Answers.Body: <p>You need to setup ssh keys.  All the commands in the script are going to use ssh to run the commands.  Note the tips here of how to setup ssh keys:</p>
  
  <p><a href="http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system#SSH_keys" rel="nofollow noreferrer">http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system#SSH_keys</a><a href="http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system#SSH_keys" rel="nofollow noreferrer">ssh key setup</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-08T16:12:15.973Z
Answers.LastActivityDate: 2018-11-08T16:12:15.973Z
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Body: <p>I am working on macOS High Sierra.</p>
  
  <p>I am following the steps described <a href="http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl" rel="nofollow noreferrer">here</a> to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the tutorial. </p>
  
  <p>At this step:</p>
  
  <pre><code>time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
        -ooc=`pwd`/<span class="math-container">${target}.ooc -fileServer=localhost -localTmp="/dev/shm" \
    -bigClusterHub=localhost -dbHost=localhost -workhorse=localhost \
    -target2Bit=`pwd`/$</span>{target}.2bit -targetSizes=`pwd`/<span class="math-container">${target}.chrom.sizes \
    -query2Bit=../$</span>{query}/<span class="math-container">${query}.2bit \
    -querySizes=../$</span>{query}/<span class="math-container">${query}.chrom.sizes $</span>{target} ${query}) &gt; do.log 2&gt;&amp;1
  </code></pre>
  
  <p>I get the following error in the <code>do.log</code> file:</p>
  
  <pre><code>Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
  username@localhost: Permission denied (publickey,password,keyboard-interactive).
  HgStepManager: executing from step 'align' through step 'cleanup'.
  HgStepManager: executing step 'align' Thu Nov  8 14:27:32 2018.
  Using localhost, /Users/username/Documents/projects/main/output/software/liftover/data/genomes/GCA_000004515.3_Glycine_max_v2.0/GCA_000004515.3_Glycine_max_v2.0.2bit and ../GCF_000004515.3_V1.1/GCF_000004515.3_V1.1.2bit
  align: localhost does not have /Users/username/Documents/projects/main/output/software/liftover/data/genomes/GCA_000004515.3_Glycine_max_v2.0/GCA_000004515.3_Glycine_max_v2.0.ooc -- if that is not the correct location, please run again with -ooc.
  </code></pre>
  
  <p>I think the main problem is here:</p>
  
  <pre><code>username@localhost: Permission denied (publickey,password,keyboard-interactive).
  </code></pre>
  
  <p>This <a href="https://stackoverflow.com/questions/1556056/permission-denied-publickey-keyboard-interactive#4398006">post</a> describes this issue. However:</p>
  
  <ul>
  <li>I do not have this file: ~/.ssh/authorized_keys. My files in ~/.ssh are: <code>github_rsa github_rsa.pub known_hosts</code>. One of the lines of <code>known_hosts</code> is localhost. Does this presumably allow me to ssh to my own laptop? I still don't understand why I need to ssh in this script if it's run locally.</li>
  <li><code>PasswordAuthentication yes</code> is already in <code>/etc/ssh/sshd_config</code></li>
  <li>If I run the command without the <code>time</code> command, I still get the same error. I am not prompted to give a password.</li>
  </ul>
  
  <p>Could anyone help me overcome this problem, please? </p>
  
Tags: <sequence-annotation><ucsc><errors><liftover>
Title: Accessing UCSC genome via ssh results in a validation error
ThreadText: # Accessing UCSC genome via ssh results in a validation error
  
  (Asked by: username_0 on 2018-11-08)
  
  I am working on macOS High Sierra.
  
  I am following the steps described [here](http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl) to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the tutorial.
  
  At this step:
  
  ```
  time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
        -ooc=`pwd`/${target}.ooc -fileServer=localhost -localTmp="/dev/shm" \
    -bigClusterHub=localhost -dbHost=localhost -workhorse=localhost \
    -target2Bit=`pwd`/${target}.2bit -targetSizes=`pwd`/${target}.chrom.sizes \
    -query2Bit=../${query}/${query}.2bit \
    -querySizes=../${query}/${query}.chrom.sizes ${target} ${query}) > do.log 2>&1
  
  ```
  
  I get the following error in the `do.log` file:
  
  ```
  Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
  username@localhost: Permission denied (publickey,password,keyboard-interactive).
  HgStepManager: executing from step 'align' through step 'cleanup'.
  HgStepManager: executing step 'align' Thu Nov  8 14:27:32 2018.
  Using localhost, /Users/username/Documents/projects/main/output/software/liftover/data/genomes/GCA_000004515.3_Glycine_max_v2.0/GCA_000004515.3_Glycine_max_v2.0.2bit and ../GCF_000004515.3_V1.1/GCF_000004515.3_V1.1.2bit
  align: localhost does not have /Users/username/Documents/projects/main/output/software/liftover/data/genomes/GCA_000004515.3_Glycine_max_v2.0/GCA_000004515.3_Glycine_max_v2.0.ooc -- if that is not the correct location, please run again with -ooc.
  
  ```
  
  I think the main problem is here:
  
  ```
  username@localhost: Permission denied (publickey,password,keyboard-interactive).
  
  ```
  
  This [post](https://stackoverflow.com/questions/1556056/permission-denied-publickey-keyboard-interactive#4398006) describes this issue. However:
  
  * I do not have this file: ~/.ssh/authorized\_keys. My files in ~/.ssh are: `github_rsa github_rsa.pub known_hosts`. One of the lines of `known_hosts` is localhost. Does this presumably allow me to ssh to my own laptop? I still don't understand why I need to ssh in this script if it's run locally.
  * `PasswordAuthentication yes` is already in `/etc/ssh/sshd_config`
  * If I run the command without the `time` command, I still get the same error. I am not prompted to give a password.
  
  Could anyone help me overcome this problem, please?
  
  **Tags:** sequence-annotation, ucsc, errors, liftover
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-11-08. Score: 2 | Accepted answer
  
  You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys:
  
  <http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system#SSH_keys>[ssh key setup](http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system#SSH_keys)
  
  
  ---
  
  