Body: <p>I have downloaded the core version of SIFTER. I am not able to run it because I get the following error.</p>
  
  <p><code>Functions gene ontology database does not exist. Get function.ontology from www.geneontology.org</code></p>
  
  <p>I have put the function.ontology into the folder <code>data</code>, but I still get the same error.</p>
  
  <p>The full error message is:</p>
  
  <pre><code>Family set to test
  ERROR: File not found.
     Functions gene ontology database does not exist. Get function.ontology from www.geneontology.org..
     To specify files, please use the options listed under Sifter's help by entering:
      java -jar sifter.jar --help
  
  
  JOB SUMMARY
  FILE ERROR: 
     Protein family file (.pli) does not exist. To obtain a .pli file, use 'pfam2pli' script. See README.txt..
     To specify files, please use the options listed under Sifter's help by entering:
      java -jar sifter.jar --help
  Exception in thread "main" java.lang.NullPointerException
      at java.io.File.&lt;init&gt;(File.java:277)
      at SifterPipelineObject.initDefaultSettings(SifterPipelineObject.java:85)
      at SifterPipelineObject.&lt;init&gt;(SifterPipelineObject.java:93)
      at Sifter.main(Sifter.java:36)
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-03T21:04:50.247Z
Comments.Text: Hi, could you explain what is "function.ontology" ? Which kind of data, in which format, which version of SIFTER or/and data are you using and how are you calling SIFTER, this should speed up the help you might receive.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-04T02:28:36.880Z
Comments.Text: Hi, I am using SIFTER 2.1.1. Actually, I do not know what a "function.ontology" is. I could not find a description for that. I run the SIFTER using the commands in its `readme` file, e.g. `java -jar sifter2.1.1.jar test -v`. That is all I know about running SIFTER.
Comments.UserDisplayName: mpourreza
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-04T07:03:48.963Z
Comments.Text: Did you read the manual or the article? Does it mention anything about requiring this data, or how to set it? Could you provide the full error? I would bet this is only the last line of your error
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-04T15:45:55.403Z
Comments.Text: Yes, I read the `readme.txt` and did all the steps. Except I could not generate the phylogeny (.nex) file. I also added the full error message to the question.
Comments.UserDisplayName: mpourreza
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-04T20:44:39.807Z
Comments.Text: So, why you could not generate the phylogeny file? (If you don't explain all the details involved we can't help) BTW, could you add a link to the software, I am not sure I [found](https://github.com/brennerlab/sifter/) the one you are referring...
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-04T22:54:14.323Z
Comments.Text: The tool is the same but I downloaded it from (http://sifter.berkeley.edu/download/).  Actually, I do not know how to create the Phylogeny, and also could not find a guide to generate one.
Comments.UserDisplayName: mpourreza
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-05T07:02:10.437Z
Comments.Text: If there is too much information missing the only solution is to contact the authors (or maintainers) of the software. Also please [edit] the question to include **all** the information, so that it can help other users in the future
Comments.UserDisplayName: llrs
Tags: <functional-annotation>
Title: How to run SIFTER stand-alone version
ThreadText: # How to run SIFTER stand-alone version
  
  (Asked by: username_0 on 2018-04-03)
  
  I have downloaded the core version of SIFTER. I am not able to run it because I get the following error.
  
  `Functions gene ontology database does not exist. Get function.ontology from www.geneontology.org`
  
  I have put the function.ontology into the folder `data`, but I still get the same error.
  
  The full error message is:
  
  ```
  Family set to test
  ERROR: File not found.
     Functions gene ontology database does not exist. Get function.ontology from www.geneontology.org..
     To specify files, please use the options listed under Sifter's help by entering:
      java -jar sifter.jar --help
  
  JOB SUMMARY
  FILE ERROR: 
     Protein family file (.pli) does not exist. To obtain a .pli file, use 'pfam2pli' script. See README.txt..
     To specify files, please use the options listed under Sifter's help by entering:
      java -jar sifter.jar --help
  Exception in thread "main" java.lang.NullPointerException
      at java.io.File.<init>(File.java:277)
      at SifterPipelineObject.initDefaultSettings(SifterPipelineObject.java:85)
      at SifterPipelineObject.<init>(SifterPipelineObject.java:93)
      at Sifter.main(Sifter.java:36)
  
  ```
  
  **Tags:** functional-annotation
  
  > **Comments:**
  > **username_1**: Hi, could you explain what is "function.ontology" ? Which kind of data, in which format, which version of SIFTER or/and data are you using and how are you calling SIFTER, this should speed up the help you might receive.  
  > **username_0**: Hi, I am using SIFTER 2.1.1. Actually, I do not know what a "function.ontology" is. I could not find a description for that. I run the SIFTER using the commands in its `readme` file, e.g. `java -jar sifter2.1.1.jar test -v`. That is all I know about running SIFTER.  
  > **username_1**: Did you read the manual or the article? Does it mention anything about requiring this data, or how to set it? Could you provide the full error? I would bet this is only the last line of your error  
  > **username_0**: Yes, I read the `readme.txt` and did all the steps. Except I could not generate the phylogeny (.nex) file. I also added the full error message to the question.  
  > **username_1**: So, why you could not generate the phylogeny file? (If you don't explain all the details involved we can't help) BTW, could you add a link to the software, I am not sure I [found](https://github.com/brennerlab/sifter/) the one you are referring...  
  > **username_0**: The tool is the same but I downloaded it from (http://sifter.berkeley.edu/download/).  Actually, I do not know how to create the Phylogeny, and also could not find a guide to generate one.  
  > **username_1**: If there is too much information missing the only solution is to contact the authors (or maintainers) of the software. Also please [edit] the question to include **all** the information, so that it can help other users in the future  
  
  ---
  
  ## 0 answers
  
  