lock on to sever line 590
Opened this issue · 2 comments
I got the following error python transfer_fast5_to_server.py --reads_dir /home/poretools/data/Lanfearlab/Volumes/LANFEARSEQ3/1003_Miriam_data_uploaded --server_name raijin.nci.org.au --dest_directory /short/xf3/bxs800/MinIon/transfer_test --user_name bxs800 --sample_name EG_AB_D
password:
('PING raijin.nci.org.au (192.43.239.23) 56(84) bytes of data.\n64 bytes from raijin3.nci.org.au (192.43.239.23): icmp_seq=1 ttl=60 time=0.661 ms\n\n--- raijin.nci.org.au ping statistics ---\n1 packets transmitted, 1 received, 0% packet loss, time 0ms\nrtt min/avg/max/mdev = 0.661/0.661/0.661/0.000 ms\n', '')
'Pertt'
Traceback (most recent call last):
File "transfer_fast5_to_server.py", line 661, in
main()
File "transfer_fast5_to_server.py", line 89, in main
check_directories()
File "transfer_fast5_to_server.py", line 590, in check_directories
if not s.login(SERVER_NAME, SERVER_USERNAME, PASSWORD):
File "/home/poretools/anaconda3/envs/poretools/lib/python2.7/site-packages/pexpect/pxssh.py", line 336, in login
raise ExceptionPxssh('could not synchronize with original prompt')
pexpect.pxssh.ExceptionPxssh: could not synchronize with original prompt
after some digging I set the original_prompt='pwd' in s (pxssh.pxssh) instead of the '[#$]'. The later appears to throw an error on raijin.
Same in line 475.
Interesting. You may need to ssh in first as this will add the server to the list of known hosts and then you don't have the 'add to known hosts' prompt when you run the script.
Hi Ben, I have added the no-sshpass option and added a mini-tutorial on how to generate a authenication key and add it to a server. I am yet to configure the add lock-file and remove lock-file scripts such that they can be completed without a password. I'm not sure if it would fix this though, which may be due to the bash_profile spitting the cwd into stdout?
Alexis.