I am encountering a segmentation fault when attempting to run featureCounts from subread-1.6.3 on even small test data. I installed featureCounts from SourceForge using the precompiled Linux binary.

Most existing help threads on this topic (1, 2, 3) 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)

1 Answer 1


I resolved this problem by installing from source; I assume the precompiled binary was not compatible with the Arch Linux kernel.

  • $\begingroup$ I encountered this with several tools on arch. It looks like most tools are compatible with Ubuntu (or Debian in general) or biolinux $\endgroup$ Oct 23, 2018 at 18:44
  • 2
    $\begingroup$ 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 ;) $\endgroup$ Oct 24, 2018 at 3:12

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