Question: Intron level featureCounts gives segfault
0
gravatar for lkmklsmn
4.8 years ago by
lkmklsmn870
United States
lkmklsmn870 wrote:

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

intron rsubread featurecounts • 1.9k views
ADD COMMENTlink modified 4.8 years ago by dbpzdbpz90 • written 4.8 years ago by lkmklsmn870

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

ADD REPLYlink written 4.8 years ago by Devon Ryan89k

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

ADD REPLYlink written 4.8 years ago by lkmklsmn870

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.

 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Martin Morgan1.6k
0
gravatar for lkmklsmn
4.8 years ago by
lkmklsmn870
United States
lkmklsmn870 wrote:

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.

ADD COMMENTlink written 4.8 years ago by lkmklsmn870
0
gravatar for dbpzdbpz
4.8 years ago by
dbpzdbpz90
Australia
dbpzdbpz90 wrote:

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

ADD COMMENTlink written 4.8 years ago by dbpzdbpz90
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