Intron level featureCounts gives segfault
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8.0 years ago
lkmklsmn ▴ 960

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 • 2.9k views
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Take a look at the memory usage when it's running. Perhaps you just run out of memory and it then segfaults.

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

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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.

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8.0 years ago
lkmklsmn ▴ 960

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.

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8.0 years ago
dbpzdbpz ▴ 170

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

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

Thank you for using our programs!

-Yang

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