Sir,
I am using MIRA assembler for whole genome assembly of a Brassica species.
I have tried it 2-3 times but I am getting an Internal
logic/programming/debugging error while running. I am attaching the
manifest file that I have used as well as the log file of MIRA. Please
provide me the solution of this problem as soon as possible.
Thanks and Regards,
Shikha Mittal
Research Associate
Centre for Agricultural Bioinformatics
Indian Agricultural Statistical Research Institute
New Delhi, India
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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http://www.chevreux.org/mira_mailinglists.html
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To report bugs or ask for features, please use the SourceForge ticketing
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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 smp2.cabgrid.res.in 3.10.0-327.el7.x86_64 #1 SMP Thu Oct
29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux
Looking for files named in data ...Pushing back filename:
"/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_1.fastq"
Pushing back filename:
"/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_2.fastq"
Manifest:
projectname: MyFirstAssembly
job: genome,denovo,accurate
parameters: COMMON_SETTINGS -NW:cmrnl=no
Manifest load entries: 1
MLE 1:
RGID: 1
RGN: DataIlluminaPairedLib autopairing SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 6 (Solexa) namschem: 4 SID: 0
DQ: 30
BB: 0 Rail: 0 CER: 0
/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_1.fastq
/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_2.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 : MyFirstAssembly
Number of threads (not) : 144
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) : [sxa] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 4
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 2
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [sxa] 20
Minimum reads per contig (mrpc) : [sxa] 10
Enforce presence of qualities (epoq) : [sxa] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [sxa] 2.5
Minimum length (ardml) : [sxa] 300
Grace length (ardgl) : [sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [sxa] 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) : [sxa] no
Read extension window length (rewl) : [sxa] 30
Read extension w. maxerrors (rewme) : [sxa] 2
First extension in pass (feip) : [sxa] 0
Last extension in pass (leip) : [sxa] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [sxa] 1
Max front gap (msvsmfg) : [sxa] 2
Max end gap (msvsmeg) : [sxa] 2
Strict front clip (msvssfc) : [sxa] 0
Strict end clip (msvssec) : [sxa] 0
Possible vector leftover clip (pvlc) : [sxa] no
maximum len allowed (pvcmla) : [sxa] 18
Min qual. threshold for entire read (mqtfer): [sxa] 5
Number of bases (mqtfernob) : [sxa] 15
Quality clip (qc) : [sxa] no
Minimum quality (qcmq) : [sxa] 20
Window length (qcwl) : [sxa] 30
Bad stretch quality clip (bsqc) : [sxa] no
Minimum quality (bsqcmq) : [sxa] 5
Window length (bsqcwl) : [sxa] 20
Masked bases clip (mbc) : [sxa] no
Gap size (mbcgs) : [sxa] 5
Max front gap (mbcmfg) : [sxa] 12
Max end gap (mbcmeg) : [sxa] 12
Lower case clip front (lccf) : [sxa] no
Lower case clip back (lccb) : [sxa] no
Clip poly A/T at ends (cpat) : [sxa] no
Keep poly-a signal (cpkps) : [sxa] no
Minimum signal length (cpmsl) : [sxa] 12
Max errors allowed (cpmea) : [sxa] 1
Max gap from ends (cpmgfe) : [sxa] 9
Clip 3 prime polybase (c3pp) : [sxa] yes
Minimum signal length (c3ppmsl) : [sxa] 15
Max errors allowed (c3ppmea) : [sxa] 3
Max gap from ends (c3ppmgfe) : [sxa] 9
Clip known adaptors right (ckar) : [sxa] yes
Ensure minimum left clip (emlc) : [sxa] no
Minimum left clip req. (mlcr) : [sxa] 0
Set minimum left clip to (smlc) : [sxa] 0
Ensure minimum right clip (emrc) : [sxa] no
Minimum right clip req. (mrcr) : [sxa] 10
Set minimum right clip to (smrc) : [sxa] 20
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : [sxa] yes
Bases per hash (pecbph) : 31
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [sxa] 0
Back freq (pbfreq) : [sxa] 0
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [sxa] yes
Back forward-rev (pbfore) : [sxa] yes
Front conf. multi-seq type (pfcmst) : [sxa] yes
Back conf. multi-seq type (pbcmst) : [sxa] yes
Front seen at low pos (pfsalp) : [sxa] no
Back seen at low pos (pbsalp) : [sxa] no
Clip bad solexa ends (cbse) : [sxa] yes
Search PhiX174 (spx174) : [sxa] yes
Filter PhiX174 (fpx174) : [sxa] no
Rare kmer mask (rkm) : [sxa] 0
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 144
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 23
Automatic increase per pass (bphaipp) : 1
Automatic incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 1
Percent required (pr) : [sxa] 95
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) : 4096
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) : [sxa] yes
Quick rule min len 1 (qrml1) : [sxa] -95
Quick rule min sim 1 (qrms1) : [sxa] 100
Quick rule min len 2 (qrml2) : [sxa] -85
Quick rule min sim 2 (qrms2) : [sxa] 100
Backbone quick overlap min len (bqoml) : [sxa] 20
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [sxa] 20
Bandwidth max (bmax) : [sxa] 80
Bandwidth min (bmin) : [sxa] 20
Minimum score (ms) : [sxa] 15
Minimum overlap (mo) : [sxa] 25
Minimum relative score in % (mrs) : [sxa] 90
Solexa_hack_max_errors (shme) : [sxa] -1
Extra gap penalty (egp) : [sxa] yes
extra gap penalty level (egpl) : [sxa] reject_codongaps
Max. egp in percent (megpp) : [sxa] 100
Contig parameters (-CO):
Name prefix (np) :
MyFirstAssembly
Reject on drop in relative alignment score in % (rodirs) : [sxa] 30
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [sxa] 4
Minimum neighbour quality needed for tagging (mnq) : [sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [sxa] 30
End-read Marking Exclusion Area in bases (emea) : [sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [sxa] yes
Also mark gap bases - need both strands (amgbnbs): [sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [sxa] no
Merge short reads (msr) : [sxa] yes
Max errors (msrme) : [sxa] 0
Keep ends unmerged (msrkeu) : [sxa] -1
Gap override ratio (gor) : [sxa] 66
Edit options (-ED):
Mira automatic contig editing (mace) : yes
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [sxa] no
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) : no
Max read name length (mrnl) : 40
Check average coverage (cac) : stop
Average coverage value (acv) : 80
Directories (-DI):
Top directory for writing files : MyFirstAssembly_assembly
For writing result files :
MyFirstAssembly_assembly/MyFirstAssembly_d_results
For writing result info files :
MyFirstAssembly_assembly/MyFirstAssembly_d_info
For writing tmp files :
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files :
MyFirstAssembly_assembly/MyFirstAssembly_d_chkpt
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [sxa] no
Save tagged singlets in project (stsip) : [sxa] 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) : no
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 : MyFirstAssembly_out.caf
MAF : MyFirstAssembly_out.maf
FASTA : MyFirstAssembly_out.unpadded.fasta
FASTA quality : MyFirstAssembly_out.unpadded.fasta.qual
FASTA (padded) : MyFirstAssembly_out.padded.fasta
FASTA qual.(pad): MyFirstAssembly_out.padded.fasta.qual
GAP4 (directory): MyFirstAssembly_out.gap4da
ACE : MyFirstAssembly_out.ace
HTML : MyFirstAssembly_out.html
Simple text : MyFirstAssembly_out.txt
TCS overview : MyFirstAssembly_out.tcs
Wiggle : MyFirstAssembly_out.wig
------------------------------------------------------------------------------
Deleting old directory MyFirstAssembly_assembly ... done.
Creating directory MyFirstAssembly_assembly ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_results ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_info ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_chkpt ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Sat Sep 15 10:32:00 2018
Loading reads from
/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_1.fastq type fastq
Localtime: Sat Sep 15 10:32:00 2018
Loading data from FASTQ file:
/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_1.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 166469020 reads, Localtime: Sat Sep 15 10:41:23 2018
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Loading reads from
/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_2.fastq type fastq
Localtime: Sat Sep 15 10:42:15 2018
Loading data from FASTQ file:
/Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis/WGBS_L1-L4-L8_2.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 166469020 reads, Localtime: Sat Sep 15 10:51:43 2018
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
List of read names which have problems with name length:
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:5903:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:6614:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:7101:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:7994:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:10348:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:10510:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:11464:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:11708:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:12033:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:12215:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:13088:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:13880:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:14651:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:14773:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:15179:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:16214:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:16315:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:16741:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:16985:1450/1
Name too long: ST-E00192:589:HCV3GCCXY:1:1101:17269:1450/1
332938038 reads had a long name length, for brevity's sake not all were listed.
WARNING!
-------- MINOR warning --------
MIRA warncode: READ_NAME_TOO_LONG
Title: Long read names
332938038 reads were detected with names longer than 40 characters (see output
log for more details).
While MIRA and many other programs have no problem with that, some older
programs have restrictions concerning the length of the read name.
Example given: the pipeline
CAF -> caf2gap -> gap2caf
will stop working at the gap2caf stage if there are read names having > 40
characters where the names differ only at >40 characters.
This is a warning only, but as a couple of people were bitten by this, the
default behaviour of MIRA is to stop when it sees that potential problem.
You might want to rename your reads to have <= 40 characters. Instead of
renaming reads in the input files, maybe the 'rename_prefix' functionality of
manifest files is useful for you there.
On the other hand, you also can ignore this potential problem and force MIRA to
continue by using the parameter: '-NW:cmrnl=warn' or '-NW:cmrnl=no'
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.
332938040 reads with valid data for assembly.
Localtime: Sat Sep 15 11:09:44 2018
Generated 166469020 unique DNA template ids for 332938040 valid reads.
TODO: Like Readpool: strain x has y reads
Have read pool with 332938040 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 332938040 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 332938040 0
Avg tot rlen 0 0 0 0 0 0 150 0
Avg rlen used 0 0 0 0 0 0 150 0
W/o clips 0 0 0 0 0 0 332938040 0
Solexa total bases: 49940706000 used bases in used reads: 49940706000
===========================================================================
Checking pairs of readgroup 1 (named: 'DataIlluminaPairedLib autopairing'):
found 332938040
-------- MINOR warning --------
MIRA warncode: READGROUP_UNEXPECTED_PAIRS
Title: Unexpected pairs in readgroup
In readgroup 1 (named: 'DataIlluminaPairedLib autopairing') paired reads were
found but no pairing information given in the manifest. MIRA will estimate
'template_size' and 'segment_placement'.
You can suppress this warning by using the keyword 'autopairing' in the
readgroup definition of the manifest file.
