[mira_talk] No such file or directory after running for approx 360 hours
- From: Joel barratt <joelbarratt43@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 14 Oct 2012 19:07:06 +1100
Hi Bastien,
I recently attempted an assembly using MIRA 3.9.4. The assembly ended with
an error though all the output files seem to be present and intact. The
assembly seemed to be running fine for about 360 hours.. Here are the last
100 lines of the output below:
Pid: 48519
PPid: 48512
TracerPid: 0
Uid: 503 503 503 503
Gid: 503 503 503 503
Utrace: 0
FDSize: 256
Groups: 503
VmPeak: 75124652 kB
VmSize: 75068216 kB
VmLck: 0 kB
VmHWM: 72407756 kB
VmRSS: 68010380 kB
VmData: 74965816 kB
VmStk: 384 kB
VmExe: 5136 kB
VmLib: 0 kB
VmPTE: 133032 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/2066390
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ffffffff,ffffffff
Cpus_allowed_list: 0-63
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Mems_allowed_list: 0-7
voluntary_ctxt_switches: 6146365
nonvoluntary_ctxt_switches: 1689789
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 26988832 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 184 (184 B)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 26988832 103 MiB 0 B 0 B
AS_skim_edges: 0 16.8 GiB 16.8 GiB 0 B
AS_adsfacts: 243715253 5.6 GiB 1.1 GiB 4 B
AS_confirmed_edges: 487430504 11.2 GiB 2.1 GiB 0 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: 26988832 103 MiB 0 B 0 B
AS_clipright: 26988832 103 MiB 0 B 0 B
AS_used_ids: 0 26 MiB 26 MiB 0 B
AS_multicopies: 26988832 26 MiB 0 B 0 B
AS_hasmcoverlaps: 0 26 MiB 26 MiB 0 B
AS_maxcoveragereached: 26988832 103 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 26988832 26 MiB 0 B 0 B
AS_isdebris: 26988832 26 MiB 0 B 0 B
AS_needalloverlaps: 26988832 26 MiB 0 B 0 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: 49 2 KiB 0 B 0 B
Total: 36638261344 (34.1 GiB)
================================================================================
Dynamic allocs: 68
Align allocs: 68
Fatal error (may be due to problems of the input data or parameters):
"Now, this is embarassing: could not rollback checkpoint rename after
failed snapshot?
Error message is boost::filesystem::rename: No such file or directory:
"Dientamoeba_scaffold_assembly/Dientamoeba_scaffold_d_chkpt_tmp",
"Dientamoeba_scaffold_assembly/Dientamoeba_scaffold_d_chkpt""
->Thrown: void Assembly::performSnapshot(uint32 actpass)
->Caught: main
Aborting process, probably due to error in the input data or
parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /scratch/work/scaffold.assembly.mira.3.9.48512
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
---------------------------------------------------------------------------------------------------------------------
Any insights into what could have caused this and how I could fix it? Let
me know if you require further information.
Thanks in advance for your support Bastien.
Cheers!
Joel
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