[mira_talk] (no subject)
- From: "Mendez Garcia, Celia" <cmendezg@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 17 Jul 2014 22:24:50 +0000
Hi,
I get this log file when mapping to a reference bacterial genome.
What's the problem here?
Thanks,
Celia
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.
To (un-)subscribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
After subscribing, mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
To report bugs or ask for features, please use the SourceForge ticketing
system at:
http://sourceforge.net/p/mira-assembler/tickets/
This ensures that requests do not get lost.
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 compute-2-3.local 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue
Nov 6 23:43:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Looking for files named in data ...Pushing back filename:
"/home/a-m/cmendezg/NC_009617.gbk"
Pushing back filename:
"/home/a-m/cmendezg/Mackie.2014527/527/527_subsampled50.fastq"
Manifest:
projectname: 527
job: genome,mapping,accurate
parameters: -NW:cmrnl=no
Manifest load entries: 2
MLE 1:
RGID: 1
RGN: SN: clostr_beij
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 5 (Text) namschem: 6 SID: 0
DQ: 30
BB: 1 Rail: 0 CER: 0
/home/a-m/cmendezg/NC_009617.gbk MLE 2:
RGID: 2
RGN: IlluminaReads SN: clost_aur
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
/home/a-m/cmendezg/Mackie.2014527/527/527_subsampled50.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 : 527
Number of threads (not) : 256
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) : 1
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 1
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
Minimum length (ardml) : [sxa] 200
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) : 0
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)) : no
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] 0
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) : no
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) : 383
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 10
Automatic increase per pass (bphaipp) : 1
Automatic incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 1
Percent required (pr) : [sxa] 60
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : yes
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) : no
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] -90
Quick rule min sim 1 (qrms1) : [sxa] 100
Quick rule min len 2 (qrml2) : [sxa] -80
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] 20
Minimum relative score in % (mrs) : [sxa] 60
Solexa_hack_max_errors (shme) : [sxa] -1
Extra gap penalty (egp) : [sxa] no
extra gap penalty level (egpl) : [sxa] reject_codongaps
Max. egp in percent (megpp) : [sxa] 100
Contig parameters (-CO):
Name prefix (np) : 527
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] 3
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) : 160
Directories (-DI):
Top directory for writing files : 527_assembly
For writing result files : 527_assembly/527_d_results
For writing result info files : 527_assembly/527_d_info
For writing tmp files : 527_assembly/527_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : 527_assembly/527_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 : 527_out.caf
MAF : 527_out.maf
FASTA : 527_out.unpadded.fasta
FASTA quality : 527_out.unpadded.fasta.qual
FASTA (padded) : 527_out.padded.fasta
FASTA qual.(pad): 527_out.padded.fasta.qual
GAP4 (directory): 527_out.gap4da
ACE : 527_out.ace
HTML : 527_out.html
Simple text : 527_out.txt
TCS overview : 527_out.tcs
Wiggle : 527_out.wig
------------------------------------------------------------------------------
Creating directory 527_assembly ... done.
Creating directory 527_assembly/527_d_results ... done.
Creating directory 527_assembly/527_d_info ... done.
Creating directory 527_assembly/527_d_chkpt ... done.
Creating directory 527_assembly/527_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Thu Jul 17 11:20:48 2014
Loading reference backbone from /home/a-m/cmendezg/NC_009617.gbk type gbf
Fishy line (110012): CONTIG join(CP000721.1:1..6000632)
Violating GenBank standard guidelines: we are in features, token is not ORIGIN,
but starts at column 0.
Loading reads from /home/a-m/cmendezg/Mackie.2014527/527/527_subsampled50.fastq
type fastq
Localtime: Thu Jul 17 11:20:52 2014
Loading data from FASTQ file:
/home/a-m/cmendezg/Mackie.2014527/527/527_subsampled50.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 9812455 reads, Localtime: Thu Jul 17 11:22:09 2014
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: HWI-ST330:422:C4AVHACXX:7:1101:1233:2167/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1329:2125/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1353:2208/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1710:2096/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1504:2235/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1755:2095/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1890:2111/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:1948:2245/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2188:2142/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2361:2067/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2304:2086/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2256:2172/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2360:2223/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2413:2245/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2568:2124/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2536:2146/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2840:2151/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2962:2169/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:2806:2204/1
Name too long: HWI-ST330:422:C4AVHACXX:7:1101:3049:2110/1
9812455 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
9812455 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'
Deleting gap columns in backbones ... Postprocessing backbone(s) ... this may
take a while.
1 to process
NC_009617_bb 6000632
Contig NC_009617_bb has strain clostr_beij
TODO: Like Readpool: strain x has y reads
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.
9812456 reads with valid data for assembly.
Localtime: Thu Jul 17 11:23:06 2014
Generated 9812456 unique DNA template ids for 9812456 valid reads.
No useful template information found.
TODO: Like Readpool: strain x has y reads
Have read pool with 9812456 reads.
