#41 Failure, wrapped MIRA process aborted.

[Yisoo Choi]

Hello, I am using MIRA very well. Thank you very much.
But I wonder bout this problem.
And i want to know what is bbcontig.
please help me.
thank you.

[66423] PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP 16395 pft 1 / 32
[66423] PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP 16395 pft 1 / 32
[66423] PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP 16395 pft 1 / 32
[66423] PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP 16395 pft 1 / 33
[66423] PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPaPPPPPPPPP 16395 pft 1 / 35
[66423] PPPPPPPPPPPPPPPPPPPaaPPPPaPPPaPPaPaPPaPaPaaPaPaaPaaaaaaaPPaP 16395 pft 1 / 87
[66423] aaaaaPaaaaaaaaPaPaaaaaPaaaaaaaaaaPaPaaaPaaaaaaaaaaaPaaaaaaPa 16395 pft 1 / 149
[66423] aaaaaaaaaaaaaaPaaaaaPaaaPaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 16395 pft 1 / 161
[66423] aPaaaaPaaaPPPaaPaPPaaaaaaPaaaPPPPPaaPaaaaaaaaaaaaaaaaPaaaaPa 16395 pft 1 / 127
[66423] aacac++cacaccc+c+aaaaaac+ccacc+ccdaaaaaaaaacaa+cc+ccaaac+ccc 16429 pft 44 / 4843
[66433] +caccaaccccacaaaaaaaaaaaaaaaaaaaaaaaaac+cac+caac+caacaaa+cac 16449 pft 1 / 1205
[66437] cccaacaaa++cccca+cccaaccc+acacccaaccaacaccaaa++a+cacccaaaaac 16453 pft 1 / 379
[66444] ac+caaaaaTaacacca+accaaacca+aca+ccaaaaaac+cc+a+cc++ccccaccca 16469 pft 1 / 1167
[66453] aaacccaacaa+cccccTcaccccacacaccacaccccccaa+accccaaaaaaa+a+aa 16475 pft 1 / 558
[66458] ++ccacac+aa+ccaaaaaacccccaaccac
ccon timings:
cct pre 104924190
cct dir 252789622
cct xcu 1073385734
cct tmp 81047174
cct sw 8905043246
cct pic 183327
cct ico 27741919
cct icm 0
cct upd 221974
cct del 0
cct rmz 196120
cct gcp 70359314

ccon i timings (134520):
ccit insglcc 40
ccit insglaro 69
ccit insglact 12
ccit insgltot 187988
ccit pr 1853921
ccit templ 447200
ccit index 177245
ccit biglccins 210068
ccit biglinterpol 12979
ccit biglupdtags 9654
ccit biglfpcri 3414
ccit bigllgap 21196218
ccit biglshiftread 75714
ccit bigltot 22142778
ccit insgr 177501
ccit ucv 1164396

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 12
ccdt itb 6
ccdt ccef 6
ccdt cceb 2
ccdt sdt 5
ccdt sr 11
ccdt smp 1
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
TU before 1001482
RIDs known 66461
TU after 935021
bfc 9/0

Finished building.
Localtime: Mon Nov 11 20:40:49 2019
Timing BFC analysereadcov: 1070626
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 20
mict_shadow 12542
mict_fallout 397634
mict_newin 36490
mict_helper1 2521087
mict_newin 36490
mict_restofloop 35006
mict_totalloop 3107553
done.

-------------- Contig statistics ----------------
Contig id: 1
Contig length: 16480

          Sanger         454      IonTor     PcBioHQ     PcBioLQ        Text      Solexa       Solid

Num. reads 0 0 0 0 0 1 66380 0
100% merged reads - - - - - - 0 0
Max. coverage 0 0 0 0 0 3 11095 0
Avg. coverage 0.000 0.000 0.000 0.000 0.000 0.984 781.769 0.000

Max. contig coverage: 11098
Avg. contig coverage: 782.753

Consensus contains: A: 4542 C: 1810 G: 2374 T: 5664 N: 0
IUPAC: 28 Funny: 0 *: 2062
GC content: 29.076%

Contig positions with coverage: 0

---

Timing BFC cout constats: 3127544
Localtime: Mon Nov 11 20:40:53 2019
bfc 10/0
Timing BFC edit tricky1: 2
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 371 new Strong RMB (SRMc)
- 10 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 13252046
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Edited 98 positions.
Localtime: Mon Nov 11 20:41:07 2019
Deleting superfluous gap columns (2) ... done, deleted 0 columns.
Localtime: Mon Nov 11 20:41:07 2019
Timing BFC edit single discrepancy, no HAF: 1011363
bfc 12/0
Timing BFC delPSHP: 20586
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering read tags to readpool.
Transfering tags to readpool.
Timing BFC crtag2rp transfer: 3471501
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Transforming CER mappings.
done transforming CER mappings.
Searching for: SROs UNSs IUPACs, preparing needed data: sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 489
mict_pre 17
mict_shadow 35376
mict_fallout 707967
mict_newin 33054
mict_helper1 2981302
mict_newin 33054
mict_restofloop 33104
mict_totalloop 3847102
done.
fetching consensus for strain0 ...makeIntelligentConsensus() complete calc .. mict_fin 2
mict_pre 14
mict_shadow 33040
mict_fallout 656171
mict_newin 33669
mict_helper1 2837689
mict_newin 33669
mict_restofloop 23936
mict_totalloop 3640989
done.
fetching consensus for strain1 ...makeIntelligentConsensus() complete calc .. mict_fin 2
mict_pre 15
mict_shadow 36803
mict_fallout 22794
mict_newin 30027
mict_helper1 29604
mict_newin 30027
mict_restofloop 22675
mict_totalloop 193230
done.
done.
Starting search:
done with search
Transfering tags to readpool.
Saving CAF ... done.
Saving MAF ... done.
Saving strains as FASTA ... ### calc AllStrains with strainid -1
### calc testpool with strainid 0
### calc ZAFER with strainid 1
done.
Saving TCS ... done.
Saving Wiggle ... done.
done.
Timing BFC store con: 30033193
Contig coverage analysis ... Last backbone mapped, not building new ones.
Moved 935021 remaining reads to debris.
Timing BFC loop total: 34711076745
Timing BFC unused: 4098
CUnused: 0
TUnused: 0
AS_used_ids.size(): 4808573
Saving debris list to file: testpool-ZAFER_assembly/testpool-ZAFER_d_info/testpool-ZAFER_info_debrislist.txt