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t0.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t1.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t2.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t3.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t4.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t5.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t6.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t7.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t8.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t9.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t10.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t11.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t12.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t13.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t14.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t15.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t16.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t17.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t18.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t19.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t20.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t21.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t22.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t23.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t24.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t25.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t26.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t27.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t28.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t29.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t30.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t31.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t32.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t33.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t34.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t35.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t36.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t37.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t38.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t39.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t40.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t41.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t42.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t43.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t44.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t45.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t46.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t47.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t48.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t49.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t50.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t51.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t52.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t53.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t54.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t55.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t56.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t57.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t58.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t59.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t60.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t61.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t62.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t63.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t64.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t65.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t66.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t67.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t68.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t69.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t70.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t71.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t72.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t73.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t74.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t75.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t76.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t77.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t78.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t79.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t80.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t81.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t82.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t83.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t84.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t85.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t86.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t87.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t88.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t89.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t90.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t91.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t92.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t93.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t94.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t95.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t96.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t97.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t98.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t99.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t100.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t101.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t102.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t103.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t104.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t105.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t106.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t107.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t108.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t109.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t110.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t111.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t112.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t113.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t114.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t115.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t116.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t117.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t118.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t119.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t120.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t121.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t122.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t123.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t124.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t125.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t126.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t127.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t128.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t129.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t130.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t131.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t132.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t133.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t134.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t135.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t136.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t137.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t138.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t139.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t140.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t141.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t142.0.txt
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_clippings_t143.0.txt
Post-load clips:
Localtime: Sat Sep 15 11:25:47 2018
Writing temporary hstat files:
freemem: 594948128768
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: Sat Sep 15 11:25:47 2018
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Sat Sep 15 11:25:47 2018
clean up temporary stat files...Localtime: Sat Sep 15 11:25:47 2018
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Sat Sep 15 11:25:47 2018
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
CLIP MSG: Adaptor right found: 179933
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 332938040 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 332345506 0
Avg tot rlen 0 0 0 0 0 0 150 0
Avg rlen used 0 0 0 0 0 0 149 0
W/o clips 0 0 0 0 0 0 330003748 0
Solexa total bases: 49940706000 used bases in used reads: 49774741808
===========================================================================
Sorting reads ... done.
Tmp directory is not on a NFS mount, good.
PRED MAXTID 166469019
Hash analysis for proposed cutbacks:Localtime: Sat Sep 15 12:32:47 2018
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: Sat Sep 15 16:29:55 2018
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Sat Sep 15 21:13:01 2018
clean up temporary stat files...Localtime: Sat Sep 15 21:14:17 2018
Raw MHI: 896652947
Raw avg. freq. : 58
HSS 1209331778 HSST: 1088398601
Localtime: Sat Sep 15 21:22:07 2018
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 58
Corrected avg. raw frequency coverage: 58
Final average frequency: 58
Deduced thresholds:
-------------------
Min normal cov: 23.2
Max normal cov: 92.8
Repeat cov: 110.2
Heavy cov: 464
Crazy cov: 1160
Mask cov: 5800
Repeat ratio histogram:
-----------------------
0 614148014
1 524759654
2 46587694
3 9410788
4 3834458
5 2092016
6 1334152
7 943504
8 711868
9 541228
10 430008
11 361328
12 300452
13 251354
14 215494
15 191524
16 168696
17 148898
18 136796
19 126128
20 115604
21 104082
22 91486
23 81022
24 74666
25 66794
26 62564
27 56492
28 51696
29 49040
30 44442
31 42130
32 39226
33 37668
34 34008
35 31740
36 30030
37 28396
38 25984
39 24384
40 22644
41 21968
42 20870
43 20058
44 19188
45 19020
46 18766
47 19426
48 19646
49 21324
50 24058
51 27894
52 32604
53 38010
54 40856
55 42460
56 42878
57 43372
58 43370
59 41398
60 36876
61 34360
62 31164
63 28862
64 25894
65 22912
66 18578
67 17346
68 16580
69 13594
70 10516
71 8686
72 8024
73 7182
74 6554
75 5936
76 6108
77 5502
78 5320
79 5144
80 5428
81 5404
82 4924
83 4748
84 4532
85 4672
86 4724
87 4626
88 4388
89 4596
90 4158
91 4216
92 4288
93 4260
94 4106
95 3748
96 3756
97 3824
98 3936
99 4308
100 4248
101 4002
102 4296
103 3882
104 3838
105 4192
106 4154
107 4042
108 3612
109 3358
110 3260
111 3390
112 3140
113 2934
