Skip to content

Canu Sorting ovlStore error #755

@HRitchie89

Description

@HRitchie89

Hi there,

I am running Canu on my MinION data and I'm having problems during the creation of the ovlStore. The bucketizing completes then when it moves onto Store I get the following error:

-- SORTING --

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

Failed with 'Aborted'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::102 in _Z17AS_UTL_catchCrashiP7siginfoPv()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
../../gcc-4.8.2/libstdc++-v3/libsupc++/vterminate.cc::95 in _ZN9__gnu_cxx27__verbose_terminate_handlerEv()
../../gcc-4.8.2/libstdc++-v3/libsupc++/eh_terminate.cc::38 in _ZN10__cxxabiv111__terminateEPFvvE()
../../gcc-4.8.2/libstdc++-v3/libsupc++/eh_terminate.cc::48 in _ZSt9terminatev()
../../gcc-4.8.2/libstdc++-v3/libsupc++/eh_throw.cc::84 in __cxa_throw()
../../gcc-4.8.2/libstdc++-v3/libsupc++/new_op.cc::56 in _Znwm()
../../gcc-4.8.2/libstdc++-v3/libsupc++/new_opv.cc::32 in _Znam()
stores/ovOverlap.H::192 in _ZN9ovOverlap16allocateOverlapsEP7gkStorem()
stores/ovStoreBuild.C::584 in main()
(null)::0 in (null)()
(null)::0 in (null)()


I have increased the available memory for Canu so I am confident it is not a memory issue. 

--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     64 GB    8 CPUs  (k-mer counting)
-- Grid:  cormhap   13 GB    8 CPUs  (overlap detection with mhap)
-- Grid:  obtovl     8 GB    8 CPUs  (overlap detection)
-- Grid:  utgovl     8 GB    8 CPUs  (overlap detection)
-- Grid:  cor       20 GB    4 CPUs  (read correction)
-- Grid:  ovb       64 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs      128 GB    1 CPU   (overlap store sorting)
-- Grid:  red        6 GB    4 CPUs  (read error detection)
-- Grid:  oea        2 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat       64 GB    8 CPUs  (contig construction)
-- Grid:  cns       48 GB    8 CPUs  (consensus)
-- Grid:  gfa        8 GB    8 CPUs  (GFA alignment and processing)

-- Finished on Fri Jan 12 18:52:35 2018 (36795 seconds) with 11934.062 GB free disk space
----------------------------------------
ERROR:
ERROR:  Failed with exit code 134.  (rc=34304)
ERROR:

ABORT:
ABORT: Canu 1.6
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:
ABORT:   failed to create the overlap store.
ABORT:
ABORT: Disk space available:  11934.062 GB

I'm fairly stumped so any suggestions would be greatly appreciated.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions