malloc error during cuffdiff in mac OS

[ytkim]

Hi all,

I am trying to analyse RNA seq data using tuxedo suit.
When I run cuffdiff(version 2.2.1) on Mac Pro (12 core, 128 GB memory, Yosemite) I encounter malloc error.

cuffdiff -o diff_CN -b genome/genome.fa -p 10 -L TH_C,TH_N --FDR 0.01 --no-update-check -u merged_asm/merged.gtf Th_C_3_bw2.tophat2/accepted_hits.bam,......... Th_N_3_bw2.tophat2/accepted_hits.bam,........
then, the following error message pops up.

cuffdiff(6462,0x7fff77d44300) malloc: *** error for object 0x7fff768d1c70: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

Any suggestion?

[GenoMax]

Are you getting the error right away or after some amount of time? Are you using the latest cufflinks binaries?

[ytkim]

It happens immediately. I am using cufflinks 2.2.1 and it is the most recent version.
it would be great if you suggest solution.

Young

[GenoMax]

If the error happens immediately then it is likely not due to exhaustion of memory.

This may be a long shot but can you try the solution suggested in this thread to fix permissions on /usr/bin: http://stackoverflow.com/questions/2...opening-termin

[ytkim]

Yes, I have done the method suggested on that web page. Deleted the com.apple.terminal.plist file and the repaired disk permission several times. However, it did not work.

[dpryan]

Given that the error indicates a free() on something not malloc()ed, I suspect you might just have to recompile cufflinks (yes, this is going to be annoying to do).

[GenoMax]

You could try pre-compiled binary: http://cole-trapnell-lab.github.io/c..._x86_64.tar.gz

[ytkim]

I copied pre-compiled files and ran brew unlinks and brew link.
It seems to work. It is running well so far.
Thank you very much GenoMax, dpryan!