114 2818
115 2774
116 2730
117 2688
118 2534
119 2446
120 2410
121 2660
122 2544
123 2356
124 2478
125 2408
126 2226
127 2440
128 2176
129 2166
130 1952
131 1836
132 1886
133 1736
134 1884
135 1980
136 1736
137 1764
138 1656
139 1532
140 1510
141 1608
142 1474
143 1572
144 1644
145 1424
146 1676
147 1530
148 1512
149 1336
150 1464
151 1538
152 1492
153 1490
154 1514
155 1372
156 1392
157 1408
158 1472
159 1304
160 1342
161 1212
162 1166
163 1168
164 1190
165 1132
166 1154
167 1208
168 1094
169 1126
170 1176
171 1206
172 1198
173 1126
174 1090
175 976
176 1116
177 1030
178 1202
179 896
180 962
181 990
182 1076
183 1092
184 1118
185 1004
186 1052
187 824
188 844
189 918
190 948
191 900
192 948
193 904
194 858
195 880
196 816
197 712
198 764
199 846
200 980
201 794
202 840
203 708
204 894
205 922
206 944
207 834
208 794
209 824
210 686
211 734
212 762
213 760
214 812
215 674
216 636
217 634
218 662
219 702
220 640
221 606
222 664
223 556
224 586
225 498
226 536
227 574
228 582
229 598
230 602
231 576
232 546
233 570
234 522
235 540
236 558
237 588
238 500
239 494
240 458
241 534
242 554
243 534
244 510
245 480
246 490
247 456
248 464
249 408
250 454
251 374
252 356
253 408
254 426
255 380
256 452
257 412
258 416
259 432
260 414
261 388
262 398
263 362
264 340
265 426
266 372
267 418
268 438
269 392
270 348
271 364
272 352
273 402
274 410
275 388
276 384
277 352
278 326
279 412
280 354
281 390
282 326
283 388
284 352
285 328
286 330
287 324
288 346
289 306
290 308
291 308
292 372
293 294
294 326
295 342
296 314
297 324
298 270
299 302
300 380
301 328
302 252
303 318
304 336
305 256
306 326
307 286
308 258
309 284
310 236
311 266
312 298
313 330
314 330
315 310
316 292
317 268
318 272
319 310
320 288
321 226
322 254
323 278
324 238
325 264
326 256
327 228
328 274
329 250
330 274
331 280
332 296
333 216
334 202
335 268
336 248
337 240
338 192
339 196
340 198
341 180
342 180
343 198
344 192
345 214
346 216
347 250
348 224
349 200
350 198
351 184
352 152
353 194
354 154
355 164
356 200
357 164
358 206
359 214
360 204
361 180
362 148
363 160
364 186
365 168
366 168
367 134
368 166
369 166
370 166
371 170
372 126
373 144
374 166
375 160
376 160
377 146
378 130
379 176
380 182
381 160
382 156
383 140
384 214
385 148
386 156
387 200
388 184
389 170
390 158
391 172
392 152
393 162
394 138
395 112
396 138
397 134
398 150
399 136
400 136
401 148
402 148
403 140
404 122
405 128
406 148
407 126
408 144
409 138
410 128
411 140
412 144
413 138
414 138
415 120
416 136
417 128
418 114
419 132
420 142
421 134
422 122
423 124
424 104
425 130
426 114
427 120
428 134
429 114
430 144
431 114
432 108
433 136
434 132
435 110
436 102
437 132
438 116
439 120
440 124
441 130
442 138
443 144
444 124
445 102
446 130
447 122
448 96
449 114
450 118
451 108
452 148
453 104
454 126
455 96
456 118
457 88
458 96
459 110
460 112
461 92
462 112
463 126
464 112
465 108
466 118
467 104
468 124
469 80
470 102
471 70
472 128
473 88
474 74
475 82
476 116
477 106
478 74
479 82
480 98
481 86
482 96
483 96
484 106
485 74
486 74
487 98
488 116
489 76
490 92
491 80
492 84
493 98
494 78
495 104
496 74
497 72
498 94
499 88
500 66
501 80
502 72
503 74
504 106
505 60
506 88
507 98
508 86
509 86
510 96
511 102
512 54
513 72
514 80
515 74
516 60
517 58
518 70
519 76
520 66
521 78
522 86
523 94
524 94
525 72
526 70
527 86
528 64
529 64
530 78
531 82
532 52
533 90
534 80
535 74
536 70
537 74
538 78
539 74
540 74
541 86
542 42
543 72
544 58
545 48
546 52
547 66
548 68
549 70
550 56
551 84
552 66
553 72
554 90
555 90
556 70
557 70
558 74
559 68
560 80
561 98
562 88
563 86
564 74
565 78
566 70
567 58
568 64
569 50
570 60
571 86
572 70
573 66
574 78
575 52
576 42
577 58
578 48
579 74
580 52
581 46
582 54
583 58
584 68
585 78
586 90
587 58
588 62
589 68
590 62
591 52
592 70
593 66
594 58
595 68
596 60
597 78
598 72
599 56
600 78
601 46
602 58
603 58
604 62
605 36
606 42
607 50
608 54
609 74
610 62
611 74
612 72
613 58
614 64
615 60
616 82
617 56
618 62
619 58
620 54
621 54
622 72
623 48
624 46
625 34
626 56
627 48
628 60
629 54
630 60
631 52
632 60
633 48
634 62
635 42
636 48
637 52
638 60
639 64
640 64
641 60
642 52
643 70
644 56
645 34
646 42
647 60
648 56
649 66
650 52
651 60
652 54
653 42
654 52
655 56
656 52
657 52
658 70
659 68
660 46
661 50
662 60
663 44
664 48
665 36
666 48
667 30
668 42
669 48
670 52
671 70
672 40
673 60
674 56
675 70
676 40
677 36
678 52
679 76
680 60
681 70
682 76
683 68
684 54
685 76
686 46
687 52
688 48
689 74
690 56
691 38
692 68
693 50
694 38
695 62
696 54
697 56
698 66
699 68
700 74
701 50
702 80
703 74
704 76
705 56
706 90
707 64
708 60
709 74
710 60
711 70
712 80
713 74
714 66
715 80
716 88
717 42
718 76
719 66
720 60
721 68
722 80
723 82
724 48
725 78
726 98
727 62
728 104
729 90
730 100
731 80
732 62
733 76
734 88
735 76
736 88
737 86
738 86
739 96
740 110
741 98
742 98
743 114
744 110
745 94
746 118
747 102
748 88
749 90
750 90
751 86
752 90
753 86
754 84
755 102
756 102
757 98
758 130
759 90
760 88
761 114
762 120
763 104
764 98
765 78
766 82
767 96
768 102
769 80
770 94
771 110
772 98
773 82
774 94
775 86
776 90
777 86
778 112
779 114
780 84
781 86
782 106
783 88
784 108
785 100
786 116
787 94
788 92
789 110
790 90
791 100
792 92
793 98
794 116
795 114
796 98
797 106
798 138
799 106
800 124
801 144
802 112
803 176
804 172
805 100
806 136
807 150
808 198
809 144
810 178
811 166
812 176
813 166
814 168
815 178
816 190
817 204
818 196
819 192
820 190
821 208
822 178
823 194
824 228
825 204
826 206
827 220
828 218
829 248
830 244
831 232
832 206
833 212
834 210
835 238
836 238
837 238
838 252
839 268
840 254
841 240
842 264
843 246
844 242
845 262
846 214
847 278
848 218
849 242
850 260
851 242
852 274
853 300
854 290
855 308
856 232
857 294
858 272
859 280
860 272
861 278
862 366
863 330
864 338
865 302
866 338
867 348
868 348
869 314
870 354
871 344
872 356
873 300
874 332
875 324
876 318
877 352
878 354
879 362
880 478
881 478
882 528
883 504
884 508
885 530
886 556
887 590
888 664
889 684
890 736
891 636
892 646
893 718
894 634
895 730
896 696
897 718
898 776
899 716
900 754
901 722
902 708
903 714
904 770
905 722
906 872
907 882
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12949 2
12968 2
13020 2
13039 4
13040 2
13043 2
13052 2
13053 2
13055 2
13058 2
13067 2
13079 4
13080 2
13092 2
13136 2
13167 2
13184 2
13226 2
13241 2
13253 2
13309 2
13354 2
13374 2
13401 2
13485 2
13562 2
13565 2
13583 2
13597 2
13605 2
13611 2
13630 2
13707 2
13764 2
13808 2
13816 2
13841 2
13847 2
13856 2
13879 2
13910 2
13918 2
14035 2
14106 2
14118 2
14147 2
14158 2
14189 2
14220 2
14228 2
14320 2
14324 2
14326 2
14371 2
14388 2
14419 2
14495 2
14515 2
14535 2
14621 2
14638 2
14641 2
14646 2
14679 2
14725 2
14731 2
14734 2
14746 2
14762 2
14763 2
14766 2
14858 2
14867 2
14887 2
15156 2
15286 2
15303 2
15331 2
15340 2
15371 2
15390 2
15402 2
15428 2
15450 2
15508 2
15517 2
15540 2
15555 2
15567 2
15588 2
15678 2
15710 2
15783 2
15794 2
15874 2
15875 2
15889 2
15922 2
15934 2
15957 2
16031 2
16060 2
16070 2
16098 2
16119 2
16135 2
16153 2
16157 2
16158 2
16222 2
16379 2
16385 2
16393 2
16420 2
16429 2
16483 2
16509 2
16527 2
16580 2
16588 2
16592 2
16636 2
16661 2
16717 2
16819 2
16849 2
16966 2
17017 2
17037 2
17060 2
17070 2
17071 2
17095 2
17197 2
17221 2
17252 2
17343 2
17451 2
17548 2
17577 2
17636 2
17638 2
17705 2
17754 2
17911 2
17941 2
18054 2
18077 2
18131 2
18181 2
18365 2
18398 2
18428 2
18466 2
18481 2
18610 2
18768 2
18783 2
18841 2
18868 2
18875 2
18914 2
18947 2
19049 2
19216 2
20407 2
20660 2
20861 2
20943 2
20965 2
20966 2
21124 2
21233 2
21298 2
21475 2
21698 2
21982 2
22585 2
22839 2
23150 2
23249 2
23294 2
23351 2
23593 2
23654 2
23658 2
23813 2
23864 2
24020 2
24145 2
24433 2
24610 2
24663 2
24766 2
24802 2
24838 2
25664 2
25868 2
26036 2
26197 2
26682 2
27219 2
27557 2
27721 2
28043 2
28928 2
29037 2
29778 2
30150 2
30747 2
30877 2
32388 2
32970 2
33099 2
33183 2
33441 2
33620 2
33893 2
34476 2
34496 2
34557 2
34691 2
35325 2
35357 2
35725 2
39287 2
39916 2
40713 2
40918 2
41235 2
41754 2
41820 2
44110 2
45398 2
45880 2
45897 2
46179 2
46201 2
47255 2
47331 2
47470 2
47582 2
47714 2
48074 2
48531 2
48601 2
49479 2
50216 2
50282 2
50638 2
50930 2
50985 2
51144 2
51277 2
51440 2
52026 2
52795 2
53232 2
53859 2
53879 2
53939 2
54017 2
54317 2
55093 2
55743 2
55965 2
56179 2
56514 2
57076 2
57149 2
57181 2
57242 2
57853 2
58367 2
58416 2
58555 2
58788 2
59020 2
59884 2
60532 2
61460 2
61515 2
61590 2
61665 2
62325 2
62906 2
63403 2
63768 2
64123 2
64242 2
64353 2
64574 2
64721 2
64998 2
65822 2
65860 2
66081 2
66340 2
66359 2
66754 2
67103 2
67254 2
67578 2
67744 2
67773 2
67849 2
68029 2
68296 2
68331 2
68566 2
68671 2
69803 2
69805 2
70341 2
70595 2
70652 2
70704 2
70748 2
72244 2
72776 2
73512 2
73781 2
73849 2
74360 2
75301 2
76172 2
76259 2
77413 2
78601 2
80092 2
83287 2
84963 2
85772 2
88341 2
90141 2
93558 2
94193 2
94221 2
94252 2
94581 2
94865 2
95419 2
100659 2
102535 2
103464 2
103567 2
104627 2
104839 2
105221 2
105864 2
106709 2
107140 2
107699 2
108076 2
109008 2
109041 2
110106 2
110268 2
110322 2
110557 2
110651 2
111880 2
112216 2
114142 2
115081 2
117291 2
118041 2
118496 2
=========================================================
Assigning statistics values:
Localtime: Sat Sep 15 21:22:19 2018
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Sat Sep 15 21:34:33 2018
Detected probable higher coverage in Illumina genome project, setting:
-CL:pmkfr=2
Localtime: Sat Sep 15 21:34:33 2018
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 11598904
Num reads cliped right: 19988398
Num reads completely killed: 1401393
Total bases clipped : 891765821
Clipping dubious poly-base stretches at end of reads ... Hash analysis for
proposed cutbacks:Localtime: Sat Sep 15 21:46:07 2018
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: Sun Sep 16 01:31:15 2018
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Sun Sep 16 06:03:56 2018
clean up temporary stat files...Localtime: Sun Sep 16 06:05:03 2018
Raw MHI: 824096962
Raw avg. freq. : 59
HSS 1130629718 HSST: 1017566747
Localtime: Sun Sep 16 06:12:34 2018
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 59
Corrected avg. raw frequency coverage: 59
Final average frequency: 59
Deduced thresholds:
-------------------
Min normal cov: 23.6
Max normal cov: 94.4
Repeat cov: 112.1
Heavy cov: 472
Crazy cov: 1180
Mask cov: 5900
Repeat ratio histogram:
-----------------------
0 546466882
1 520363166
2 40819684
3 8922966
4 3698868
5 2025028
6 1301020
7 923696
8 694548
9 527870
10 421242
11 356054
12 294212
13 244576
14 213068
15 188290
16 164498
17 147980
18 135328
19 124516
20 114362
21 100406
22 87750
23 80100
24 73166
25 65448
26 61160
27 54516
28 51538
29 47454
30 43830
31 40870
32 39306
33 36036
34 33320
35 30890
36 29684
37 27408
38 25216
39 23518
40 22666
41 21384
42 20808
43 19426
44 19526
45 19048
46 19600
47 19818
48 21450
49 24158
50 27644
51 32490
52 38400
53 41244
54 43224
55 43568
56 44058
57 44130
58 42058
59 37522
