text: user1075: I am running the following command to index my genome:
  STAR --runThreadN 8 --runMode genomeGenerate --genomeDir output/index/star --genomeFastaFiles ref.fa --sjdbGTFfile ref.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 100
  and I get the following output:
  Feb 27 10:27:37 ..... started STAR run
  Feb 27 10:27:37 ... starting to generate Genome files
  Feb 27 10:27:40 ... starting to sort Suffix Array. This may take a long time...
  Feb 27 10:27:42 ... sorting Suffix Array chunks and saving them to disk...
  Feb 27 10:28:26 ... loading chunks from disk, packing SA...
  Feb 27 10:28:30 ... finished generating suffix array
  Feb 27 10:28:30 ... generating Suffix Array index
  terminate called after throwing an instance of 'std::bad_alloc'
    what():  std::bad_alloc
  
  Searches for the GNU/Linux error lead to some pages about C++ that I don't understand. 
  Submitting it as a batch job works fine but I would like to know why it does not work on a node. It is quite practical for me to test small code like this without submitting a batch job.
  The command above works fine on my laptop running Mac OSX.
  The STAR version is STAR_2.5.3a on both computers: STAR_2.5.3a
  The memory usage of the node is the following:
  total            used       free     shared    buffers       cached
  
  251              251         0         0       0             232
  
  so, is there 0 memory for me to use on this node?
  Why is my indexing aborting? 
  
  user77: A std::bad_alloc error tends to mean that you've run out of memory. It's not unusual for head nodes to be fairly limited in capacity, so presumably that's the issue.
  
original_text: 1075: <p>I am running the following command to index my genome:</p>
  
  <p><code>STAR --runThreadN 8 --runMode genomeGenerate --genomeDir output/index/star --genomeFastaFiles ref.fa --sjdbGTFfile ref.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 100</code></p>
  
  <p>and I get the following output:</p>
  
  <pre><code>Feb 27 10:27:37 ..... started STAR run
  Feb 27 10:27:37 ... starting to generate Genome files
  Feb 27 10:27:40 ... starting to sort Suffix Array. This may take a long time...
  Feb 27 10:27:42 ... sorting Suffix Array chunks and saving them to disk...
  Feb 27 10:28:26 ... loading chunks from disk, packing SA...
  Feb 27 10:28:30 ... finished generating suffix array
  Feb 27 10:28:30 ... generating Suffix Array index
  terminate called after throwing an instance of 'std::bad_alloc'
    what():  std::bad_alloc
  </code></pre>
  
  <p>Searches for the GNU/Linux error lead to some pages about C++ that I don't understand. </p>
  
  <p>Submitting it as a batch job works fine but I would like to know why it does not work on a node. It is quite practical for me to test small code like this without submitting a batch job.</p>
  
  <p>The command above works fine on my laptop running Mac OSX.</p>
  
  <p>The STAR version is STAR_2.5.3a on both computers: STAR_2.5.3a</p>
  
  <p>The memory usage of the node is the following:</p>
  
  <pre><code>total            used       free     shared    buffers       cached
  
  251              251         0         0       0             232
  </code></pre>
  
  <p>so, is there 0 memory for me to use on this node?</p>
  
  <p>Why is my indexing aborting? </p>
   77: <p>A <code>std::bad_alloc</code> error tends to mean that you've run out of memory. It's not unusual for head nodes to be fairly limited in capacity, so presumably that's the issue.</p>
  