Practical-6-MAG-analyses.md

@@ -106,7 +106,7 @@ Now we need to submit the script to Slurm with:
 
 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, it's in the `marmic_NGS2021/results/day_4/` directory. There's an arb database in there 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) and open the `MarMic-gtdbtk-example.arb` database. 
+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, it's in the `marmic_NGS2021/results/day_4/gtdbtk` directory. There's an arb database in there 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) and open the `MarMic-gtdbtk-example.arb` database. 
 
 # (
 If you _really_ want to view your own tree (you have to be a bit masochistic but whatever, you do you), you'll need to click 'create and import', then choose the file `gtdbtk.bac120.msa.fasta` in your `gtdbtk_denovo` directory, set the Type in the dropdown menu to 'protein', and choose 'fasta_wgap.ift' from the list on the right. When prompted, select 'Generate unique species IDs', then 'None (only 'acc')'. Now you have a database. In the top row of icons you'll see a padlock, and below it a dropdown set of numbers. Change that from '0' to '6'. Then in the top row of menus, click 'Species', then 'Search and Query'. In the new window, click the 'Search' button. Then in the 'More functions' tab, click 'Set Protection of Fields of Listed Species'. This gives you yet another window. Here click on 'name' in the right panel, then '0 temporary' from the list on the left, then click the 'Assign protection to field of listed' button. Nothing will obviously happen but trust me, that's how it's meant to be. Go ahead and click close on this window and also on the 'Search and Query' window. Now click 'File' from the top row, then 'Export', then 'Export fields (to calc-sheet using NDS)', make sure the Column output at the bottom is 'TAB separated', then hit 'Save', then 'close'.