60 34732
61 31538
62 29172
63 26066
64 22774
65 18482
66 17458
67 16490
68 13526
69 10114
70 8556
71 7942
72 7154
73 6450
74 6168
75 5908
76 5642
77 5278
78 5328
79 5524
80 5284
81 5010
82 4740
83 4642
84 4678
85 4804
86 4676
87 4468
88 4390
89 4270
90 4404
91 4296
92 4348
93 3940
94 3724
95 3840
96 3988
97 4246
98 4406
99 4042
100 4390
101 4050
102 3822
103 4186
104 4242
105 4170
106 3754
107 3482
108 3300
109 3406
110 3290
111 2976
112 2898
113 2784
114 2778
115 2736
116 2578
117 2476
118 2464
119 2674
120 2596
121 2406
122 2542
123 2402
124 2336
125 2448
126 2158
127 2182
128 1948
129 1872
130 1884
131 1784
132 1976
133 1928
134 1800
135 1750
136 1594
137 1576
138 1586
139 1508
140 1610
141 1678
142 1510
143 1552
144 1646
145 1558
146 1398
147 1442
148 1574
149 1446
150 1508
151 1610
152 1512
153 1318
154 1514
155 1452
156 1336
157 1352
158 1250
159 1206
160 1210
161 1206
162 1126
163 1228
164 1180
165 1114
166 1160
167 1168
168 1242
169 1226
170 1138
171 1100
172 1014
173 1136
174 1040
175 1222
176 904
177 1018
178 1000
179 1074
180 1124
181 1108
182 1018
183 1022
184 886
185 854
186 940
187 984
188 904
189 996
190 902
191 846
192 868
193 780
194 746
195 790
196 956
197 896
198 800
199 822
200 764
201 960
202 974
203 886
204 828
205 796
206 780
207 718
208 758
209 796
210 832
211 708
212 670
213 666
214 622
215 724
216 652
217 640
218 672
219 566
220 598
221 520
222 520
223 600
224 606
225 592
226 590
227 610
228 548
229 582
230 526
231 552
232 566
233 610
234 506
235 478
236 486
237 540
238 572
239 548
240 516
241 482
242 490
243 450
244 488
245 382
246 460
247 406
248 354
249 408
250 416
251 422
252 446
253 434
254 420
255 430
256 396
257 402
258 410
259 326
260 396
261 414
262 414
263 436
264 390
265 398
266 346
267 388
268 390
269 400
270 398
271 396
272 378
273 342
274 406
275 370
276 360
277 356
278 386
279 370
280 332
281 334
282 328
283 342
284 314
285 332
286 324
287 374
288 288
289 334
290 346
291 318
292 320
293 296
294 304
295 388
296 314
297 264
298 328
299 346
300 256
301 318
302 292
303 256
304 276
305 280
306 252
307 332
308 338
309 312
310 312
311 298
312 270
313 282
314 310
315 254
316 270
317 246
318 258
319 270
320 256
321 242
322 282
323 246
324 256
325 300
326 306
327 232
328 204
329 248
330 282
331 238
332 204
333 210
334 198
335 176
336 190
337 182
338 222
339 192
340 240
341 246
342 222
343 206
344 206
345 186
346 164
347 186
348 156
349 178
350 198
351 176
352 196
353 224
354 206
355 178
356 160
357 146
358 200
359 166
360 166
361 124
362 182
363 178
364 162
365 152
366 154
367 134
368 178
369 164
370 162
371 126
372 170
373 162
374 184
375 164
376 162
377 160
378 194
379 160
380 158
381 212
382 170
383 184
384 144
385 176
386 178
387 144
388 116
389 128
390 134
391 152
392 150
393 126
394 154
395 156
396 142
397 130
398 122
399 152
400 144
401 140
402 130
403 142
404 142
405 142
406 134
407 136
408 124
409 148
410 128
411 100
412 140
413 148
414 140
415 126
416 112
417 108
418 148
419 110
420 116
421 142
422 126
423 138
424 132
425 112
426 154
427 102
428 112
429 134
430 122
431 122
432 106
433 134
434 144
435 140
436 126
437 102
438 142
439 104
440 110
441 112
442 118
443 104
444 150
445 108
446 114
447 118
448 120
449 88
450 104
451 110
452 124
453 96
454 112
455 120
456 114
457 112
458 116
459 108
460 118
461 88
462 106
463 68
464 136
465 88
466 76
467 90
468 112
469 110
470 74
471 92
472 102
473 96
474 96
475 106
476 86
477 76
478 84
479 108
480 94
481 88
482 84
483 84
484 90
485 80
486 104
487 90
488 74
489 84
490 74
491 98
492 64
493 72
494 82
495 96
496 80
497 84
498 94
499 100
500 76
501 96
502 118
503 58
504 74
505 74
506 78
507 72
508 62
509 68
510 74
511 66
512 82
513 90
514 78
515 110
516 68
517 80
518 86
519 62
520 66
521 74
522 78
523 50
524 98
525 86
526 72
527 76
528 78
529 82
530 58
531 74
532 88
533 50
534 68
535 64
536 48
537 62
538 70
539 78
540 88
541 60
542 84
543 82
544 88
545 82
546 84
547 74
548 70
549 84
550 72
551 74
552 84
553 104
554 64
555 74
556 88
557 54
558 72
559 44
560 70
561 72
562 78
563 58
564 74
565 68
566 54
567 66
568 48
569 68
570 64
571 56
572 66
573 60
574 72
575 74
576 88
577 54
578 52
579 72
580 62
581 50
582 62
583 64
584 64
585 60
586 66
587 66
588 76
589 58
590 76
591 62
592 68
593 60
594 70
595 40
596 46
597 52
598 80
599 58
600 52
601 80
602 66
603 64
604 58
605 64
606 76
607 50
608 62
609 52
610 76
611 52
612 62
613 42
614 44
615 36
616 48
617 82
618 56
619 64
620 52
621 62
622 44
623 66
624 40
625 50
626 52
627 58
628 72
629 56
630 56
631 68
632 66
633 60
634 34
635 48
636 62
637 54
638 74
639 48
640 54
641 64
642 46
643 44
644 58
645 62
646 56
647 56
648 66
649 40
650 58
651 50
652 44
653 60
654 40
655 54
656 42
657 52
658 58
659 74
660 54
661 56
662 66
663 52
664 62
665 34
666 64
667 58
668 70
669 72
670 94
671 60
672 72
673 56
674 58
675 48
676 52
677 66
678 50
679 56
680 54
681 64
682 58
683 56
684 42
685 46
686 74
687 80
688 54
689 62
690 84
691 70
692 82
693 62
694 84
695 78
696 70
697 82
698 58
699 80
700 88
701 68
702 58
703 74
704 90
705 56
706 78
707 60
708 54
709 80
710 68
711 78
712 52
713 90
714 72
715 66
716 114
717 98
718 98
719 86
720 76
721 92
722 86
723 78
724 76
725 82
726 86
727 96
728 130
729 94
730 110
731 114
732 98
733 112
734 96
735 96
736 86
737 94
738 98
739 92
740 78
741 78
742 114
743 112
744 96
745 100
746 110
747 104
748 94
749 112
750 88
751 94
752 82
753 86
754 106
755 112
756 68
757 96
758 106
759 94
760 76
761 90
762 62
763 100
764 94
765 124
766 86
767 84
768 102
769 110
770 92
771 112
772 140
773 100
774 94
775 82
776 130
777 98
778 108
779 82
780 134
781 126
782 128
783 88
784 126
785 124
786 146
787 144
788 134
789 156
790 182
791 120
792 134
793 168
794 184
795 192
796 208
797 188
798 164
799 178
800 202
801 158
802 206
803 196
804 196
805 200
806 204
807 194
808 196
809 176
810 232
811 216
812 242
813 196
814 256
815 210
816 234
817 218
818 232
819 210
820 238
821 246
822 206
823 266
824 244
825 246
826 250
827 230
828 290
829 250
830 236
831 220
832 232
833 248
834 258
835 252
836 240
837 250
838 274
839 290
840 286
841 256
842 274
843 304
844 286
845 256
846 286
847 368
848 306
849 336
850 310
851 362
852 324
853 340
854 316
855 376
856 326
857 366
858 318
859 318
860 332
861 328
862 352
863 348
864 360
865 480
866 492
867 548
868 508
869 518
870 544
871 596
872 594
873 654
874 712
875 738
876 648
877 654
878 718
879 674
880 748
881 694
882 748
883 776
884 710
885 798
886 672
887 750
888 762
889 764
890 776
891 886
892 850
893 846
894 1018
895 796
896 926
897 942
898 852
899 866
900 980
901 986
902 1002
903 996
904 1106
905 1072
906 1096
907 1152
908 1222
909 1206
910 1274
911 1166
912 1240
913 1180
914 1266
915 1190
916 1300
917 1210
918 1244
919 1246
920 1388
921 1434
922 1326
923 1452
924 1316
925 1332
926 1356
927 1252
928 1394
929 1368
930 1404
931 1384
932 1350
933 1344
934 1472
935 1450
936 1352
937 1462
938 1540
939 1424
940 1504
941 1416
942 1512
943 1344
944 1422
945 1378
946 1446
947 1390
948 1320
949 1322
950 1352
951 1234
952 1302
953 1326
954 1252
955 1224
956 1238
957 1284
958 1186
959 1260
960 1294
961 1170
962 1320
963 1234
964 1192
965 1186
966 1278
967 1240
968 1310
969 1196
970 1250
971 1332
972 1202
973 1232
974 1234
975 1226
976 1184
977 1260
978 1208
979 1076
980 1102
981 1130
982 1142
983 1106
984 1104
985 1134
986 1106
987 1064
988 1048
989 1048
990 1040
991 1108
992 1056
993 1004
994 1002
995 1020
996 1026
997 924
998 940
999 958
1000 1000
1001 900
1002 918
1003 896
1004 940
1005 832
1006 824
1007 744
1008 752
1009 724
1010 654
1011 748
1012 656
1013 690
1014 632
1015 696
1016 594
1017 598
1018 600
1019 574
1020 514
1021 492
1022 560
1023 512
1024 484
1025 388
1026 472
1027 448
1028 432
1029 436
1030 374
1031 396
1032 354
1033 342
1034 350
1035 346
1036 314
1037 300
1038 310
1039 292
1040 292
1041 280
1042 328
1043 282
1044 232
1045 224
1046 220
1047 224
1048 220
1049 194
1050 214
1051 224
1052 234
1053 242
1054 180
1055 212
1056 156
1057 166
1058 138
1059 138
1060 136
1061 132
1062 96
1063 134
1064 84
1065 94
1066 114
1067 80
1068 108
1069 96
1070 108
1071 90
1072 92
1073 122
1074 82
1075 90
1076 84
1077 88
1078 60
1079 74
1080 62
1081 50
1082 62
1083 52
1084 82
1085 46
1086 50
1087 66
1088 48
1089 44
1090 56
1091 36
1092 32
1093 30
1094 52
1095 36
1096 22
1097 28
1098 20
1099 32
1100 26
1101 26
1102 22
1103 30
1104 34
1105 24
1106 20
1107 10
1108 12
1109 8
1110 16
1111 26
1112 12
1113 22
1114 8
1115 12
1116 14
1117 18
1118 10
1119 8
1120 14
1121 12
1122 18
1123 10
1124 20
1125 14
1126 8
1127 16
1128 14
1129 14
1130 22
1131 16
1132 12
1133 10
1134 18
1135 8
1136 8
1137 10
1138 14
1139 6
1140 22
1141 12
1142 14
1143 22
1144 4
1145 16
1146 6
1147 14
1148 14
1149 10
1150 10
1151 10
1152 16
1153 30
1154 10
1155 22
1156 10
1157 28
1158 20
1159 22
1160 12
1161 16
1162 12
1163 12
1164 12
1165 24
1166 8
1167 16
1168 10
1169 10
1170 24
1171 12
1172 20
1173 16
1174 16
1175 16
1176 16
1177 6
1178 12
1179 14
1180 8
1181 20
1182 4
1183 10
1184 14
1185 8
1186 14
1187 16
1188 12
1189 14
1190 14
1191 16
1192 10
1193 10
1194 8
1195 12
1196 10
1197 12
1198 24
1199 12
1200 12
1201 8
1202 8
1203 16
1204 12
1205 10
1206 2
1207 16
1208 12
1209 4
1210 6
1211 6
1212 20
1213 10
1214 12
1215 8
1216 10
1217 14
1218 16
1219 8
1220 10
1221 6
1222 24
1223 18
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4532 6
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5960 6
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9912 2
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10000 2
10065 2
10072 2
10088 2
10102 2
10131 2
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10213 2
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10280 2
10315 2
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12858 4
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105324 2
105874 2
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107161 2
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108399 2
108452 2
108683 2
108776 2
109984 2
110314 2
112208 2
113130 2
115303 2
116040 2
116487 2
=========================================================
Assigning statistics values:
Localtime: Sun Sep 16 06:12:43 2018
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Sun Sep 16 06:23:50 2018
Localtime: Sun Sep 16 06:23:50 2018
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 2260309
Num reads cliped right: 4625996
Num reads completely killed: 676090
Total bases clipped : 139690678
Clipping dubious poly-base stretches at end of reads ...
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 332938040 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 330269488 0
Avg tot rlen 0 0 0 0 0 0 150 0
Avg rlen used 0 0 0 0 0 0 147 0
W/o clips 0 0 0 0 0 0 298680736 0
Solexa total bases: 49940706000 used bases in used reads: 48727921234
===========================================================================
Performing snapshot 1
Localtime: Sun Sep 16 06:34:46 2018
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_chkpt ... done.
