Nono of the scp, sftp, rysinc command connect to the server. I tried two different VPNs to connect to baobab.
The only thing that seems to work is my atom-plugin for remote editing, which is also based on sftp, but this is not very convenient to copy files.
You should keep the shell initialization as minimal as possible (simply
set up the shell and its prompt). If you need to load some other
programs, you will do it via a script once the shell is available. This
has the advantage of letting you login even if the other programs you
need are broken.
Please remove any conda* stuff in your ~/.bashrc and try again to connect, everything should work as expected.
NB , while I could have fixed your ~/.bashrc , I have refrained to do that given that you have running jobs.