I am using MIRA for the first time for a bacterial whole genome de novo
assembly project. I use ion torrent data with average read length163 bp
with 4,675,076 reads and the assembly aborts with error saying very high
average coverage. How can I solve this problem? If I have to cut down the
data volume how to do that without sampling bias.
Another one comment by mira was "Skewed distribution".Is there any way to
view and analyse the portion of data which contribute skewness? For
reference purpose I am attaching the assembly log here with.
This is MIRA 4.0.2 .
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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Compiled by: bach
Fri Apr 18 14:57:20 CEST 2014
On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012
x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux lab445-T1700 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10
19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Looking for files named in data ...Pushing back filename:
"/home/user/Desktop/SST/sstiontorrent.fastq"
Manifest:
projectname: SST1
job: genome,denovo,accurate
parameters: -GE:not=4
Manifest load entries: 1
MLE 1:
RGID: 1
RGN: SSTiontorrent SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 2 (IonTor) namschem: 4 SID: 0
DQ: 20
BB: 0 Rail: 0 CER: 0
/home/user/Desktop/SST/sstiontorrent.fastq
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data
Used parameter settings:
General (-GE):
Project name : SST1
Number of threads (not) : 4
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Wants quality file (wqf) : [ion] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 5
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 3
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [ion] 40
Minimum reads per contig (mrpc) : [ion] 5
Enforce presence of qualities (epoq) : [ion] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [ion] 2
Minimum length (ardml) : [ion] 200
Grace length (ardgl) : [ion] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [ion] 1.5
Spoiler detection (sd) : yes
Last pass only (sdlpo) : yes
Use genomic pathfinder (ugpf) : yes
Use emergency search stop (uess) : yes
ESS partner depth (esspd) : 500
Use emergency blacklist (uebl) : yes
Use max. contig build time (umcbt) : no
Build time in seconds (bts) : 10000
Strain and backbone options (-SB):
Bootstrap new backbone (bnb) : yes
Start backbone usage in pass (sbuip) : 3
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Trim overhanging reads (tor) : yes
(Also build new contigs (abnc)) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [ion] no
Read extension window length (rewl) : [ion] 15
Read extension w. maxerrors (rewme) : [ion] 2
First extension in pass (feip) : [ion] 0
Last extension in pass (leip) : [ion] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [ion] 8
Max front gap (msvsmfg) : [ion] 8
Max end gap (msvsmeg) : [ion] 12
Strict front clip (msvssfc) : [ion] 0
Strict end clip (msvssec) : [ion] 0
Possible vector leftover clip (pvlc) : [ion] no
maximum len allowed (pvcmla) : [ion] 18
Min qual. threshold for entire read (mqtfer): [ion] 0
Number of bases (mqtfernob) : [ion] 0
Quality clip (qc) : [ion] no
Minimum quality (qcmq) : [ion] 20
Window length (qcwl) : [ion] 30
Bad stretch quality clip (bsqc) : [ion] no
Minimum quality (bsqcmq) : [ion] 5
Window length (bsqcwl) : [ion] 20
Masked bases clip (mbc) : [ion] yes
Gap size (mbcgs) : [ion] 5
Max front gap (mbcmfg) : [ion] 12
Max end gap (mbcmeg) : [ion] 12
Lower case clip front (lccf) : [ion] yes
Lower case clip back (lccb) : [ion] yes
Clip poly A/T at ends (cpat) : [ion] no
Keep poly-a signal (cpkps) : [ion] no
Minimum signal length (cpmsl) : [ion] 12
Max errors allowed (cpmea) : [ion] 1
Max gap from ends (cpmgfe) : [ion] 9
Clip 3 prime polybase (c3pp) : [ion] no
Minimum signal length (c3ppmsl) : [ion] 15
Max errors allowed (c3ppmea) : [ion] 3
Max gap from ends (c3ppmgfe) : [ion] 9
Clip known adaptors right (ckar) : [ion] yes
Ensure minimum left clip (emlc) : [ion] no
Minimum left clip req. (mlcr) : [ion] 4
Set minimum left clip to (smlc) : [ion] 4
Ensure minimum right clip (emrc) : [ion] no
Minimum right clip req. (mrcr) : [ion] 10
Set minimum right clip to (smrc) : [ion] 15
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : [ion] yes
Bases per hash (pecbph) : 27
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [ion] 1
Back freq (pbfreq) : [ion] 1
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [ion] no
Back forward-rev (pbfore) : [ion] no
Front conf. multi-seq type (pfcmst) : [ion] no
Back conf. multi-seq type (pbcmst) : [ion] no
Front seen at low pos (pfsalp) : [ion] no
Back seen at low pos (pbsalp) : [ion] no
Clip bad solexa ends (cbse) : [ion] no
Search PhiX174 (spx174) : [ion] no
Filter PhiX174 (fpx174) : [ion] no
Rare kmer mask (rkm) : [ion] 0
