What to do when you are disconnected from Uppmax?

It happens from time to time that you get disconnected from Uppmax after loosing the connection to the network for example. Here, we summarize the steps you have to repeat before continuing doing your work.

Type the following command but replace username with your login name.

  1. Connect to Uppmax:
ssh -X username@milou.uppmax.uu.se
  1. Type the following command to see the node you are affected to:
squeue -u username
  1. The nodelist column gives you the name of the node that has been reserved for you.
    To log in to compute node run the following command (replace mXX with the actual compute node you are assigned to)
ssh -X mXX
  1. Make sure that you can launch graphical tools in your node by typing this command:
xclock

If you see the clock then you should be able to launch GUI-based tools. Close the clock.

  1. Load all necessary softwares to complete all exercices 
    source /proj/g2015028/nobackup/single_cell_exercises/scripts/modules_load

Now we can check that all softwares have been correctly loaded, please type the following command in your terminal and check that all element of the list below is listed contact the teachers if not.

module list

If you have reached the part 3: Single cell genome assembly, continue with the next steps

Since we use the variables sample and trim, the following commands will set those variables. In case you loose your connection, you will need to redo this step again.

If you assemble Hiseq data without trimming:

sample=Hiseq
trim=''
cd ~/single_cell_exercises/dataset1

If you assemble Hiseq data with trimming:

sample=Hiseq
trim=_Trimmomatic
cd ~/single_cell_exercises/dataset1

If you assemble Miseq data without trimming:

sample=Miseq
trim=''
cd ~/single_cell_exercises/dataset2

If you assemble Miseq data with merging:

sample=Miseq
trim=_Trimmomatic
cd ~/single_cell_exercises/dataset2
Previous page