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.
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