For this exercise 10 Dehalococcoides genomes with the file extension fasta should be in the directory $HOME/miga_genomes/dehalo. This will be the case if you followed the instructions in the section Get Example Data. Otherwise you will have to make adjustments to the commands below.
This exercise takes approximately 90 minutes to run interactively. The same execise is included under Submitting MiGA Jobs if you would rather run it that way.
Log into the HPCC with your user name and password.
Create a directory for your project in your home directory:
cd
mkdir dehalo
Still from your home directory, start MiGA, create a new project named dehalo, and move into the dehalo directory:
singularity shell MiGA
miga new -P ~/dehalo -t clade
cd dehalo
The -t argument is needed to specify what kind of project you are running. Acceptable types are :
genomesfor the genomes from isolatescladefor genomes of closely related species
For this example, we are using closely related genomes (expected ANI >= 90%), so we choose clade.
It is not necessary to add a reference database to a clade project. The genomes submitted will be compared among themelves.
Add your data set to the MiGA project. In doing this, turn off mytaxa scan, as in the command below. Here the -t flag specifies that the data being uploaded are genomes and the -i flag specifies that they are already assembled.
miga add -P . -t genome -i assembly ~/miga_genomes/dehalo/*.fna -m run_mytaxa_scan=false
Launch the daemon to start MiGA processing your data:
miga daemon start -P . --shutdown-when-done
The shutdown-when-done argument automatically stops the daemon when processing is complete. After the job starts, you can display the project information with the command:
miga about -P .
Also after the job starts, you can display the dataset information:
miga ls -P . -i
And you can monitor its progress by entering:
miga ls -P . -p
which should return something like:
name raw_reads trimmed_reads read_quality trimmed_fasta assembly cds essential_genes ssu mytaxa mytaxa_scan distances taxonomy stats
---- --------- ------------- ------------ ------------- -------- --- --------------- --- ------ ----------- --------- -------- -----
GCF_000011905_1_ASM1190v1_genomic - - - - done done done done done done queued queued queued
GCF_000341655_1_ASM34165v1_genomic - - - - done done done done done done queued queued queued
GCF_000341695_1_ASM34169v1_genomic - - - - done done done done done done done done done
GCF_000830925_1_ASM83092v1_genomic - - - - done done done done done done done done done
GCF_001010485_1_ASM101048v1_genomic - - - - done done done done done done done done done
GCF_001547795_1_ASM154779v1_genomic - - - - done done done done done done done done done
GCF_001610775_1_ASM161077v1_genomic - - - - done done done done done done done done done
GCF_001889305_1_ASM188930v1_genomic - - - - done done done done done done done done done
GCF_002007845_1_ASM200784v1_genomic - - - - done done done done done done queued queued queued
GCF_004684285_1_ASM468428v1_genomic - - - - done done done done done done queued queued queued
When all entries in the stats column read "done," the project is finished.
If you did not use the --shutdown-when-done arguement when starting the daemon, you can stop it with:
miga daemon stop -P .
Exit the MiGA singularity containeer with:
exit
See the section "Exploring Results" for how to access the results of your project.