===========================================================================
Pool statistics:
Backbones: 1 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 9812455 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 9812455 0
Avg tot rlen 0 0 0 0 0 0 100 0
Avg rlen used 0 0 0 0 0 0 100 0
W/o clips 0 0 0 0 0 0 9812455 0
Solexa total bases: 981245500 used bases in used reads: 981245500
===========================================================================
Checking pairs of readgroup 1 (named: ''): found 0
Checking pairs of readgroup 2 (named: 'IlluminaReads'): found 0
527_assembly/527_d_tmp/527_int_clippings_t0.0.txt
527_assembly/527_d_tmp/527_int_clippings_t1.0.txt
527_assembly/527_d_tmp/527_int_clippings_t2.0.txt
527_assembly/527_d_tmp/527_int_clippings_t3.0.txt
527_assembly/527_d_tmp/527_int_clippings_t4.0.txt
527_assembly/527_d_tmp/527_int_clippings_t5.0.txt
527_assembly/527_d_tmp/527_int_clippings_t6.0.txt
527_assembly/527_d_tmp/527_int_clippings_t7.0.txt
527_assembly/527_d_tmp/527_int_clippings_t8.0.txt
527_assembly/527_d_tmp/527_int_clippings_t9.0.txt
527_assembly/527_d_tmp/527_int_clippings_t10.0.txt
527_assembly/527_d_tmp/527_int_clippings_t11.0.txt
527_assembly/527_d_tmp/527_int_clippings_t12.0.txt
527_assembly/527_d_tmp/527_int_clippings_t13.0.txt
527_assembly/527_d_tmp/527_int_clippings_t14.0.txt
527_assembly/527_d_tmp/527_int_clippings_t15.0.txt
527_assembly/527_d_tmp/527_int_clippings_t16.0.txt
527_assembly/527_d_tmp/527_int_clippings_t17.0.txt
527_assembly/527_d_tmp/527_int_clippings_t18.0.txt
527_assembly/527_d_tmp/527_int_clippings_t19.0.txt
527_assembly/527_d_tmp/527_int_clippings_t20.0.txt
527_assembly/527_d_tmp/527_int_clippings_t21.0.txt
527_assembly/527_d_tmp/527_int_clippings_t22.0.txt
527_assembly/527_d_tmp/527_int_clippings_t23.0.txt
527_assembly/527_d_tmp/527_int_clippings_t24.0.txt
527_assembly/527_d_tmp/527_int_clippings_t25.0.txt
527_assembly/527_d_tmp/527_int_clippings_t26.0.txt
527_assembly/527_d_tmp/527_int_clippings_t27.0.txt
527_assembly/527_d_tmp/527_int_clippings_t28.0.txt
527_assembly/527_d_tmp/527_int_clippings_t29.0.txt
527_assembly/527_d_tmp/527_int_clippings_t30.0.txt
527_assembly/527_d_tmp/527_int_clippings_t31.0.txt
527_assembly/527_d_tmp/527_int_clippings_t32.0.txt
527_assembly/527_d_tmp/527_int_clippings_t33.0.txt
527_assembly/527_d_tmp/527_int_clippings_t34.0.txt
527_assembly/527_d_tmp/527_int_clippings_t35.0.txt
527_assembly/527_d_tmp/527_int_clippings_t36.0.txt
527_assembly/527_d_tmp/527_int_clippings_t37.0.txt
527_assembly/527_d_tmp/527_int_clippings_t38.0.txt
527_assembly/527_d_tmp/527_int_clippings_t39.0.txt
527_assembly/527_d_tmp/527_int_clippings_t40.0.txt
527_assembly/527_d_tmp/527_int_clippings_t41.0.txt
527_assembly/527_d_tmp/527_int_clippings_t42.0.txt
527_assembly/527_d_tmp/527_int_clippings_t43.0.txt
527_assembly/527_d_tmp/527_int_clippings_t44.0.txt
527_assembly/527_d_tmp/527_int_clippings_t45.0.txt
527_assembly/527_d_tmp/527_int_clippings_t46.0.txt
527_assembly/527_d_tmp/527_int_clippings_t47.0.txt
527_assembly/527_d_tmp/527_int_clippings_t48.0.txt
527_assembly/527_d_tmp/527_int_clippings_t49.0.txt
527_assembly/527_d_tmp/527_int_clippings_t50.0.txt
527_assembly/527_d_tmp/527_int_clippings_t51.0.txt
527_assembly/527_d_tmp/527_int_clippings_t52.0.txt
527_assembly/527_d_tmp/527_int_clippings_t53.0.txt
527_assembly/527_d_tmp/527_int_clippings_t54.0.txt
527_assembly/527_d_tmp/527_int_clippings_t55.0.txt
527_assembly/527_d_tmp/527_int_clippings_t56.0.txt
527_assembly/527_d_tmp/527_int_clippings_t57.0.txt