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 4
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 19
Automatic increase per pass (bphaipp) : 1
Automatic incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 1
Percent required (pr) : [ion] 50
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : no
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048
Parameters for Hash Statistics (-HS):
Freq. cov. estim. min (fcem) : 0
Freq. estim. min normal (fenn) : 0.4
Freq. estim. max normal (fexn) : 1.6
Freq. estim. repeat (fer) : 1.9
Freq. estim. heavy repeat (fehr) : 8
Freq. estim. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Nasty repeat coverage (nrc) : 0
Lossless digital normalisation (ldn) : no
Repeat level in info file (rliif) : 6
Million hashes per buffer (mhpb) : 16
Rare kmer early kill (rkek) : no
Pathfinder options (-PF):
Use quick rule (uqr) : [ion] yes
Quick rule min len 1 (qrml1) : [ion] 80
Quick rule min sim 1 (qrms1) : [ion] 90
Quick rule min len 2 (qrml2) : [ion] 60
Quick rule min sim 2 (qrms2) : [ion] 95
Backbone quick overlap min len (bqoml) : [ion] 80
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [ion] 20
Bandwidth max (bmax) : [ion] 80
Bandwidth min (bmin) : [ion] 20
Minimum score (ms) : [ion] 15
Minimum overlap (mo) : [ion] 19
Minimum relative score in % (mrs) : [ion] 70
Solexa_hack_max_errors (shme) : [ion] -1
Extra gap penalty (egp) : [ion] yes
extra gap penalty level (egpl) : [ion] reject_codongaps
Max. egp in percent (megpp) : [ion] 100
Contig parameters (-CO):
Name prefix (np) : SST1
Reject on drop in relative alignment score in % (rodirs) : [ion] 25
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [ion] 4
Minimum neighbour quality needed for tagging (mnq) : [ion] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [ion] 25
End-read Marking Exclusion Area in bases (emea) : [ion] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [ion] no
Also mark gap bases - even multicolumn (amgbemc) : [ion] yes
Also mark gap bases - need both strands (amgbnbs): [ion] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [ion] no
Merge short reads (msr) : [ion] no
Max errors (msrme) : [ion] 0
Keep ends unmerged (msrkeu) : [ion] -1
Gap override ratio (gor) : [ion] 66
Edit options (-ED):
Mira automatic contig editing (mace) : yes
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [ion] yes
Misc (-MI):
Large contig size (lcs) : 500
Large contig size for stats (lcs4s) : 5000
I know what I do (ikwid) : no
Extra flag 1 / sanity track check (ef1) : no
Extra flag 2 / dnredreadsatpeaks (ef2) : yes
Extra flag 3 / pelibdisassemble (ef3) : yes
Extended log (el) : no
Nag and Warn (-NW):
Check NFS (cnfs) : stop
Check multi pass mapping (cmpm) : stop
Check template problems (ctp) : stop
Check duplicate read names (cdrn) : stop
Check max read name length (cmrnl) : stop
Max read name length (mrnl) : 40
Check average coverage (cac) : stop
Average coverage value (acv) : 80
Directories (-DI):
Top directory for writing files : SST1_assembly
For writing result files : SST1_assembly/SST1_d_results
For writing result info files : SST1_assembly/SST1_d_info
For writing tmp files : SST1_assembly/SST1_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : SST1_assembly/SST1_d_chkpt
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [ion] no
Save tagged singlets in project (stsip) : [ion] yes
Remove rollover tmps (rrot) : yes
Remove tmp directory (rtd) : no
Result files:
Saved as CAF (orc) : yes
Saved as MAF (orm) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : no
Saved as GFF3 (org3) : no
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : yes
Saved as wiggle (orw) : yes
Temporary result files:
Saved as CAF (otc) : yes
Saved as MAF (otm) : no
Saved as FASTA (otf) : no
Saved as GAP4 (directed assembly) (otg) : no
Saved as phrap ACE (ota) : no
Saved as HTML (oth) : no
Saved as Transposed Contig Summary (ots) : no
Saved as simple text format (ott) : no
Extended temporary result files:
Saved as CAF (oetc) : no
Saved as FASTA (oetf) : no
Saved as GAP4 (directed assembly) (oetg) : no
Saved as phrap ACE (oeta) : no
Saved as HTML (oeth) : no
Save also singlets (oetas) : no
Alignment output customisation:
TEXT characters per line (tcpl) : 60
HTML characters per line (hcpl) : 60
TEXT end gap fill character (tegfc) :
HTML end gap fill character (hegfc) :
File / directory output names:
CAF : SST1_out.caf
MAF : SST1_out.maf
FASTA : SST1_out.unpadded.fasta
FASTA quality : SST1_out.unpadded.fasta.qual
FASTA (padded) : SST1_out.padded.fasta
FASTA qual.(pad): SST1_out.padded.fasta.qual
GAP4 (directory): SST1_out.gap4da
ACE : SST1_out.ace
HTML : SST1_out.html
Simple text : SST1_out.txt
TCS overview : SST1_out.tcs
Wiggle : SST1_out.wig
------------------------------------------------------------------------------
Creating directory SST1_assembly ... done.
