Intron level featureCounts gives segfault

Question

[lkmklsmn]

Hi,

I am trying to use the featureCounts function in the Rsubread (1.12.6) package in R (3.0.1). I have done this without problems before. This time I am summarizing reads for each intron, meaning my count table should have about 600000 rows for each intron feature. R keeps on crashing, giving me a segfault error.

Any ideas what I could be doing wrong? Does featureCounts run into problem when summarizing across a very large numbers of features? Did anyone successfully use featureCounts on over 500k features?

Thanks

[Devon Ryan]

Take a look at the memory usage when it's running. Perhaps you just run out of memory and it then segfaults.

[lkmklsmn]

I have monitored the memory usage, but its very low, so I dont think I am actually running out of memory.

[Martin Morgan]

This is really a question for maintainer("Rsubread"). Perhaps they'll want the output of sessionInfo(), in particular the version of Rsubread you're using.

Answer 1

[lkmklsmn]

I got it to work using the subread standalone. I think the segfault problem was caused by a problem in the file system I was using. Using the standalone I have no problem summarizing across 600k features.

Answer 2

[dbpzdbpz]

Sorry for the segmentation faults.

There were two bugs in the old version of featureCounts in R that were related to the annotation files and were able to crash the R session. These two bugs have been fixed in the new Rsubread package. The new package is available on BioC 2.14. The version of the new Rsubread package is 1.14.1

(see http://www.bioconductor.org/packages/release/bioc/html/Rsubread.html)

Can you please upgrade to the new version and see if the error is reproduced?

Thank you for using our programs!

-Yang