Hi,
i also got 2 times the same error with MIRA 3.9.4 and paired-end
Illumina set of 11M reads or so:
---------------------------------
Could not create directory
'8dsw_denovo_assembly/8dsw_denovo_d_chkpt'.: Cannot allocate
memory
"Could not create new snapshot directory? Disk full? changed
permissions?"
---------------------------------
I got enough space and i think memory(64GB) as well. But yeah i
think MIRA wanted to create a directory which already existed and
was full so i suppose the system did not allow it, hence the
error. Well waiting for MIRA 3.9.5 or debugging the code by
ourselves :)
Btw, i think ive read before that MIRA uses around 1.5Gb RAM per
million of Illumina reads. I have 2 questions regarding this:
1. Is it still so?
2. Is this 1.5Gb per million single reads? I mean that for
paired-end it will be 3GB.
Cheers
Dimitar
On 09/20/2012 02:40 PM, Andrej Benjak wrote:
Dear Bastien, dear "bioinfo" friends,
I got the same error running mira 3.9.4 with similar conditions as previously reported (mapping genome (454+Illu+PacBio+IonTor), HDD not mounted, lots of free space).
One warning got my attention though.Just before the exit error I got this:
"Could not create directory '18b_hybrid_assembly_1_assembly/18b_hybrid_assembly_1_d_chkpt'.: Cannot allocate memory"
This was the only instance of "Cannot allocate memory" in the log file.
Following in the log was the "Memory self assessment" and then exit (see below) .
As the RAM was not sufficient for mira the computer was swapping a lot (over 30%). The "amm" was on and "kpmf=5".
Has anybody else also got the same "Cannot allocate memory" before "Could not create new snapshot directory? Disk full? changed permissions?"?
All the best,
Andrej Benjak
Localtime: Wed Sep 19 22:46:50 2012
Creating directory 18b_hybrid_assembly_1_assembly/18b_hybrid_assembly_1_d_chkpt ...
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 16285528 kB
MemFree: 90808 kB
Buffers: 1480 kB
Cached: 60888 kB
SwapCached: 2323544 kB
Active: 11673376 kB
Inactive: 1424376 kB
Active(anon): 11646316 kB
Inactive(anon): 1389604 kB
Active(file): 27060 kB
Inactive(file): 34772 kB
Unevictable: 32 kB
Mlocked: 32 kB
SwapTotal: 28141472 kB
SwapFree: 15847912 kB
Dirty: 1404 kB
Writeback: 0 kB
AnonPages: 12202224 kB
Mapped: 43996 kB
Shmem: 560 kB
Slab: 78552 kB
SReclaimable: 46616 kB
SUnreclaim: 31936 kB
KernelStack: 3848 kB
PageTables: 73880 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 36284236 kB
Committed_AS: 25489504 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 170972 kB
VmallocChunk: 34359550460 kB
HardwareCorrupted: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 7489536 kB
DirectMap2M: 9113600 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 11092
Pid: 11092
PPid: 4885
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 256
Groups: 4 20 24 46 105 109 119 127 128 1000
VmPeak: 23122696 kB
VmSize: 23122680 kB
VmLck: 0 kB
VmHWM: 14880196 kB
VmRSS: 12077020 kB
VmData: 23111852 kB
VmStk: 4184 kB
VmExe: 5136 kB
VmLib: 0 kB
VmPTE: 44468 kB
Threads: 1
SigQ: 0/16382
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 5720061
nonvoluntary_ctxt_switches: 1922767
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 8445926 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 1 contigs.
Mem used for reads: 184 (184 B)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 8445926 32 MiB 0 B 0 B
AS_skim_edges: 0 4.2 GiB 4.2 GiB 0 B
AS_adsfacts: 8004887 176 MiB 23 MiB 4 B
AS_confirmed_edges: 16009772 351 MiB 46 MiB 4 B
AS_permanent_overlap_bans: 1 24 B 0 B 0 B
AS_readhitmiss: 0 24 B 0 B 0 B
AS_readhmcovered: 0 24 B 0 B 0 B
AS_count_rhm: 0 24 B 0 B 0 B
AS_clipleft: 8445926 32 MiB 0 B 0 B
AS_clipright: 8445926 32 MiB 0 B 0 B
AS_used_ids: 0 8 MiB 8 MiB 2 B
AS_multicopies: 8445926 8 MiB 0 B 2 B
AS_hasmcoverlaps: 0 8 MiB 8 MiB 2 B
AS_maxcoveragereached: 8445926 32 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 8445926 8 MiB 0 B 2 B
AS_isdebris: 8445926 8 MiB 0 B 2 B
AS_needalloverlaps: 8445926 8 MiB 0 B 2 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 24 B 0 B 0 B
AS_probablermbsnotok: 0 24 B 0 B 0 B
AS_weakrmbsnotok: 0 24 B 0 B 0 B
AS_readmaytakeskim: 0 40 B 0 B 0 B
AS_skimstaken: 0 40 B 0 B 0 B
AS_numskimoverlaps: 0 24 B 0 B 0 B
AS_numleftextendskims: 0 24 B 0 B 0 B
AS_rightextendskims: 0 24 B 0 B 0 B
AS_skimleftextendratio: 0 24 B 0 B 0 B
AS_skimrightextendratio: 0 24 B 0 B 0 B
AS_usedtmpfiles: 34 1 KiB 0 B 0 B
Total: 5247869632 (4.9 GiB)
================================================================================
Dynamic allocs: 57
Align allocs: 276
Fatal error (may be due to problems of the input data or parameters):
"Could not create new snapshot directory? Disk full? changed permissions?"
->Thrown: void Assembly::performSnapshot(uint32 actpass)
->Caught: main
Aborting process, probably due to error in the input data or parametrisation.
--
Dimitar Kenanov
Bioinformatician
Tel:+65 6778 6822 (ext 114)
Fax:+65 6778 2962
email:
Dimitar@xxxxxxxxxxxxxx