Creating directory SST1_assembly/SST1_d_results ... done.
Creating directory SST1_assembly/SST1_d_info ... done.
Creating directory SST1_assembly/SST1_d_chkpt ... done.
Creating directory SST1_assembly/SST1_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Mon May 25 12:24:55 2015
Loading reads from /home/user/Desktop/SST/sstiontorrent.fastq type fastq
Localtime: Mon May 25 12:24:55 2015
Loading data from FASTQ file: /home/user/Desktop/SST/sstiontorrent.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 4675076 reads, Localtime: Mon May 25 12:25:07 2015
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Checking reads for trace data (loading qualities if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
No SCF data present in any read, EdIt automatic contig editing for Sanger data
is now switched off.
4675076 reads with valid data for assembly.
Localtime: Mon May 25 12:25:11 2015
Generated 4675076 unique DNA template ids for 4675076 valid reads.
No useful template information found.
TODO: Like Readpool: strain x has y reads
Have read pool with 4675076 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 4675076 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 4491990 0 0 0 0 0
Avg tot rlen 0 0 163 0 0 0 0 0
Avg rlen used 0 0 168 0 0 0 0 0
W/o clips 0 0 4675076 0 0 0 0 0
IonTor total bases: 762480053 used bases in used reads: 757939345
===========================================================================
Checking pairs of readgroup 1 (named: 'SSTiontorrent'): found 0
SST1_assembly/SST1_d_tmp/SST1_int_clippings_t0.0.txt
SST1_assembly/SST1_d_tmp/SST1_int_clippings_t1.0.txt
SST1_assembly/SST1_d_tmp/SST1_int_clippings_t2.0.txt
SST1_assembly/SST1_d_tmp/SST1_int_clippings_t3.0.txt
Post-load clips:
Localtime: Mon May 25 12:25:15 2015
Writing temporary hstat files:
freemem: 12795125760
TNH: 5356
XME 1: 0.000212828
XME 2: 0.1
NEPB 1: 104857
NEPB 2: 104857
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Mon May 25 12:25:15 2015
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon May 25 12:25:15 2015
clean up temporary stat files...Localtime: Mon May 25 12:25:15 2015
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Mon May 25 12:25:15 2015
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
CLIP MSG: Adaptor right found: 2397
CLIP MSG: Partial adaptor right found: 10
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 4675076 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 4491919 0 0 0 0 0
Avg tot rlen 0 0 163 0 0 0 0 0
Avg rlen used 0 0 168 0 0 0 0 0
W/o clips 0 0 4672669 0 0 0 0 0
IonTor total bases: 762480053 used bases in used reads: 757867930
===========================================================================
Sorting reads ... done.
Tmp directory is not on a NFS mount, good.
PRED MAXTID 4675075
Hash analysis for proposed cutbacks:Localtime: Mon May 25 12:25:35 2015
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Mon May 25 12:28:17 2015
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon May 25 12:30:21 2015
clean up temporary stat files...Localtime: Mon May 25 12:30:22 2015
Raw MHI: 34784109
Raw avg. freq. : 129
HSS 38191160 HSST: 34372044
Corrected MHI: 33054667
Corrected avg. freq. : 55
HSS 38191160 HSST: 34372044
Localtime: Mon May 25 12:30:32 2015
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 129
Corrected avg. raw frequency coverage: 55 SKEWED DISTRIBUTION!
