I am trying to run minirosetta.linuxgccrelease on our cluster.
I got the following message at the end of the log file:
[ERROR] EXCN_utility_exit has been thrown from: src/core/fragment/FragmentIO.cc line: 233
ERROR: ERROR: FragmentIO: could not open file $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC09_05.200_v1_3
This problem seems to be Rosetta specific and not relate to the cluster. However, I do not think there is anything wrong with “aaC226S_HC09_05.200_v1_3” and it works fine on my Ubuntu.
The “test.sh” file attached is to submit the batch job on cluster.
The options file and output log file are also attached.
Could you please help me solve this? Thank you very much.
You can’t use $HOME inside a Rosetta flags file. $HOME is a shell variable – if it is used in a command line argument, the shell substitutes it before Rosetta sees it. The shell does not interact with the inside of the flags file, so Rosetta sees a literal “$HOME”, (as the error shows), which is not a valid path.
Replace $HOME in your flags file with the actual path and it will probably work.
Thank you for correcting my usage. Yes, it works fine now after change the $HOME into a full path directory.
However, as I said in another post, https://www.rosettacommons.org/node/3868
the output structure is still of coordinate shift compared to the input structure (attached). Is there some way to prevent this? I would appreciate it very much if this can be solved and I can combine light chain and heavy chain together in a PDB file for my further work. Thank you very much.