Localtime: Sun Sep 16 07:33:51 2018
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 242226
Ngid: 242226
Pid: 242226
PPid: 242225
TracerPid: 0
Uid: 1002 1002 1002 1002
Gid: 1002 1002 1002 1002
FDSize: 256
Groups: 1002
VmPeak: 562952752 kB
VmSize: 553514992 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 545671692 kB
VmRSS: 545670268 kB
VmData: 553405440 kB
VmStk: 136 kB
VmExe: 5792 kB
VmLib: 0 kB
VmPTE: 1065860 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/4124734
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000001
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed:
ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff
Cpus_allowed_list: 0-287
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Mems_allowed_list: 0-7
voluntary_ctxt_switches: 373096
nonvoluntary_ctxt_switches: 72232
--------------------------------------------------------------------------------
Pass: 1 / 4
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 332938040 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 330269488 0
Avg tot rlen 0 0 0 0 0 0 150 0
Avg rlen used 0 0 0 0 0 0 147 0
W/o clips 0 0 0 0 0 0 298680736 0
Solexa total bases: 49940706000 used bases in used reads: 48727921234
===========================================================================
Localtime: Sun Sep 16 07:34:56 2018
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: Sun Sep 16 11:35:21 2018
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Sun Sep 16 16:20:18 2018
clean up temporary stat files...Localtime: Sun Sep 16 16:21:06 2018
Raw MHI: 644292860
Raw avg. freq. : 67
HSS 921464630 HSST: 829318167
Localtime: Sun Sep 16 16:28:02 2018
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 67
Corrected avg. raw frequency coverage: 67
Final average frequency: 67
Deduced thresholds:
-------------------
Min normal cov: 26.8
Max normal cov: 107.2
Repeat cov: 127.3
Heavy cov: 536
Crazy cov: 1340
Mask cov: 6700
Repeat ratio histogram:
-----------------------
0 384869910
1 479531414
2 33898146
3 8943602
4 3763384
5 2043414
6 1311676
7 938552
8 687846
9 526250
10 428514
11 352950
12 291732
13 245662
14 211896
15 187556
16 166182
17 150848
18 137610
19 125326
20 111592
21 99730
22 90920
23 81282
24 72520
25 66214
26 61264
27 57132
28 53386
29 49296
30 47318
31 44028
32 39754
33 37212
34 34944
35 33222
36 29740
37 28344
38 27028
39 25000
40 24258
41 23378
42 21810
43 21422
44 22860
45 22342
46 24956
47 28692
48 32908
49 40488
50 44548
51 48288
52 46680
53 48180
54 47114
55 45192
56 40826
57 37242
58 32920
59 30742
60 27352
61 22082
62 20240
63 18728
64 15984
65 12844
66 10420
67 9912
68 8682
69 8050
70 7598
71 6832
72 6672
73 6422
74 6178
75 6034
76 5828
77 5926
78 5660
79 5172
80 5192
81 5022
82 5078
83 4808
84 4904
85 5128
86 4882
87 4730
88 4432
89 4270
90 4386
91 4280
92 4932
93 5058
94 5230
95 4992
96 5056
97 4902
98 5164
99 5102
100 4322
101 4362
102 4188
103 3828
104 3886
105 3802
106 3314
107 3550
108 3282
109 3172
110 2836
111 2990
112 2886
113 2892
114 2776
115 2676
116 2814
117 2590
118 2824
119 2614
120 2382
121 2328
122 2328
123 2224
124 2076
125 2192
126 2080
127 2158
128 2232
129 1982
130 1756
131 1814
132 1688
133 1718
134 1878
135 1838
136 1694
137 1914
138 1740
139 1736
140 1758
141 1818
142 1790
143 1828
144 1768
145 1776
146 1700
147 1748
148 1558
149 1518
150 1598
151 1456
152 1390
153 1240
154 1332
155 1352
156 1408
157 1516
158 1400
159 1384
160 1394
161 1422
162 1382
163 1302
164 1398
165 1426
166 1300
167 1320
168 1246
169 1124
170 1178
171 1156
172 1222
173 1100
174 1008
175 964
176 974
177 956
178 984
179 1008
180 984
181 942
182 822
183 872
184 876
185 898
186 922
187 1014
188 1018
189 970
190 850
191 812
192 974
193 912
194 866
195 906
196 888
197 816
198 902
199 870
200 854
201 902
202 806
203 776
204 828
205 734
206 816
207 744
208 698
209 734
210 698
211 624
212 552
213 642
214 618
215 584
216 612
217 626
218 642
219 582
220 580
221 632
222 630
223 564
224 588
225 558
226 620
227 674
228 626
229 636
230 606
231 594
232 594
233 668
234 582
235 580
236 614
237 588
238 528
239 500
240 570
241 542
242 540
243 596
244 514
245 518
246 534
247 540
248 520
249 506
250 502
251 532
252 538
253 456
254 496
255 518
256 472
257 492
258 534
259 488
260 424
261 500
262 482
263 436
264 464
265 454
266 378
267 396
268 394
269 390
270 428
271 428
272 384
273 368
274 356
275 358
276 392
277 444
278 452
279 398
280 380
281 424
282 406
283 430
284 396
285 382
286 408
287 456
288 422
289 404
290 348
291 334
292 398
293 346
294 372
295 322
296 364
297 372
298 346
299 320
300 362
301 308
302 336
303 348
304 324
305 316
306 396
307 332
308 380
309 348
310 312
311 304
312 288
313 314
314 378
315 288
316 304
317 266
318 310
319 318
320 288
321 236
322 250
323 272
324 228
325 230
326 246
327 232
328 250
329 276
330 238
331 250
332 236
333 264
334 246
335 230
336 272
337 244
338 200
339 230
340 218
341 212
342 204
343 240
344 202
345 202
346 208
347 206
348 196
349 216
350 228
351 184
352 194
353 222
354 160
355 192
356 200
357 206
358 174
359 180
360 204
361 168
362 186
363 184
364 174
365 248
366 152
367 158
368 160
369 140
370 130
371 142
372 148
373 150
374 202
375 192
376 176
377 174
378 162
379 190
380 146
381 166
382 124
383 158
384 156
385 162
386 178
387 168
388 146
389 158
390 170
391 162
392 134
393 176
394 142
395 160
396 124
397 160
398 154
399 144
400 172
401 136
402 184
403 130
404 124
405 128
406 122
407 162
408 160
409 134
410 150
411 166
412 144
413 134
414 128
415 140
416 142
417 160
418 96
419 154
420 122
421 118
422 146
423 128
424 160
425 136
426 132
427 190
428 154
429 138
430 130
431 118
432 130
433 116
434 136
435 140
436 120
437 126
438 98
439 126
440 128
441 122
442 138
443 110
444 126
445 118
446 126
447 128
448 118
449 82
450 148
451 112
452 110
453 94
454 120
455 124
456 110
457 120
458 112
459 116
460 130
461 130
462 128
463 148
464 152
465 144
466 156
467 116
468 118
469 106
470 130
471 102
472 86
473 148
474 92
475 92
476 102
477 128
478 98
479 90
480 126
481 114
482 76
483 70
484 96
485 64
486 68
487 80
488 76
489 82
490 96
491 66
492 82
493 76
494 96
495 80
496 62
497 112
498 94
499 52
500 114
501 94
502 76
503 82
504 90
505 74
506 76
507 82
508 102
509 68
510 80
511 72
512 106
513 82
514 86
515 68
516 112
517 108
518 74
519 66
520 90
521 98
522 84
523 90
524 92
525 68
526 74
527 88
528 100
529 82
530 60
531 92
532 86
533 100
534 82
535 100
536 66
537 72
538 72
539 64
540 96
541 84
542 54
543 78
544 80
545 78
546 54
547 76
548 60
549 68
550 60
551 80
552 78
553 74
554 78
555 64
556 98
557 60
558 80
559 64
560 80
561 84
562 64
563 58
564 58
565 50
566 64
567 68
568 60
569 82
570 34
571 76
572 82
573 58
574 78
575 80
576 80
577 68
578 66
579 88
580 72
581 80
582 88
583 78
584 56
585 76
586 58
587 66
588 68
589 56
590 68
591 54
592 52
593 58
594 66
595 70
596 42
597 46
598 70
599 52
600 58
601 62
602 70
603 80
604 68
605 58
606 58
607 84
608 70
609 60
610 72
611 38
612 40
613 54
614 40
615 68
616 48
617 54
618 70
619 76
620 60
621 66
622 72
623 48
624 64
625 64
626 64
627 62
628 74
629 66
630 42
631 80
632 64
633 54
634 40
635 34
636 62
637 44
638 58
639 62
640 58
641 56
642 54
643 66
644 60
645 52
646 54
647 62
648 62
649 70
650 70
651 90
652 60
653 74
654 82
655 70
656 76
657 82
658 84
659 70
660 64
661 96
662 84
663 70
664 94
665 64
666 106
667 92
668 92
669 102
670 62
671 82
672 70
673 102
674 88
675 76
676 96
677 98
678 86
679 84
680 66
681 78
682 72
683 82
684 102
685 86
686 82
687 114
688 104
689 124
690 96
691 102
692 72
693 88
694 80
695 120
696 100
697 88
698 102
699 92
700 102
701 124
702 100
703 96
704 86
705 114
706 112
707 134
708 112
709 108
710 92
711 100
712 116
713 124
714 116
715 116
716 74
717 112
718 118
719 102
720 116
721 114
722 106
723 82
724 116
725 124
726 122
727 120
728 78
729 108
730 108
731 92
732 114
733 102
734 100
735 82
736 110
737 94
738 116
739 148
740 126
741 128
742 130
743 142
744 126
745 128
746 114
747 112
748 162
749 142
750 178
751 176
752 162
753 198
754 196
755 180
756 142
757 192
758 204
759 194
760 192
761 220
762 218
763 174
764 188
765 208
766 198
767 232
768 238
769 252
770 242
771 238
772 216
773 226
774 248
775 216
776 214
777 264
778 266
779 234
780 196
781 236
782 234
783 272
784 272
785 184
786 232
787 196
788 194
789 258
790 244
791 268
792 250
793 278
794 288
795 262
796 254
797 314
798 328
799 292
800 318
801 304
802 316
803 290
804 318
805 300
806 296
807 350
808 386
809 342
810 346
811 330
812 370
813 382
814 440
815 340
816 394
817 442
818 478
819 424
820 528
821 528
822 544
823 600
824 590
825 552
826 590
827 610
828 588
829 704
830 644
831 700
832 742
833 792
834 746
835 892
836 732
837 850
838 852
839 792
840 802
841 828
842 840
843 788
844 862
845 908
846 924
847 940
848 1054
849 1000
850 1044
851 1030
852 1070
853 1040
854 1084
855 1222
856 1180
857 1286
858 1300
859 1164
860 1192
861 1340
862 1324
863 1354
864 1278
865 1346
866 1440
867 1306
868 1404
869 1394
870 1440
871 1434
872 1456
873 1490
874 1512
875 1418
876 1388
877 1436
878 1444
879 1356
880 1540
881 1472
882 1520
883 1624
884 1568
885 1682
886 1678
887 1708
888 1654
889 1618
890 1572
891 1482
892 1434
893 1602
894 1526
895 1566
896 1566
897 1568
898 1506
899 1500