Final average frequency: 55
Deduced thresholds:
-------------------
Min normal cov: 22
Max normal cov: 88
Repeat cov: 104.5
Heavy cov: 440
Crazy cov: 1100
Mask cov: 5500
Repeat ratio histogram:
-----------------------
0 31933576
1 1845918
2 1172410
3 966354
4 798608
5 641150
6 434598
7 226490
8 98450
9 34308
10 13580
11 6378
12 2994
13 1690
14 1182
15 1162
16 1044
17 926
18 916
19 932
20 898
21 1176
22 1030
23 1152
24 1280
25 832
26 776
27 568
28 292
29 200
30 78
31 52
32 90
33 48
34 16
72 4
73 2
=========================================================
Assigning statistics values:
Localtime: Mon May 25 12:30:32 2015
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Mon May 25 12:31:10 2015
-------- MEDIUM warning --------
MIRA warncode: ASCOV_VERY_HIGH
Title: Very high average coverage
You are running a genome de-novo assembly and the current best estimation for
average coverage is 129x (note that this number can be +/- 20% off the real
value). This is a pretty high coverage,higher than the current warning threshold
of 80x.
You should try to get the average coverage not higher than, say, 60x to 100x for
Illumina data or 40x to 60x for 454 and Ion Torrent data. Hybrid assemblies
should target a total coverage of 80x to 100x as upper bound. For that, please
downsample your input data.
This warning has two major reasons:
- for MIRA and other overlap based assemblers, the runtime and memory
requirements for ultra-high coverage projects grow exponentially, so reducing
the data helps you there
- for all assemblers, the contiguity of an assembly can also suffer if the
coverage is too high, i.e. you get more contigs than you would otherwise.
Causes for this effect can be non-random sequencing errors or low frequency
sub-populations with SNPs which become strong enough to be mistaken for
possible repeats.
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 32890056 kB
MemFree: 17948724 kB
Buffers: 19660 kB
Cached: 2501448 kB
SwapCached: 388 kB
Active: 10921428 kB
Inactive: 3597484 kB
Active(anon): 10554384 kB
Inactive(anon): 1456848 kB
Active(file): 367044 kB
Inactive(file): 2140636 kB
Unevictable: 32 kB
Mlocked: 32 kB
SwapTotal: 31249404 kB
SwapFree: 31216088 kB
Dirty: 16 kB
Writeback: 0 kB
AnonPages: 11997516 kB
Mapped: 128944 kB
Shmem: 13360 kB
Slab: 139976 kB
SReclaimable: 108672 kB
SUnreclaim: 31304 kB
KernelStack: 3464 kB
PageTables: 47940 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 47694432 kB
Committed_AS: 14460644 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 186968 kB
VmallocChunk: 34359539508 kB
HardwareCorrupted: 0 kB
AnonHugePages: 286720 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 84448 kB
DirectMap2M: 4050944 kB
DirectMap1G: 29360128 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 2936
Ngid: 0
Pid: 2936
PPid: 2935
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 64
Groups: 4 24 27 30 46 108 124 1000
VmPeak: 11935736 kB
VmSize: 11673576 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 11581108 kB
VmRSS: 11581108 kB
VmData: 11660556 kB
VmStk: 136 kB
VmExe: 5792 kB
VmLib: 0 kB
VmPTE: 22688 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/256785
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 18569
nonvoluntary_ctxt_switches: 31002
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 4675076 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: 0 24 B 0 B 0 B
AS_skim_edges: 0 24 B 0 B 0 B
AS_adsfacts: 0 24 B 0 B 0 B
AS_confirmed_edges: 0 24 B 0 B 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: 4675076 18 MiB 0 B 0 B
AS_clipright: 4675076 18 MiB 0 B 0 B
AS_used_ids: 4675076 4 MiB 0 B 4 B
AS_multicopies: 0 4 MiB 4 MiB 4 B
AS_hasmcoverlaps: 0 4 MiB 4 MiB 4 B
AS_maxcoveragereached: 4675076 18 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 4675076 4 MiB 0 B 4 B
AS_isdebris: 4675076 4 MiB 0 B 4 B
AS_needalloverlaps: 4675076 4 MiB 0 B 4 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 18 MiB 18 MiB 0 B
AS_probablermbsnotok: 0 18 MiB 18 MiB 0 B
AS_weakrmbsnotok: 0 18 MiB 18 MiB 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: 5 176 B 0 B 0 B
Total: 140253408 (134 MiB)
================================================================================
Dynamic s allocs: 0
Dynamic m allocs: 0
Align allocs: 0
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* High average coverage detected, see output log above respectively the *
* 'WARNING' files in the info directory for more information. In case you wish *
* to force MIRA to disregard this safety check, consider using '-NW:cac=warn' *
* or '-NW:cac=no' *
********************************************************************************
->Thrown: void Assembly::performProposedCutbackClips(const string & logname,
const string & logprefix)
->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: /home/user/Desktop/SST
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, wrapped MIRA process aborted.