Buildstats - RM positions : 371 0
Buildstats - overcall edits : 0 0
Buildstats - hash edits : 98 0
Buildstats - contig disassemblies: 0 0

ATG PREDICTIONS
rgid: 2 c: 985 sp: -2 m: 190.6637596899 d: 23.0334694876 s: 0.8776294181 -: 149 +: 241
rgid: 2 c: 27385 sp: -1 m: 260.3825812536 d: 56.1390662411 s: 0.3836896661 -: 153 +: 378
Final prediction: rgid: 2 c: 27385 sp: -1 m: 260.3825812536 d: 56.1390662411 s: 0.3836896661 -: 153 +: 378
ATG PREDICTIONS
rgid: 2 c: 985 sp: -2 m: 190.6637596899 d: 23.0334694876 s: 0.8776294181 -: 149 +: 241
rgid: 2 c: 27385 sp: -1 m: 260.3825812536 d: 56.1390662411 s: 0.3836896661 -: 153 +: 378
Final prediction: rgid: 2 c: 27385 sp: -1 m: 260.3825812536 d: 56.1390662411 s: 0.3836896661 -: 153 +: 378
Performing snapshot 2
Localtime: Mon Nov 11 20:41:42 2019

========================== Memory self assessment ==============================
Running in 64 bit mode.

Dump from /proc/meminfo

---

MemTotal: 131678636 kB
MemFree: 5359544 kB
MemAvailable: 103934576 kB
Buffers: 894464 kB
Cached: 96575844 kB
SwapCached: 520 kB
Active: 75411144 kB
Inactive: 47593768 kB
Active(anon): 23814212 kB
Inactive(anon): 1696664 kB
Active(file): 51596932 kB
Inactive(file): 45897104 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 8388604 kB
SwapFree: 8363516 kB
Dirty: 8988 kB
Writeback: 0 kB
AnonPages: 25533900 kB
Mapped: 340336 kB
Shmem: 1888 kB
Slab: 2694368 kB
SReclaimable: 2333420 kB
SUnreclaim: 360948 kB
KernelStack: 11888 kB
PageTables: 64168 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 74096848 kB
Committed_AS: 30015860 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 0 kB
VmallocChunk: 0 kB
HardwareCorrupted: 0 kB
AnonHugePages: 8192 kB
ShmemHugePages: 0 kB
ShmemPmdMapped: 0 kB
CmaTotal: 0 kB
CmaFree: 0 kB
HugePages_Total: 128
HugePages_Free: 122
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 1402420 kB
DirectMap2M: 54865920 kB
DirectMap1G: 79691776 kB

---

Dump from /proc/self/status

---

Name: mira
Umask: 0022
State: R (running)
Tgid: 28112
Ngid: 0
Pid: 28112
PPid: 28111
TracerPid: 0
Uid: 0 0 0 0
Gid: 0 0 0 0
FDSize: 64
Groups: 0
NStgid: 28112
NSpid: 28112
NSpgid: 5022
NSsid: 2917
VmPeak: 8102336 kB
VmSize: 8102336 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 8026520 kB
VmRSS: 8026520 kB
RssAnon: 8021188 kB
RssFile: 5332 kB
RssShmem: 0 kB
VmData: 8096224 kB
VmStk: 300 kB
VmExe: 5792 kB
VmLib: 8 kB
VmPTE: 15796 kB
VmSwap: 0 kB
HugetlbPages: 0 kB
CoreDumping: 0
Threads: 1
SigQ: 0/514114
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000001
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000003fffffffff
CapEff: 0000003fffffffff
CapBnd: 0000003fffffffff
CapAmb: 0000000000000000
NoNewPrivs: 0
Seccomp: 0
Speculation_Store_Bypass: thread vulnerable
Cpus_allowed: ffff
Cpus_allowed_list: 0-15
Mems_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 4904
nonvoluntary_ctxt_switches: 3107333

---

Information on current assembly object:

AS_readpool: 4808573 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: 4808573 18 MiB 0 B 4 B
AS_skim_edges: 0 382 MiB 382 MiB 0 B
AS_adsfacts: 1001401 22 MiB 3 MiB 4 B
AS_confirmed_edges: 2002802 44 MiB 6 MiB 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: 4808573 18 MiB 0 B 4 B
AS_clipright: 4808573 18 MiB 0 B 4 B
AS_used_ids: 0 5 MiB 5 MiB 3 B
AS_multicopies: 4808573 5 MiB 0 B 3 B
AS_hasmcoverlaps: 0 5 MiB 5 MiB 3 B
AS_maxcoveragereached: 4808573 18 MiB 0 B 4 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 4808573 5 MiB 0 B 3 B
AS_isdebris: 4808573 5 MiB 0 B 3 B
AS_needalloverlaps: 4808573 5 MiB 0 B 3 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: 42 1 KiB 0 B 0 B
Total: 575554120 (549 MiB)

================================================================================
Failure, wrapped MIRA process aborted.

MIRA seems to have failed - see detailed output above