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Troubleshooting_checklist.md

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Approaches to troubleshooting in bioinformatics – A checklist

When a command is not working, you are getting an unexpected output, etc, it might help you to go through this list to solve the issue!

Common issues

  • Are you in the right folder / directory? ('mapp' in Swedish) (use pwd)
  • Is your input file in the right folder or are you providing the right path to it? (use ls)
  • Is your input file what it should be? E.g. is the format correct? (use less)
  • Double check the command - any typo in the name of the software, of the files etc, will make it impossible for the command to be executed.
  • If -Y forwarding is not working on Uppmax: maybe you connected with ssh -Y from an existing Uppmax session. In that case log out completely from Uppmax and try again.
  • To interrupt a process: press 'Ctrl' and 'C'.
  • Try to read the error message. Sometimes they are not very informative, but sometimes they are!

Useful commands:

  • pwd
  • cd
  • less (exit with 'q')
  • cat
  • nano
  • cp from_folder/filename to_folder/filename If you want to copy entire folders, use cp -r. If you are in 'to_folder' already and you want the same filename, you can use cp from_folder/filename . .

Transfer files between your computer and Uppmax

Open a new terminal window. Navigate to the folder where you want to work (i.e. either the folder containing the files you want to transfer to Uppmax, or the folder where you want to copy the files currently on Uppmax).

Log in to Uppmax with the sftp protocol instead of ssh: ssh [email protected]

Navigate to the right folder using cd.

If you need to navigate on your own computer, use lcd (or lpwd to know where you are).

To copy files FROM your computer TO Uppmax: use put and the name of the file.

To copy files FROM Uppmax TO your computer: use get and the name of the file.

If you wish to copy entire folders, use the -r flag.