Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-06T21:01:10.527Z
Answers.LastActivityDate: 2020-02-06T21:01:10.527Z
Answers.UserDisplayName: Seanny123
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-06T22:43:46.147Z
Comments.Text: 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...
Comments.UserDisplayName: Matteo Ferla
Tags: <protein-structure><computational-biochemistry><rosetta>
Title: How to specify input resfile for Rosetta?
ThreadText: # How to specify input resfile for Rosetta?
  
  (Asked by: username_0 on 2020-02-06)
  
  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?
  
  **Tags:** protein-structure, computational-biochemistry, rosetta
  
  > **Comments:**
  > **username_1**: 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...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2020-02-06. Score: 2 | Accepted answer
  
  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>
  
  ```
  
  
  ---
  
  