text: user6966: 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?
  
  user6966: 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>
  
  
original_text: 6966: <p>I'm trying to run the following Rosetta command.</p>
  
  <pre><code>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
  </code></pre>
  
  <p>However, I keep getting the error:</p>
  
  <pre><code>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.
  </code></pre>
  
  <p>The error resolves itself if I move <code>resfile.txt</code> to the current working directory. Why can't <code>resfile.txt</code> be found?</p>
   6966: <p>The problem is my <code>pack.xml</code> specified a <code>resfile.txt</code> location which over-wrote my command-line option.</p>
  
  <pre><code>    &lt;TASKOPERATIONS&gt;
         &lt;ReadResfile name="Design_Resfile" filename="resfile.txt"/&gt;
      &lt;/TASKOPERATIONS&gt;
  </code></pre>
  
  <p>If you remove the <code>filename</code> option in the XML file, you are then able to specify the path.</p>
  
  <pre><code>    &lt;TASKOPERATIONS&gt;
         &lt;ReadResfile name="Design_Resfile"/&gt;
      &lt;/TASKOPERATIONS&gt;
  </code></pre>
  