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I'm trying to run the following Rosetta command.

rosetta_scripts.linuxgccrelease -s data/binding/dataset/test/protein.pdb \ 
    -parser:protocol data/binding/test/scripts/pack.xml \
    -out:path:all data/binding/test/output/ \
    -resfile data/binding/test/output/resfile.txt \
    -out:prefix RosettaOutput_ \
    -nstruct 1 -ignore_zero_occupancy false -overwrite

However, I keep getting the error:

core.pack.task.operation.TaskOperations: {0} [ ERROR ] File:resfile.txt not found!

ERROR: Cannot open file resfile.txt
ERROR:: Exit from: /home/sean/src/rosetta_src_2019.35.60890_bundle/main/source/src/core/pack/task/operation/TaskOperations.cc line: 1645
Error: {0} [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'RosettaOutput_2MWY_0001'
Error: {0} [ ERROR ] Treating failure as bad input; canceling similar jobs

[ ERROR ]: Caught exception:


File: /home/sean/src/rosetta_src_2019.35.60890_bundle/main/source/src/core/pack/task/operation/TaskOperations.cc:1645
[ ERROR ] UtilityExitException
ERROR: Cannot open file resfile.txt




AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.


protocols.jd2.FileSystemJobDistributor: {0} job failed, reporting bad input; other jobs of same input will be canceled: RosettaOutput_2MWY_0001
protocols.jd2.JobDistributor: {0} no more batches to process... 
protocols.jd2.JobDistributor: {0} 1 jobs considered, 1 jobs attempted in 13 seconds

[ ERROR ]: Caught exception:


File: /home/sean/src/rosetta_src_2019.35.60890_bundle/main/source/src/protocols/jd2/JobDistributor.cc:327
1 jobs failed; check output for error messages


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

The error resolves itself if I move resfile.txt to the current working directory. Why can't resfile.txt be found?

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  • $\begingroup$ A Rosetta question here? Excitement! Wait it’s solved. Darn. For future questions... Rosetta commons forum is the ideal place for questions about Rosetta. Some users appear in both here and there, but there are more experts... $\endgroup$ Feb 6 '20 at 22:43
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The problem is my pack.xml specified a resfile.txt location which over-wrote my command-line option.

    <TASKOPERATIONS>
       <ReadResfile name="Design_Resfile" filename="resfile.txt"/>
    </TASKOPERATIONS>

If you remove the filename option in the XML file, you are then able to specify the path.

    <TASKOPERATIONS>
       <ReadResfile name="Design_Resfile"/>
    </TASKOPERATIONS>
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