malloc error on OS X 10.11 (El Capitan) with Fastx_collapser

[adisaxena]

Hi,

I am trying to calculate duplicate and singleton sequences in my RNASeq reads with fastx_collapser (Fastx-Toolkit, Hannon lab) on a Mac Mini (2 core, 16 GB memory, OS X El Capital/10.11).

Every time I run the fastx_collapser command in terminal I get this message:

fastx_collapser(536,0xa2a32000) malloc: *** mach_vm_map(size=1048576) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
Abort trap: 6

OS X 10.11 doesn't allow one to "Repair Disk Permissions" (http://stackoverflow.com/questions/3...ach-vm-mapsize) and Disabling System Integrity Protection (http://osxdaily.com/2015/10/05/disab...tion-mac-os-x/) didnt help.

Has anyone else encountered this problem? Shall be most grateful for any suggestions and advice!

Thanks in advance-
Adi

[adisaxena]

malloc error on OS X 10.11 (El Capitan) with Fastx_collapser

Hi,

I am trying to calculate duplicate and singleton sequences in my RNASeq reads with fastx_collapser (Fastx-Toolkit, Hannon lab) on a Mac Mini (2 core, 16 GB memory, OS X El Capital/10.11).

Every time I run the fastx_collapser command in terminal I get this message:

fastx_collapser(536,0xa2a32000) malloc: *** mach_vm_map(size=1048576) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
Abort trap: 6

OS X 10.11 doesn't allow one to "Repair Disk Permissions" (http://stackoverflow.com/questions/3...ach-vm-mapsize) and Disabling System Integrity Protection (http://osxdaily.com/2015/10/05/disab...tion-mac-os-x/) didnt help.

Has anyone else encountered this problem? Shall be most grateful for any suggestions and advice!

Thanks in advance-
Adi

[GenoMax]

What size is your data file? Perhaps the thing to do would be to align the data and then use Picard to mark the duplicates.

[adisaxena]

@Genomax, Many thanks for your reply. My file is 25gb and I have 2TB storage on my mac mini. Will look into Picard too.

[GenoMax]

Did you compile the toolkit yourself?

[adisaxena]

@Genomax
Yes I did. I have used other tools from the kit (fastx_clipper, fastq_quality_trimmer) and they all worked fine.

[GenoMax]

Have you considered splitting the file in multiple and running rounds of fastx_collapser (since it appears to be trying to do this in memory)?

You could also use dedupe.sh from BBMap to get an idea of perfect duplicates.