Answers.Body: <p>I resolved this problem by installing from source; I assume the precompiled binary was not compatible with the Arch Linux kernel.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-23T18:44:16.600Z
Answers.Text: I encountered this with several tools on arch. It looks like most tools are compatible with Ubuntu (or Debian in general) or biolinux
Answers.UserDisplayName: engineercoding
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-24T03:12:58.380Z
Answers.Text: Perhaps the authors should note the distribution of the binary build rather than denoting it as "linux"... or perhaps I shouldn't be so naive as to think such a thing could exist ;)
Answers.UserDisplayName: Scott Gigante
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-23T01:37:03.230Z
Answers.LastActivityDate: 2018-10-23T01:37:03.230Z
Answers.UserDisplayName: Scott Gigante
Body: <p>I am encountering a segmentation fault when attempting to run <a href="http://bioinf.wehi.edu.au/featureCounts/" rel="nofollow noreferrer">featureCounts</a> from <code>subread-1.6.3</code> on even small test data. I installed featureCounts from <a href="https://sourceforge.net/projects/subread/files/subread-1.6.3/" rel="nofollow noreferrer">SourceForge</a> using the precompiled Linux binary.</p>
  
  <p>Most existing help threads on this topic (<a href="http://seqanswers.com/forums/showthread.php?t=50353" rel="nofollow noreferrer">1</a>, <a href="https://www.biostars.org/p/169712/" rel="nofollow noreferrer">2</a>, <a href="https://support.bioconductor.org/p/59473/" rel="nofollow noreferrer">3</a>) show some splash screen output before the error, but I get a segmentation fault before any error is shown.</p>
  
  <pre><code>$ featureCounts -T 1 -p -t exon -g gene_id -a /data/sai/annots/musmus_cdna_all_ensembl92.gtf -o test.txt test.bam test2.bam
  Segmentation fault (core dumped)
  </code></pre>
  
Tags: <rna-seq><sam><subread><featurecounts>
Title: featureCounts segmentation fault on Arch Linux
ThreadText: # featureCounts segmentation fault on Arch Linux
  
  (Asked by: username_0 on 2018-10-23)
  
  I am encountering a segmentation fault when attempting to run [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) from `subread-1.6.3` on even small test data. I installed featureCounts from [SourceForge](https://sourceforge.net/projects/subread/files/subread-1.6.3/) using the precompiled Linux binary.
  
  Most existing help threads on this topic ([1](http://seqanswers.com/forums/showthread.php?t=50353), [2](https://www.biostars.org/p/169712/), [3](https://support.bioconductor.org/p/59473/)) show some splash screen output before the error, but I get a segmentation fault before any error is shown.
  
  ```
  $ featureCounts -T 1 -p -t exon -g gene_id -a /data/sai/annots/musmus_cdna_all_ensembl92.gtf -o test.txt test.bam test2.bam
  Segmentation fault (core dumped)
  
  ```
  
  **Tags:** rna-seq, sam, subread, featurecounts
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-10-23. Score: 3 | Accepted answer
  
  I resolved this problem by installing from source; I assume the precompiled binary was not compatible with the Arch Linux kernel.
  
  > **Comments:**
  > **username_1**: I encountered this with several tools on arch. It looks like most tools are compatible with Ubuntu (or Debian in general) or biolinux  
  > **username_0**: Perhaps the authors should note the distribution of the binary build rather than denoting it as "linux"... or perhaps I shouldn't be so naive as to think such a thing could exist ;)  
  
  ---
  
  