cufflinks memory allocation error.

[billthebrute]

Hi all,

I have been successful in using cufflinks on sam alignments in the past
but am currently faced with a tricky problem. When I use tophat to
generate accepted_hits.sam and use cufflinks on this file, I get the very
uninformative error:

Processing bundle [ 10:12183975-12184040 ] with 1 non-redundant alignments
Processing bundle [ 10:12184440-12184505 ] with 1 non-redundant alignments
Processing bundle [ 10:12184986-12434174 ] with 1816 non-redundant alignments
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted

Strangely, when I extract this bundle by searching for all reads that
align between positions 12184986-12434174, and use cufflinks only on this
bundle, the error message disappears. I doubt that it is really a memory
problem because sometimes the same error occurs on tiny bundles.
Do you have any ideas of where this is coming from ?

Thanks in advance !

[joro]

Hi billthebrute,

I know this was a while ago but did you resolve this? I'm having the same problem.

Cheers.

[mauro.pala]

Hi all,


I have the same problem. I'm using samtools 0.1.16, TopHat v1.3.1 and cufflinks v1.0.3. has anyone solved this?

My data is 50M of reads PE. I'm running this with 16Gb of RAM


thanks


M.

[lakshmaa]

I had the same problem std:bad_alloc() with my cufflinks run. I was running it on the cluster. When I increased the free memory option to 10G and number of single processors to use to 24, it worked fine. Hope this of some help.