updates to liftoff and moddotplot

fixed memory of moddotplot. changed things to use hap1 instead of dip asm.
added new mashmap for hap2 with pi 90 for the moddotplot prep. generally fixed
text for the asms in action. This commit will likely conflict with other
changes made and will need to be merged.

assembly/genomics_aotearoa/pages/day3b_assembly_cleanup_annotation.md

@@ -248,8 +248,8 @@ ln -s /nesi/nobackup/nesi02659/LRA/resources/chm13/CHM13-T2T.renamed.gff.gz chm1
 ln -s /nesi/nobackup/nesi02659/LRA/resources/chm13/CHM13-T2T.renamed.gff.liftoff.sqlite3 chm13-annotations.gff.liftoff.sqlite3
 ln -s /nesi/nobackup/nesi02659/LRA/resources/chm13/chm13v2.0.fa chm13.fa
 ln -s /nesi/nobackup/nesi02659/LRA/resources/chm13/chm13v2.0.fa.fai chm13.fa.fai
-ln -s /nesi/nobackup/nesi02659/LRA/resources/verkko_trio_prebaked/asm_hifiont/assembly.fasta asm.fa
-ln -s /nesi/nobackup/nesi02659/LRA/resources/verkko_trio_prebaked/asm_hifiont/assembly.fasta asm.fa.fai
+ln -s /nesi/nobackup/nesi02659/LRA/resources/assemblies/verkko/full/trio/assembly/assembly.haplotype1.fasta asm.hap1.fa
+ln -s /nesi/nobackup/nesi02659/LRA/resources/assemblies/verkko/full/trio/assembly/assembly.haplotype1.fasta.fai asm.hap1.fa.fai
 ```
 
 <details>
@@ -269,8 +269,8 @@ ln -s /nesi/nobackup/nesi02659/LRA/resources/verkko_trio_prebaked/asm_hifiont/as
     the input GFF file) and <code>-db</code> (to provide the input SQLite
     database) are interchangeable. We&rsquo;ll be using the database to save
     time, but we could instead use the other option and supply the GFF file.
-	If you haven&rsquo;t yet viewed a GFF file, now would be a good time to
-	check one out: <pre><code>less -S chm13-annotations.gff.gz</code></pre>
+    If you haven&rsquo;t yet viewed a GFF file, now would be a good time to
+    check one out: <pre><code>less -S chm13-annotations.gff.gz</code></pre>
 </details>
 
 **Run Liftoff**
@@ -286,8 +286,8 @@ module load Liftoff/1.6.3.2-gimkl-2022a-Python-3.11.3
 liftoff \
     -p 8 \
     -db chm13-annotations.gff.liftoff.sqlite3 \
-    -o asm.annotations.gff \
-    asm.fa \
+    -o asm.hap1.annotations.gff \
+    asm.hap1.fa \
     chm13.fa
 ```
 
@@ -315,15 +315,19 @@ liftoff \
     -copies # possibly with -sc 2 # diploid vs haploid assembly liftover
 -->
 
+<!--
+    Expect this to take just over 1 hour w/ 8 cpus. MaxRSS was reported as
+    ~36 GB, but it failed when I gave it only 36 GB previously.
+-->
 Then submit it as a job with `sbatch`:
 ```
-sbatch -J liftoff -N1 -n1 -c8 --mem=20G -t 0-01:30 -A nesi02659 -o %x.%j.log liftoff.sh
+sbatch -J liftoff -N1 -n1 -c8 --mem=48G -t 0-02:00 -A nesi02659 -o %x.%j.log liftoff.sh
 ```
 
 **Look at the output GFF3 file**
 
 ```shell
-less -S asm.annotations.gff
+less -S asm.hap1.annotations.gff
 ```
 
 You can also explore the files in Liftoff's intermediate directory:
@@ -335,8 +339,8 @@ Before we visualize the annotations in IGV, it is best if we sort and index the
 output GFF file:
 ```
 module load IGV/2.9.4
-igvtools sort asm.annotations.gff asm.annotations.sorted.gff
-igvtools index asm.annotations.sorted.gff
+igvtools sort asm.hap1.annotations.gff asm.hap1.annotations.sorted.gff
+igvtools index asm.hap1.annotations.sorted.gff
 ```
 These operations are small enough that you should not need to submit a job for
 them.
@@ -351,7 +355,7 @@ To open IGV and view the annotations, do the following:
        igv.sh
        ```
 2. Load the CHM13-T2T genome (instead of the default hg19): Genome > Load Genome from File... > `chm13.fa`
-3. Load the GFF file: File > Load from File... > `asm.annotations.sorted.gff`
+3. Load the GFF file: File > Load from File... > `asm.hap1.annotations.sorted.gff`
 4. Explore
 
 **What do you observe? Do you have any questions?**