Answers.Body: <p>Like gringer already commented, the cause of your error is nicely given by the <code>java</code> program. Your default <code>max heap</code> settings are probably too low for the program. If you have more memory on your machine you can give <code>max heap</code> a higher value. See this <a href="https://stackoverflow.com/questions/37335/how-to-deal-with-java-lang-outofmemoryerror-java-heap-space-error-64mb-heap">post</a> and answers on Stack overflow.</p>
  
  <p>You'll probably need to use the <code>-Xmxn</code> argument in <code>java</code>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-17T08:12:13.840Z
Answers.LastActivityDate: 2017-11-17T08:12:13.840Z
Answers.UserDisplayName: benn
Answers.Body: <p>"If pilon was installed by condo, edit the file "/Users/user/anaconda/bin/pilon" by changing the maximum memory limit from 1G to higher numbers like "14G". It works. " 
  check the thread: <a href="https://github.com/broadinstitute/pilon/issues/26" rel="nofollow noreferrer">https://github.com/broadinstitute/pilon/issues/26</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-18T10:19:54.737Z
Answers.LastActivityDate: 2020-04-18T10:19:54.737Z
Answers.UserDisplayName: LucasY
Body: <p>I am trying to use Pilon to improve a reference based on some Illumina data I have got. So, I aligned the Illumina reads to the reference using bwa. Then, I want to use Pilon to improve the reference using the alignment file in BAM format.</p>
  
  <p>Information about Pilon is found <a href="https://github.com/broadinstitute/pilon/wiki/Requirements-&amp;-Usage" rel="nofollow noreferrer" title="Requirements of Pilon">here</a>. I installed Pilon using conda.</p>
  
  <p>The output of 'pilon' is:</p>
  
  <pre><code>Pilon version 1.22 Wed Mar 15 16:38:30 2017 -0400
  
      Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]
                   [...other options...]
             pilon --help for option details
  </code></pre>
  
  <p>The output of:</p>
  
  <pre><code>pilon --genome ref.fa --frags readsSorted.bam --output pilo --outdir output/scaffold
  </code></pre>
  
  <p>is:</p>
  
  <pre><code> Exception in thread "main" java.lang.reflect.InvocationTargetException
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at com.simontuffs.onejar.Boot.run(Boot.java:340)
      at com.simontuffs.onejar.Boot.main(Boot.java:166)
  Caused by: java.lang.OutOfMemoryError: Java heap space
      at org.broadinstitute.pilon.GenomeRegion.&lt;init&gt;(GenomeRegion.scala:55)
      at org.broadinstitute.pilon.GenomeFile$$anonfun$contigRegions$1.apply(GenomeFile.scala:72)
   at org.broadinstitute.pilon.GenomeFile$$anonfun$contigRegions$1.apply(GenomeFile.scala:72)
      at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
   at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
      at scala.collection.immutable.Range.foreach(Range.scala:160)
      at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
   at scala.collection.AbstractTraversable.map(Traversable.scala:104)
   at org.broadinstitute.pilon.GenomeFile.contigRegions(GenomeFile.scala:72)
   at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:52)
      at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:52)
      at scala.collection.immutable.List.map(List.scala:277)
      at org.broadinstitute.pilon.GenomeFile.&lt;init&gt;(GenomeFile.scala:52)
      at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:98)
      at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
      ... 6 more
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-16T22:12:21.557Z
Comments.Text: Note that the error is a memory issue:
  
  `java.lang.OutOfMemoryError: Java heap space`
Comments.UserDisplayName: gringer
Tags: <assembly><reference-genome>
Title: Java error when launching Pilon
ThreadText: # Java error when launching Pilon
  
  (Asked by: username_0 on 2017-11-16)
  
  I am trying to use Pilon to improve a reference based on some Illumina data I have got. So, I aligned the Illumina reads to the reference using bwa. Then, I want to use Pilon to improve the reference using the alignment file in BAM format.
  
  Information about Pilon is found [here](https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage "Requirements of Pilon"). I installed Pilon using conda.
  
  The output of 'pilon' is:
  
  ```
  Pilon version 1.22 Wed Mar 15 16:38:30 2017 -0400
  
      Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]
                   [...other options...]
             pilon --help for option details
  
  ```
  
  The output of:
  
  ```
  pilon --genome ref.fa --frags readsSorted.bam --output pilo --outdir output/scaffold
  
  ```
  
  is:
  
  ```
   Exception in thread "main" java.lang.reflect.InvocationTargetException
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at com.simontuffs.onejar.Boot.run(Boot.java:340)
      at com.simontuffs.onejar.Boot.main(Boot.java:166)
  Caused by: java.lang.OutOfMemoryError: Java heap space
      at org.broadinstitute.pilon.GenomeRegion.<init>(GenomeRegion.scala:55)
      at org.broadinstitute.pilon.GenomeFile$$anonfun$contigRegions$1.apply(GenomeFile.scala:72)
   at org.broadinstitute.pilon.GenomeFile$$anonfun$contigRegions$1.apply(GenomeFile.scala:72)
      at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
   at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
      at scala.collection.immutable.Range.foreach(Range.scala:160)
      at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
   at scala.collection.AbstractTraversable.map(Traversable.scala:104)
   at org.broadinstitute.pilon.GenomeFile.contigRegions(GenomeFile.scala:72)
   at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:52)
      at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:52)
      at scala.collection.immutable.List.map(List.scala:277)
      at org.broadinstitute.pilon.GenomeFile.<init>(GenomeFile.scala:52)
      at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:98)
      at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
      ... 6 more
  
  ```
  
  **Tags:** assembly, reference-genome
  
  > **Comments:**
  > **username_1**: Note that the error is a memory issue:  `java.lang.OutOfMemoryError: Java heap space`  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2017-11-17. Score: 2 | Accepted answer
  
  Like username_1 already commented, the cause of your error is nicely given by the `java` program. Your default `max heap` settings are probably too low for the program. If you have more memory on your machine you can give `max heap` a higher value. See this [post](https://stackoverflow.com/questions/37335/how-to-deal-with-java-lang-outofmemoryerror-java-heap-space-error-64mb-heap) and answers on Stack overflow.
  
  You'll probably need to use the `-Xmxn` argument in `java`.
  
  
  ---
  
  ### Answer by username_3 on 2020-04-18. Score: 0
  
  "If pilon was installed by condo, edit the file "/Users/user/anaconda/bin/pilon" by changing the maximum memory limit from 1G to higher numbers like "14G". It works. "
  check the thread: <https://github.com/broadinstitute/pilon/issues/26>
  
  
  ---
  
  