I am new to rosetta. I am studying the Rosetta tutorials and I am there is a problem with output path control. I followed the tutorial 4 (controlling input and output) and type the following command in the section "Setting output paths" of this tutorial into my CentOS 7 linux shell:
$> $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb -out:pdb -out:path output_files
After the common is excuted there is no result file generated in the target directory (output_files). The last few lines in the log are: protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed input_files/1qys.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: no jobs were attempted, did you forget to pass -overwrite?
I cannot understand the last line. How to pass -overwrite? If I just add " -overwrite" to the above command:
$> $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb -out:pdb -out:path output_files -overwrite
A error message is given:
[ERROR] EXCN_utility_exit has been thrown from: src/protocols/jd2/wwPDBJobOutputter.cc line: 89 ERROR: Unable to open file: 1qys_0001.pdb
But if I carryout the command with root previlege:
sudo $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb -out:pdb -out:path output_files
The result files "1qys_0001.pdb" and "score.sc" appear in the currect working directory (/home/sunyp/app/rosetta_src_2017.08.59291_bundle/demos/tutorials/input_and_output_learning) rather than the target directory "output_files".
I feel this is very strange and don't know how to sovle it. Could anyone help me? I very appreciate any help and advise.
Thank you in advance.