Practical-6-MAG-analyses.md

@@ -91,7 +91,7 @@ Then copy and paste the following into it, and change the path to your MAGs, and
 #SBATCH --ntasks=1                               # Run a single task
 #SBATCH --cpus-per-task=16                       # Number of cpus to allocate for each task
 #SBATCH --mem=250gb                              # Job Memory
-#SBATCH --time=05:00:00                          # Time limit hrs:min:sec
+#SBATCH --time=15:00:00                          # Time limit hrs:min:sec
 #SBATCH --output=slurm-%A_%a.out                 # Standard output and error log
 #SBATCH --array=1                                # Array range
 #SBATCH --partition=CLUSTER                      # Partition
@@ -104,7 +104,7 @@ Now we need to submit the script to Slurm with:
     $ sbatch slurm-submit.sh
 
 
-Now you can run `squeue` and see if your job is running! Also you'll see a new file has been created for the output that would otherwise print to screen. Check this file to make sure you don't have any errors. Run time for GTDB-tk is pretty long (after all it has to compare your MAGs to a database of over 20,000 other genomes), so carry on with the stuff below while you wait.
+Now you can run `squeue` and see if your job is running! Also you'll see a new file has been created for the output that would otherwise print to screen. Check this file to make sure you don't have any errors. Run time for GTDB-tk, especially the `de_novo_wf`, is pretty long (after all it has to compare your MAGs to a database of over 20,000 other genomes - check out the run-time we've reserved in the slurm script!), so carry on with the stuff below and you can take a look at the GTDB-tk outputs later today (`classify_wf` should finish today), or tomorrow.
 
 It's also possible to load the phylogenetic tree output from GTDB-tk into arb, but it's a bit of a faff. We prepared an example of what it looks like for you to explore. There's an arb tree you can view (you first have to go to an arb server `$ ssh arb-X` (put in an number from 1 to 3 in place of the X), then run `arb` from the command line).