900 1432
901 1394
902 1396
903 1344
904 1314
905 1376
906 1474
907 1498
908 1364
909 1468
910 1420
911 1430
912 1396
913 1354
914 1416
915 1324
916 1360
917 1296
918 1366
919 1332
920 1256
921 1358
922 1252
923 1300
924 1272
925 1236
926 1226
927 1244
928 1200
929 1256
930 1228
931 1150
932 1210
933 1130
934 1118
935 1158
936 1172
937 1162
938 1138
939 1252
940 1188
941 1146
942 1046
943 1038
944 1086
945 1116
946 924
947 918
948 930
949 842
950 862
951 830
952 834
953 736
954 706
955 740
956 790
957 776
958 726
959 664
960 606
961 570
962 610
963 592
964 506
965 506
966 512
967 466
968 472
969 424
970 376
971 372
972 408
973 412
974 406
975 334
976 358
977 334
978 310
979 350
980 358
981 330
982 340
983 338
984 300
985 304
986 336
987 326
988 256
989 244
990 224
991 212
992 256
993 212
994 198
995 198
996 152
997 156
998 154
999 172
1000 172
1001 138
1002 158
1003 118
1004 86
1005 102
1006 104
1007 114
1008 90
1009 76
1010 124
1011 96
1012 80
1013 94
1014 76
1015 86
1016 90
1017 82
1018 78
1019 68
1020 60
1021 66
1022 54
1023 62
1024 86
1025 60
1026 68
1027 58
1028 36
1029 52
1030 52
1031 48
1032 28
1033 32
1034 10
1035 28
1036 20
1037 18
1038 16
1039 18
1040 14
1041 12
1042 14
1043 30
1044 14
1045 28
1046 16
1047 8
1048 16
1049 14
1050 16
1051 30
1052 26
1053 14
1054 16
1055 10
1056 24
1057 18
1058 12
1059 6
1060 12
1061 14
1062 16
1063 18
1064 14
1065 18
1066 8
1067 18
1068 14
1069 8
1070 16
1071 8
1072 10
1073 26
1074 14
1075 16
1076 24
1077 24
1078 12
1079 10
1080 14
1081 8
1082 18
1083 22
1084 16
1085 14
1086 20
1087 22
1088 26
1089 20
1090 20
1091 4
1092 2
1093 12
1094 12
1095 12
1096 14
1097 10
1098 14
1099 18
1100 24
1101 8
1102 6
1103 6
1104 10
1105 18
1106 4
1107 20
1108 18
1109 12
1110 8
1111 20
1112 4
1113 14
1114 6
1115 20
1116 10
1117 10
1118 6
1119 12
1120 10
1121 8
1122 6
1123 14
1124 12
1125 2
1126 4
1127 8
1128 12
1129 12
1130 10
1131 10
1132 12
1133 20
1134 16
1135 12
1136 6
1137 12
1138 18
1139 26
1140 10
1141 10
1142 14
1143 24
1144 28
1145 24
1146 16
1147 26
1148 14
1149 16
1150 16
1151 16
1152 8
1153 12
1154 12
1155 12
1156 10
1157 8
1158 12
1159 6
1160 22
1161 22
1162 18
1163 22
1164 16
1165 16
1166 12
1167 16
1168 20
1169 30
1170 20
1171 14
1172 18
1173 14
1174 10
1175 8
1176 20
1177 10
1178 8
1179 10
1180 14
1181 16
1182 10
1183 14
1184 14
1185 10
1186 18
1187 8
1188 4
1189 12
1190 14
1191 16
1192 10
1193 18
1194 22
1195 4
1196 10
1197 20
1198 16
1199 18
1200 24
1201 4
1202 18
1203 10
1204 16
1205 12
1206 10
1207 10
1208 10
1209 10
1210 8
1211 10
1212 12
1213 12
1214 14
1215 12
1216 2
1217 12
1218 10
1219 16
1220 18
1221 4
1222 10
1223 10
1224 10
1225 24
1226 14
1227 6
1228 14
1229 18
1230 22
1231 16
1232 12
1233 14
1234 8
1235 10
1236 14
1237 8
1238 2
1239 4
1240 4
1241 4
1242 18
1243 10
1244 16
1245 8
1246 16
1247 12
1248 14
1249 8
1250 10
1251 12
1252 14
1253 12
1254 8
1255 10
1256 10
1257 20
1258 20
1259 22
1260 14
1261 14
1262 10
1263 10
1264 14
1265 18
1266 14
1267 8
1268 4
1269 2
1270 8
1271 12
1272 10
1273 6
1274 8
1275 14
1276 14
1277 12
1278 8
1279 8
1280 8
1281 18
1282 14
1283 12
1284 16
1285 18
1286 4
1287 12
1288 8
1289 26
1290 16
1291 14
1292 10
1293 8
1294 16
1295 16
1296 8
1297 4
1298 14
1299 4
1300 8
1301 16
1302 18
1303 8
1304 16
1305 12
1306 8
1307 8
1308 8
1309 10
1310 10
1311 8
1312 8
1313 2
1314 10
1315 4
1316 10
1317 18
1318 10
1319 8
1320 14
1321 16
1322 10
1323 12
1324 8
1325 2
1326 20
1327 16
1328 8
1329 10
1330 14
1331 16
1332 12
1333 6
1334 10
1335 8
1336 6
1337 12
1338 8
1339 10
1340 14
1341 26
1342 16
1343 6
1344 8
1345 8
1346 14
1347 12
1348 8
1349 10
1350 8
1351 22
1352 16
1353 6
1354 22
1355 4
1356 12
1357 14
1358 12
1359 12
1360 20
1361 22
1362 10
1363 26
1364 24
1365 14
1366 14
1367 14
1368 8
1369 8
1370 10
1371 18
1372 30
1373 18
1374 18
1375 12
1376 6
1377 18
1378 10
1379 14
1380 10
1381 18
1382 14
1383 22
1384 20
1385 24
1386 14
1387 10
1388 16
1389 22
1390 22
1391 8
1392 16
1393 16
1394 16
1395 16
1396 16
1397 8
1398 14
1399 8
1400 8
1401 16
1402 6
1403 18
1404 10
1405 14
1406 8
1407 10
1408 12
1409 8
1410 10
1411 8
1412 12
1413 14
1414 16
1415 12
1416 14
1417 8
1418 16
1419 24
1420 14
1421 14
1422 10
1423 20
1424 18
1425 12
1426 8
1427 6
1428 16
1429 8
1430 18
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3933 2
3934 2
3935 2
3937 2
3938 2
3939 2
3941 2
3947 2
3950 2
3951 2
3952 2
3953 2
3954 2
3962 6
3965 4
3967 2
3968 2
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3981 2
3982 2
3985 2
3986 2
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4001 2
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4024 4
4030 4
4032 2
4040 2
4047 4
4050 2
4055 2
4059 2
4060 2
4063 2
4064 2
4065 2
4068 2
4072 2
4073 2
4074 2
4078 2
4079 2
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4083 2
4084 2
4086 2
4089 2
4096 2
4098 2
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4110 2
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4299 2
4318 4
4325 2
4330 4
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4357 2
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4429 6
4434 2
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4443 2
4445 2
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4473 4
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4503 4
4507 2
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4581 2
4583 2
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4598 2
4600 4
4601 2
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4607 2
4609 2
4611 2
4621 2
4622 2
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4625 2
4626 2
4627 4
4640 2
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4680 2
4685 2
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4695 2
4697 2
4715 4
4720 2
4727 2
4738 2
4739 2
4742 4
4751 2
4756 4
4768 2
4771 2
4772 4
4773 2
4774 2
4778 2
4782 2
4784 2
4787 2
4805 2
4807 4
4818 2
4830 2
4832 2
4838 2
4839 2
4853 2
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4869 2
4873 2
4875 2
4876 4
4898 2
4902 2
4907 2
4914 2
4919 2
4922 2
4935 4
4938 4
4940 2
4941 2
4942 2
4946 2
4952 4
4954 2
4960 2
4964 2
4973 2
4974 2
4977 2
4983 2
4985 6
4987 2
4988 4
4990 2
4995 2
4996 4
4997 2
4998 2
5000 2
5002 2
5009 2
5013 2
5019 2
5021 2
5025 2
5034 2
5037 2
5038 2
5047 2
5048 2
5052 2
5055 2
5063 2
5064 4
5067 2
5070 2
5075 2
5084 2
5087 2
5090 2
5096 4
5098 4
5102 2
5104 6
5106 2
5107 2
5110 2
5112 2
5114 2
5116 2
5125 2
5129 2
5134 2
5136 2
5139 2
5146 2
5148 2
5152 2
5156 2
5158 2
5161 2
5163 4
5164 4
5173 2
5180 2
5181 2
5185 2
5187 2
5188 6
5190 4
5191 2
5193 2
5194 2
5198 2
5199 2
5212 2
5216 2
5222 2
5223 4
5228 4
5238 2
5239 2
5245 2
5246 4
5248 2
5250 2
5257 2
5260 2
5265 2
5268 4
5269 2
5270 2
5272 2
5275 2
5277 2
5280 2
5281 2
5283 2
5285 2
5286 2
5287 2
5290 2
5297 2
5301 4
5303 2
5307 4
5318 2
5330 2
5340 2
5343 2
5361 2
5364 2
5367 2
5369 2
5377 2
5392 2
5397 2
5401 2
5403 2
5405 2
5406 4
5409 2
5410 2
5412 2
5422 2
5423 2
5429 4
5430 2
5433 2
5442 2
5443 2
5444 2
5447 2
5448 2
5450 2
5457 2
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5467 2
5471 2
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5498 2
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5523 2
5527 2
5528 2
5533 2
5558 2
5561 2
5565 2
5577 2
5580 2
5581 2
5590 2
5596 2
5602 2
5612 2
5616 4
5624 2
5625 2
5633 2
5642 2
5659 2
5664 2
5665 2
5666 2
5669 2
5670 2
5672 2
5687 2
5693 2
5699 2
5701 2
5706 2
5709 2
5713 2
5719 2
5724 2
5726 2
5735 2
5745 4
5753 2
5765 2
5766 2
5770 2
5777 2
5779 2
5783 2
5793 2
5794 2
5817 2
5819 4
5820 2
5828 2
5832 2
5849 4
5857 2
5863 2
5864 2
5872 2
5875 2
5878 2
5879 2
5886 2
5887 2
5888 2
5892 2
5909 2
5912 2
5913 2
5918 2
5921 4
5931 2
5944 4
5947 6
5948 2
5951 4
5953 4
5964 6
5968 2
5971 2
5975 4
5976 2
5977 2
5978 2
5980 4
5981 2
5984 2
5987 2
5992 2
6000 4
6001 2
6002 2
6003 2
6007 2
6009 2
6011 2
6023 2
6027 2
6030 2
6034 4
6035 2
6038 4
6045 2
6046 2
6054 4
6055 2
6058 2
6071 2
6080 2
6084 2
6085 2
6090 4
6092 2
6093 2
6095 2
6098 2
6103 2
6104 2
6108 2
6113 2
6122 2
6127 2
6136 8
6138 2
6142 2
6144 2
6145 2
6148 2
6150 2
6151 2
6152 4
6154 2
6159 2
6162 4
6163 2
6164 2
6165 2
6173 2
6174 4
6182 2
6185 2
6189 2
6192 2
6197 2
6205 2
6213 2
6214 2
6219 2
6220 2
6224 6
6225 2
6230 2
6232 4
6234 6
6237 2
6238 2
6239 2
6241 2
6249 2
6261 2
6265 2
6266 2
6273 2
6274 2
6276 2
6278 2
6290 2
6291 2
6292 2
6298 2
6300 2
6304 2
6309 2
6311 2
6312 2
6330 4
6332 2
6338 2
6341 2
6352 2
6360 2
6362 2
6367 2
6369 2
6371 2
6373 2
6384 2
6386 2
6391 2
6400 2
6401 2
6415 2
6416 2
6432 2
6446 2
6452 2
6454 2
6456 2
6464 2
6480 2
6481 2
6489 2
6490 2
6495 2
6496 2
6497 2
6500 2
6508 2
6517 2
6520 2
6522 2
6528 2
6551 2
6557 2
6561 2
6566 2
6583 2
6589 2
6592 2
6600 2
6619 2
6620 2
6624 4
6625 2
6631 2
6633 2
6648 2
6655 2
6661 2
6668 2
6672 2
6680 2
6688 2
6693 2
6704 2
6705 2
6707 2
6708 2
6710 2
6713 2
6714 2
6715 4
6735 2
6737 2
6743 2
6750 2
6753 2
6756 2
6760 4
6762 2
6766 2
6767 2
6777 4
6778 2
6787 2
6790 2
6796 4
6798 2
6803 2
6816 2
6820 2
6830 2
6837 2
6852 2
6854 4
6880 2
6892 2
6905 2
6907 2
6909 4
6913 2
6927 2
6938 2
6953 2
6955 2
6967 2
6981 2
6984 2
6990 2
6992 2
6994 2
7025 2
7029 2
7031 2
7038 2
7054 2
7062 2
7068 2
7081 2
7091 2
7116 2
7138 2
