.
+
+<p>See <a href="SystemHelp.html#concat" class="ext" target="_blank">CPU and Concat</a> for a description of these
+two options.
 <p>Then select <ttb>All Pairs</ttb> or <ttb>Selected Pair</ttb>
 to run the Alignment&amp;Synteny.
 <td><a href="img/projAnS.png"><img src="img/projAnS.png" alt="align and synteny" style="border: 1px solid black; width: 450px"></a>
@@ -756,11 +789,27 @@ <h3>Alignment&amp;Synteny</h3>
 <p>The log files are in the <ttx>/logs</ttx> directory, see
 <a href="MUMmer.html#log" class="ext" target="_blank">Running MUMmer</a> for more details.
 
-<p>See <a href="MUMmer.html#cmd"  class="ext" target="_blank">Using MUMmer with SyMAP</a>
+<p>See <a href="MUMmer.html"  class="ext" target="_blank">Using MUMmer with SyMAP</a>
 for a discussion on how it works in SyMAP, trouble-shooting, and running MUMmer externally
 (i.e. if your local machine does not have enough memory or CPUs, you may need to run it on
 a bigger machine).
 
+<p><u>Incomplete alignment</u>
+If SyMAP completed the alignment, e.g. the demo <tt>/align</tt> directory will have the following files:
+<pre>
+-rw-r--r--@ 1 cari  staff     0B Apr 10 10:28 all.done
+-rw-r--r--@ 1 cari  staff   1.2M Apr 10 10:28 demo_seq_cc.demo_seq2_f1.mum
+-rw-r--r--@ 1 cari  staff     0B Apr 10 10:28 demo_seq_cc.demo_seq2_f1.mum.done
+-rw-r--r--@ 1 cari  staff   541K Apr 10 10:27 demo_seq_cc.demo_seq2_f2.mum
+-rw-r--r--@ 1 cari  staff     0B Apr 10 10:27 demo_seq_cc.demo_seq2_f2.mum.done
+</pre>
+<ol>
+<li>The 'all.done' indicates that the all alignments completed.
+<li>If 'all.done' does not exist, SyMAP will perform any alignments that do NOT have a corresponding 'mum.done'.
+If the <ttl>Concat</ttl> setting has been switched between the previous and current run, this will not work correctly.
+<li>If the user supplied the alignments (<a href="MUMmer.html#cmd"  class="ext" target="_blank">Supply MUMmer files</a>),
+there may not be 'mum.done' files but there should be an 'all.done', so it is assumed they are all done.
+</ol>
 <!--------------------------------------------------------------------->
 <a id="draft2"></a>
 <table style="width: 95%"><tr><td style="text-align: left">
@@ -928,9 +977,12 @@ <h3>How SyMAP Works</h3>
 The query is the one with alphabetically the first name. The query sequences
 are written into one large file, while smaller target sequences are grouped
 into larger FASTA files of size up to 60Mb, for more efficient processing
-in MUMmer. There is an option <ttl>Concat</ttl> that if unchecked, the query sequences
+in MUMmer.
+
+There is an option <ttl>Concat</ttl> that if unchecked, the query sequences
 are treated the same as the target; i.e. generally there will be more sequence files to
  processed, but they will be smaller.
+ See <a href="SystemHelp.html#concat" class="ext" target="_blank">Concat</a> for a description and timing results.
 <p>
 <i>Anchor Clustering and Filtering:</i><br>
 The raw anchor set consists of the hits found by MUMmer, which are filtered and clustered for input to the synteny algorithm.