7140 2
7145 2
7146 2
7148 2
7179 2
7182 2
7191 2
7193 2
7194 4
7204 2
7217 2
7261 2
7269 2
7289 2
7292 2
7308 2
7347 2
7363 2
7376 2
7385 2
7397 2
7405 2
7412 2
7539 2
7575 2
7583 2
7596 2
7598 2
7603 2
7613 2
7616 2
7617 2
7637 2
7640 2
7672 2
7682 2
7684 2
7689 2
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7723 2
7742 2
7758 2
7761 2
7767 2
7778 4
7800 2
7816 2
7830 2
7833 2
7845 2
7917 2
7949 2
7973 2
7989 2
8000 2
8004 2
8007 2
8015 2
8020 2
8034 2
8043 2
8048 2
8050 2
8090 2
8091 2
8145 2
8161 2
8174 2
8178 2
8198 2
8240 2
8245 2
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8268 2
8314 2
8346 2
8349 2
8357 2
8461 2
8465 2
8498 2
8502 2
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8507 2
8593 2
8606 2
8650 2
8653 2
8662 2
8701 2
8734 2
8749 2
8755 2
8756 2
8833 2
8834 2
8837 4
8840 2
8846 4
8851 2
8862 2
8879 2
8883 2
8889 2
8900 2
8902 2
8924 2
8930 2
8933 2
8934 2
8937 2
8970 2
8984 2
8993 2
9035 2
9038 2
9045 2
9074 2
9078 2
9091 4
9108 2
9146 2
9147 2
9149 2
9195 4
9228 2
9234 2
9274 2
9284 2
9302 2
9303 2
9305 2
9312 2
9313 2
9320 2
9342 2
9361 4
9383 2
9398 2
9402 2
9414 2
9438 2
9442 2
9463 2
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9490 2
9499 4
9509 4
9515 2
9529 2
9555 2
9573 2
9612 2
9614 2
9625 2
9641 2
9643 2
9648 2
9684 2
9686 2
9707 4
9729 2
9733 2
9737 2
9744 2
9755 2
9771 2
9777 2
9788 2
9806 2
9823 2
9828 2
9836 2
9840 2
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9877 2
9916 2
9945 2
9957 2
9994 2
10010 2
10025 2
10032 2
10111 2
10120 2
10131 2
10144 2
10164 4
10172 2
10220 2
10234 2
10272 2
10282 2
10287 2
10365 2
10375 2
10379 2
10387 2
10403 2
10410 2
10418 2
10445 2
10454 2
10565 2
10595 2
10606 2
10626 2
10703 2
10728 2
10762 2
10839 2
11032 2
11038 2
11040 2
11132 2
11276 2
11287 2
11288 2
11313 2
11348 2
11360 2
11429 2
11495 2
11538 2
11583 2
11599 2
11617 2
11631 2
11641 2
11652 2
11657 2
11670 2
11722 2
11767 2
11817 2
11835 2
11863 2
11883 2
11892 2
11907 2
11988 2
11993 2
12002 2
12009 2
12020 2
12036 2
12058 2
12074 2
12113 2
12130 4
12150 2
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12197 2
12203 2
12213 2
12242 2
12261 2
12293 2
12312 2
12345 2
12374 2
12570 2
12574 2
12577 2
12602 2
12604 2
12648 2
12668 2
12685 2
12841 2
12920 2
12942 2
13187 2
13280 2
13296 2
13305 2
13336 2
13361 2
13373 2
13402 2
13450 2
13474 2
13476 2
13485 2
13504 2
13507 2
13513 2
13568 2
13569 2
13577 2
13581 2
13596 2
13631 2
13653 2
13718 2
13745 2
13768 2
13802 2
13852 2
13877 2
13888 2
13893 2
13916 2
13975 2
14044 2
14066 2
14077 2
14187 2
14188 2
14230 2
14275 2
14283 2
14290 2
14393 2
14473 2
14488 2
14490 2
14525 2
14531 2
14568 2
14595 2
14622 2
14643 2
14645 4
14672 2
14692 2
14734 2
14741 2
14761 2
14763 2
14765 2
14806 2
14808 2
14816 2
14841 2
14848 2
14892 4
14895 2
14915 2
14917 2
14929 2
14937 2
14974 2
15017 2
15033 2
15051 2
15117 2
15133 2
15168 2
15203 2
15221 2
15235 2
15414 2
15424 2
15425 2
15431 2
15445 2
15461 2
15485 2
15525 2
15559 2
15594 2
15680 2
15694 2
15717 2
15729 2
15742 2
15771 2
15778 2
15831 2
15843 2
15867 2
15939 2
15972 2
16081 2
16103 2
16109 2
16112 2
16149 2
16155 2
16202 2
16215 2
16219 2
16237 2
16257 2
16279 2
16342 2
16416 2
16566 2
16619 2
16652 2
16671 2
16683 2
16747 2
16768 2
16824 6
16838 2
16863 2
16919 2
16925 2
16958 2
17017 2
17086 2
17111 2
17192 2
17205 2
17265 2
17346 2
17464 2
17494 2
17550 2
17734 2
17799 2
17837 2
17931 2
18054 2
18093 2
18211 2
18294 2
18311 2
18321 2
18335 2
18341 2
18348 2
18398 2
18415 2
18453 2
18464 2
18525 2
18583 4
18601 2
18735 2
18736 2
18776 4
18801 2
18866 2
18905 2
18921 2
18962 2
19081 2
19090 2
19107 2
19114 2
19115 2
19137 2
19376 2
19554 2
19557 2
19559 2
19620 2
19666 2
19681 2
19773 2
19808 2
19817 2
19930 2
20045 2
20209 2
20340 2
20557 2
20593 2
20611 2
20843 2
20914 2
21014 2
21081 2
21235 2
21238 2
21249 2
21297 2
21400 2
21448 2
21449 2
21514 2
21557 2
21622 2
21625 2
21637 2
21710 2
21810 2
21909 2
21965 2
22000 2
22152 2
22429 2
22463 2
22489 4
22543 2
22687 2
22714 2
22760 2
22813 2
23052 2
23174 2
23191 2
23284 2
23398 2
23584 2
23598 2
23826 2
23996 2
24296 2
24500 2
24659 2
24718 2
24764 2
24984 2
25802 2
26567 2
27433 2
28019 2
28217 2
28366 2
28473 2
29318 2
29940 2
30005 2
30446 2
30561 2
30786 2
31082 2
31162 2
31224 2
31656 2
31904 2
32300 2
33400 2
34103 2
34632 2
34911 2
34993 2
35094 2
35148 2
35275 2
35789 2
36418 2
36429 2
36601 2
37094 2
37213 2
37301 2
37812 2
37825 2
38710 2
39046 2
40401 2
40420 2
40422 2
41007 2
41691 2
42696 2
42731 2
42827 2
42851 2
43173 2
43295 2
43489 2
43529 2
43818 2
44635 2
46282 2
46803 2
47300 2
47320 2
47405 2
48415 2
48966 2
49227 2
49782 2
49946 2
50025 2
50220 2
50234 2
50738 2
52710 2
53659 2
55635 2
55695 2
56540 2
57824 2
58256 2
58766 2
59532 2
59734 2
59846 2
60366 2
60608 2
60938 2
61154 2
62533 2
65427 2
66164 2
66212 2
66318 2
66439 2
66643 2
66709 2
66989 2
67648 2
67885 2
70153 2
70790 2
71458 2
71752 2
73972 2
75011 2
75755 2
76003 2
76059 2
76286 2
76701 2
76862 2
77882 2
77926 2
77966 2
78578 2
78587 2
78608 2
78618 2
78738 2
79274 2
79435 2
79645 2
79756 2
79824 2
79955 2
80350 2
80414 2
80477 2
80556 2
80574 2
80816 2
81037 2
81055 2
81245 2
81259 2
81684 2
82019 2
82170 2
82240 2
82303 2
82393 2
82448 2
82480 4
82595 2
82769 2
82895 2
83055 2
83180 2
83229 2
83561 2
84240 2
84515 2
84920 2
85009 2
85706 2
86508 2
87040 2
87657 2
88676 2
91029 2
92885 2
95527 2
100304 2
100565 2
102028 2
104676 2
105039 2
105383 2
105485 2
105851 2
106633 2
106905 2
108249 2
109699 2
110462 2
111783 2
111842 2
112592 2
113198 2
113294 2
114590 2
114989 2
115072 2
115475 2
116528 2
116751 2
116898 2
117256 2
118191 2
118454 2
118549 2
118626 2
119202 2
119530 2
121229 2
123755 2
126804 2
127005 2
127438 2
127509 2
129040 2
130487 2
131646 2
132410 2
133063 2
133554 2
133676 2
135311 2
135807 2
136921 2
141446 2
=========================================================
Estimator of average coverage: 67
Assigning statistics values:
Localtime: Sun Sep 16 16:28:11 2018
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Sun Sep 16 16:53:33 2018
Buntifying reads (this may take a while) ... done.
Adding fork tags (this may take a while) ... done.
Writing read repeat info to:
MyFirstAssembly_assembly/MyFirstAssembly_d_info/MyFirstAssembly_info_readrepeats.lst
... 130384718 sequences with 291463944 masked stretches.
AS_resumeasembly 0
AS_resumeisok 0
fileExists(MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_signal_findpossibleoverlaps_pass.1.ok)
0
Localtime: Sun Sep 16 17:42:12 2018
Searching for possible overlaps:
Localtime: Sun Sep 16 17:42:13 2018
Now running threaded and partitioned skimmer with 3249 partitions in 144
threads:
[0%]
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
from 11149558560 to 7250456064
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
from 10938854784 to 7016288688
.
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
from 21908035512 to 13438167000
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
from 22572147768 to 13466587464
.
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
from 32474810256 to 19044428376
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
from 33296052168 to 19098648120
.
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
from 43486292976 to 24062992920
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.1.bin
from 43168195320 to 23841337440
.|
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.1.bin
from 53763553416 to 28340806248
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from 178884669960 to 114187180488
Hits chosen: 19356878180
Localtime: Fri Sep 21 21:42:07 2018
Total megahubs: 0
Cutting back possible chimeras ... done.
Chimeras were searched for ... looking for hits to purge.
truncating
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from 118095357672 to 118065311304
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from 114187180488 to 114163824288
System memory: 1081855930368
Mem2keepfree: 162278389555
Used by MIRA: 686068211712
Mem avail: 233509329101
rsh increased memtouse to: 233509329101
Edge vector capacity: 563719451
Can load up to 563714451 skim edges at once.
Partitioning into 37 blocks.
Blocks: 4965931 10052210 17184776 25604414 34130334
42802503 51695633 60709106 69826763 79038853
88342737 97672580 107026845 116176987 125486249
135018031 144700571 154329107 164099122 173865173
183685627 193556279 203207923 213102779 223033686
233001028 242924922 252820126 262555803 272054916
282085819 292116478 302217858 312241259 322321445
332463525 332938040
We have 19352427966 skims in file.
Localtime: Fri Sep 21 22:05:24 2018
De-normalising SKIM hits ... (this will take a while)
Localtime: Fri Sep 21 22:21:32 2018
Localtime: Fri Sep 21 22:26:35 2018
Writing normalised skimblock 0 ( 16.0 GiB) ... done.
Localtime: Fri Sep 21 22:43:28 2018
Localtime: Fri Sep 21 22:50:54 2018
Writing normalised skimblock 4965931 ( 16.0 GiB) ... done.
Localtime: Fri Sep 21 23:07:50 2018
Localtime: Fri Sep 21 23:13:21 2018
Writing normalised skimblock 10052210 ( 16.0 GiB) ... done.
Localtime: Fri Sep 21 23:30:27 2018
Localtime: Fri Sep 21 23:35:16 2018
Writing normalised skimblock 17184776 ( 16.0 GiB) ... done.
Localtime: Fri Sep 21 23:52:28 2018
Localtime: Fri Sep 21 23:57:16 2018
Writing normalised skimblock 25604414 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 00:14:41 2018
Localtime: Sat Sep 22 00:19:27 2018
Writing normalised skimblock 34130334 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 00:36:34 2018
Localtime: Sat Sep 22 00:41:07 2018
Writing normalised skimblock 42802503 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 00:58:20 2018
Localtime: Sat Sep 22 01:02:21 2018
Writing normalised skimblock 51695633 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 01:19:15 2018
Localtime: Sat Sep 22 01:22:32 2018
Writing normalised skimblock 60709106 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 01:37:45 2018
Localtime: Sat Sep 22 01:41:20 2018
Writing normalised skimblock 69826763 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 01:56:26 2018
Localtime: Sat Sep 22 01:59:33 2018
Writing normalised skimblock 79038853 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 02:14:40 2018
Localtime: Sat Sep 22 02:18:21 2018
Writing normalised skimblock 88342737 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 02:35:24 2018
Localtime: Sat Sep 22 02:39:39 2018
Writing normalised skimblock 97672580 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 02:57:02 2018
Localtime: Sat Sep 22 03:01:17 2018
Writing normalised skimblock 107026845 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 03:18:49 2018
Localtime: Sat Sep 22 03:22:57 2018
Writing normalised skimblock 116176987 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 03:38:36 2018
Localtime: Sat Sep 22 03:41:53 2018
Writing normalised skimblock 125486249 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 03:57:56 2018
Localtime: Sat Sep 22 04:01:56 2018
Writing normalised skimblock 135018031 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 04:19:12 2018
Localtime: Sat Sep 22 04:23:08 2018
Writing normalised skimblock 144700571 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 04:40:36 2018
Localtime: Sat Sep 22 04:44:33 2018
Writing normalised skimblock 154329107 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 05:01:09 2018
Localtime: Sat Sep 22 05:04:54 2018
Writing normalised skimblock 164099122 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 05:20:35 2018
Localtime: Sat Sep 22 05:23:54 2018
Writing normalised skimblock 173865173 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 05:41:15 2018
Localtime: Sat Sep 22 05:45:11 2018
Writing normalised skimblock 183685627 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 06:02:35 2018
Localtime: Sat Sep 22 06:06:26 2018
Writing normalised skimblock 193556279 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 06:23:47 2018
Localtime: Sat Sep 22 06:27:34 2018
Writing normalised skimblock 203207923 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 06:44:51 2018
Localtime: Sat Sep 22 06:48:21 2018
Writing normalised skimblock 213102779 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 07:05:39 2018
Localtime: Sat Sep 22 07:09:25 2018
Writing normalised skimblock 223033686 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 07:26:41 2018
Localtime: Sat Sep 22 07:30:33 2018
Writing normalised skimblock 233001028 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 07:47:58 2018
Localtime: Sat Sep 22 07:51:16 2018
Writing normalised skimblock 242924922 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 08:08:34 2018
Localtime: Sat Sep 22 08:11:48 2018
Writing normalised skimblock 252820126 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 08:28:49 2018
Localtime: Sat Sep 22 08:32:00 2018
Writing normalised skimblock 262555803 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 08:49:26 2018
Localtime: Sat Sep 22 08:52:50 2018
Writing normalised skimblock 272054916 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 09:09:53 2018
Localtime: Sat Sep 22 09:13:35 2018
Writing normalised skimblock 282085819 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 09:30:45 2018
Localtime: Sat Sep 22 09:34:25 2018
Writing normalised skimblock 292116478 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 09:51:52 2018
Localtime: Sat Sep 22 09:55:27 2018
Writing normalised skimblock 302217858 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 10:12:57 2018
Localtime: Sat Sep 22 10:16:14 2018
Writing normalised skimblock 312241259 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 10:33:31 2018
Localtime: Sat Sep 22 10:36:40 2018
Writing normalised skimblock 322321445 ( 16.0 GiB) ... done.
Localtime: Sat Sep 22 10:52:38 2018
Localtime: Sat Sep 22 10:52:45 2018
Writing normalised skimblock 332463525 ( 765 MiB) ... done.
Localtime: Sat Sep 22 10:52:46 2018
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Localtime: Sat Sep 22 15:01:25 2018
Only short reads
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Loaded 536870807 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 866440697
Step 20
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Loaded 536870886 elements
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Loaded 536870892 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 2103855558
Step 30
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Loaded 536869464 elements
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Loaded 536870886 elements
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Loaded 536870892 elements
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Loaded 536870692 elements
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870896 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 2103855558
Step 40
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Loaded 536869464 elements
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Loaded 536870886 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870888 elements
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Loaded 536870856 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 2103855558
Step 50
Total skims taken: 2103855558
Step 53
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Loaded 536869464 elements
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Loaded 536870807 elements
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Loaded 536870905 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 3499405611
Step 55
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Loaded 536870886 elements
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Loaded 536870396 elements
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Loaded 536870850 elements
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Loaded 536870811 elements
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Loaded 536870892 elements
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Loaded 536870807 elements
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Loaded 536870692 elements
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Loaded 536870905 elements
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 3635566041
Step 56
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Loaded 536870886 elements
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Loaded 536870396 elements
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Loaded 536870850 elements
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Loaded 536870811 elements
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Loaded 536870892 elements
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Loaded 536870807 elements
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Loaded 536870692 elements
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Loaded 536870905 elements
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Total skims taken: 3655790772
Step 60
Loading block 0
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Loaded 536869464 elements
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Loaded 536870886 elements
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Loaded 536870396 elements
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Loaded 536870850 elements
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Loaded 536870811 elements
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Loaded 536870892 elements
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Loaded 536870807 elements
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Loaded 536870692 elements
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Loaded 536870905 elements
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
Loading block 36
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Loaded 25079580 elements
Total skims taken: 3715934407
Step solexa by critlevel
rsh4_takeSolexaByCritLevel.
Loading block 0
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Loaded 536869464 elements
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Loaded 536870886 elements
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Loaded 536870396 elements
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Loaded 536870850 elements
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Loaded 536870811 elements
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Loaded 536870892 elements
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Loaded 536870807 elements
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Loaded 536870692 elements
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Loaded 536870905 elements
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Taken 495716247 hits.
rsh4_takeSolexaByCritLevel.
Loading block 0
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Loaded 536869464 elements
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Loaded 536870886 elements
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Loaded 536870396 elements
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Loaded 536870850 elements
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Loaded 536870811 elements
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Loaded 536870892 elements
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Loaded 536870807 elements
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Loaded 536870692 elements
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Loaded 536870905 elements
Loading block 9
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Taken 316372739 hits.
Step template overlaps
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Loaded 536869464 elements
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Loaded 536870886 elements
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Loaded 536870396 elements
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Loaded 536870850 elements
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Loaded 536870811 elements
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Loaded 536870892 elements
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Loaded 536870807 elements
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Loaded 536870692 elements
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Loaded 536870905 elements
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Loaded 536870864 elements
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Loaded 536870702 elements
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Loaded 536870795 elements
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Loaded 536870844 elements
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Loaded 536870789 elements
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Loaded 536870903 elements
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Loaded 536870889 elements
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Loaded 536870875 elements
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Loaded 536870896 elements
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Loaded 536870843 elements
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Loaded 536870888 elements
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Loaded 536870806 elements
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Loaded 536870856 elements
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Loaded 536870721 elements
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Loaded 536870775 elements
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Loaded 536870886 elements
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Loaded 536870890 elements
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Loaded 536870876 elements
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Loaded 536870828 elements
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Loaded 536870895 elements
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Loaded 536870848 elements
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Loaded 536870844 elements
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Loaded 536870906 elements
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Loaded 536870807 elements
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Loaded 536870870 elements
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Loaded 536870750 elements
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Loaded 536870837 elements
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Loaded 25079580 elements
Step NAO
rsh4_takeNeedAllOverlaps.
None needed.
Total skims taken: 4543858836
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 1056499932 kB
MemFree: 323418124 kB
MemAvailable: 511348844 kB
Buffers: 20 kB
Cached: 188147048 kB
SwapCached: 206496 kB
Active: 511784372 kB
Inactive: 211827156 kB
Active(anon): 509518988 kB
Inactive(anon): 25989232 kB
Active(file): 2265384 kB
Inactive(file): 185837924 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 4194300 kB
SwapFree: 131088 kB
Dirty: 736 kB
Writeback: 0 kB
AnonPages: 535310664 kB
Mapped: 64252 kB
Shmem: 43436 kB
Slab: 1554728 kB
SReclaimable: 672056 kB
SUnreclaim: 882672 kB
KernelStack: 55232 kB
PageTables: 1326748 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 532444264 kB
Committed_AS: 684873896 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 1974204 kB
VmallocChunk: 33418288128 kB
HardwareCorrupted: 0 kB
AnonHugePages: 128735232 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 472812 kB
DirectMap2M: 50792448 kB
DirectMap1G: 1024458752 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 242226
Ngid: 145499
Pid: 242226
PPid: 242225
TracerPid: 0
Uid: 1002 1002 1002 1002
Gid: 1002 1002 1002 1002
FDSize: 256
Groups: 1002
VmPeak: 679426256 kB
VmSize: 669988488 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 661968504 kB
VmRSS: 524764276 kB
VmData: 669878936 kB
VmStk: 136 kB
VmExe: 5792 kB
VmLib: 0 kB
VmPTE: 1288536 kB
VmSwap: 3920012 kB
Threads: 1
SigQ: 0/4124734
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000001
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed:
ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff
Cpus_allowed_list: 0-287
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Mems_allowed_list: 0-7
voluntary_ctxt_switches: 216925984
nonvoluntary_ctxt_switches: 458914
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 332938040 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: 332938040 1.2 GiB 0 B 0 B
AS_skim_edges: 25079580 16.8 GiB 16.1 GiB 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: 332938040 1.2 GiB 0 B 0 B
AS_clipright: 332938040 1.2 GiB 0 B 0 B
AS_used_ids: 332938040 318 MiB 0 B 0 B
AS_multicopies: 332938040 318 MiB 0 B 0 B
AS_hasmcoverlaps: 0 318 MiB 318 MiB 0 B
AS_maxcoveragereached: 332938040 1.2 GiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 332938040 318 MiB 0 B 0 B
AS_isdebris: 332938040 318 MiB 0 B 0 B
AS_needalloverlaps: 332938040 318 MiB 0 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1.2 GiB 1.2 GiB 0 B
AS_probablermbsnotok: 0 1.2 GiB 1.2 GiB 0 B
AS_weakrmbsnotok: 0 1.2 GiB 1.2 GiB 0 B
AS_readmaytakeskim: 332938040 318 MiB 8 B 0 B
AS_skimstaken: 19352427966 18.0 GiB 2 B 0 B
AS_numskimoverlaps: 332938040 1.2 GiB 0 B 0 B
AS_numleftextendskims: 332938040 1.2 GiB 0 B 0 B
AS_rightextendskims: 332938040 1.2 GiB 0 B 0 B
AS_skimleftextendratio: 332938040 318 MiB 0 B 0 B
AS_skimrightextendratio: 332938040 318 MiB 0 B 0 B
AS_usedtmpfiles: 156 5 KiB 0 B 0 B
Total: 53705420304 (50.0 GiB)
================================================================================
Dynamic s allocs: 0
Dynamic m allocs: 0
Align allocs: 0
Internal logic/programming/debugging error (*sigh* this should not have
happened)
********************************************************************************
* More than 2^31 skim hits would be taken ... this was not foreseen yet. *
* Please contact the author. *
********************************************************************************
->Thrown: void Assembly::reduceSkimHits4(int32 version, const string prefix,
const string postfix, const string logname)
->Caught: main
Aborting process, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/p/mira-assembler/tickets/
and also give a short notice on the mira talk mailing list.
If reporting, please do not delete the log and checkpoint directories, there may
be files in them which could be needed to find the problem.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /Backup/rao1/Shikha/B.fruticulosa/MIRA_analysis
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, wrapped MIRA process aborted.
Attachment:
manifest.conf
Description: Binary data