527_assembly/527_d_tmp/527_int_clippings_t58.0.txt
527_assembly/527_d_tmp/527_int_clippings_t59.0.txt
527_assembly/527_d_tmp/527_int_clippings_t60.0.txt
527_assembly/527_d_tmp/527_int_clippings_t61.0.txt
527_assembly/527_d_tmp/527_int_clippings_t62.0.txt
527_assembly/527_d_tmp/527_int_clippings_t63.0.txt
527_assembly/527_d_tmp/527_int_clippings_t64.0.txt
527_assembly/527_d_tmp/527_int_clippings_t65.0.txt
527_assembly/527_d_tmp/527_int_clippings_t66.0.txt
527_assembly/527_d_tmp/527_int_clippings_t67.0.txt
527_assembly/527_d_tmp/527_int_clippings_t68.0.txt
527_assembly/527_d_tmp/527_int_clippings_t69.0.txt
527_assembly/527_d_tmp/527_int_clippings_t70.0.txt
527_assembly/527_d_tmp/527_int_clippings_t71.0.txt
527_assembly/527_d_tmp/527_int_clippings_t72.0.txt
527_assembly/527_d_tmp/527_int_clippings_t73.0.txt
527_assembly/527_d_tmp/527_int_clippings_t74.0.txt
527_assembly/527_d_tmp/527_int_clippings_t75.0.txt
527_assembly/527_d_tmp/527_int_clippings_t76.0.txt
527_assembly/527_d_tmp/527_int_clippings_t77.0.txt
527_assembly/527_d_tmp/527_int_clippings_t78.0.txt
527_assembly/527_d_tmp/527_int_clippings_t79.0.txt
527_assembly/527_d_tmp/527_int_clippings_t80.0.txt
527_assembly/527_d_tmp/527_int_clippings_t81.0.txt
527_assembly/527_d_tmp/527_int_clippings_t82.0.txt
527_assembly/527_d_tmp/527_int_clippings_t83.0.txt
527_assembly/527_d_tmp/527_int_clippings_t84.0.txt
527_assembly/527_d_tmp/527_int_clippings_t85.0.txt
527_assembly/527_d_tmp/527_int_clippings_t86.0.txt
527_assembly/527_d_tmp/527_int_clippings_t87.0.txt
527_assembly/527_d_tmp/527_int_clippings_t88.0.txt
527_assembly/527_d_tmp/527_int_clippings_t89.0.txt
527_assembly/527_d_tmp/527_int_clippings_t90.0.txt
527_assembly/527_d_tmp/527_int_clippings_t91.0.txt
527_assembly/527_d_tmp/527_int_clippings_t92.0.txt
527_assembly/527_d_tmp/527_int_clippings_t93.0.txt
527_assembly/527_d_tmp/527_int_clippings_t94.0.txt
527_assembly/527_d_tmp/527_int_clippings_t95.0.txt
527_assembly/527_d_tmp/527_int_clippings_t96.0.txt
527_assembly/527_d_tmp/527_int_clippings_t97.0.txt
527_assembly/527_d_tmp/527_int_clippings_t98.0.txt
527_assembly/527_d_tmp/527_int_clippings_t99.0.txt
527_assembly/527_d_tmp/527_int_clippings_t100.0.txt
527_assembly/527_d_tmp/527_int_clippings_t101.0.txt
527_assembly/527_d_tmp/527_int_clippings_t102.0.txt
527_assembly/527_d_tmp/527_int_clippings_t103.0.txt
527_assembly/527_d_tmp/527_int_clippings_t104.0.txt
527_assembly/527_d_tmp/527_int_clippings_t105.0.txt
527_assembly/527_d_tmp/527_int_clippings_t106.0.txt
527_assembly/527_d_tmp/527_int_clippings_t107.0.txt
527_assembly/527_d_tmp/527_int_clippings_t108.0.txt
527_assembly/527_d_tmp/527_int_clippings_t109.0.txt
527_assembly/527_d_tmp/527_int_clippings_t110.0.txt
527_assembly/527_d_tmp/527_int_clippings_t111.0.txt
527_assembly/527_d_tmp/527_int_clippings_t112.0.txt
527_assembly/527_d_tmp/527_int_clippings_t113.0.txt
527_assembly/527_d_tmp/527_int_clippings_t114.0.txt
527_assembly/527_d_tmp/527_int_clippings_t115.0.txt
527_assembly/527_d_tmp/527_int_clippings_t116.0.txt
527_assembly/527_d_tmp/527_int_clippings_t117.0.txt
527_assembly/527_d_tmp/527_int_clippings_t118.0.txt
527_assembly/527_d_tmp/527_int_clippings_t119.0.txt
527_assembly/527_d_tmp/527_int_clippings_t120.0.txt
527_assembly/527_d_tmp/527_int_clippings_t121.0.txt
527_assembly/527_d_tmp/527_int_clippings_t122.0.txt
527_assembly/527_d_tmp/527_int_clippings_t123.0.txt
527_assembly/527_d_tmp/527_int_clippings_t124.0.txt
527_assembly/527_d_tmp/527_int_clippings_t125.0.txt
527_assembly/527_d_tmp/527_int_clippings_t126.0.txt
527_assembly/527_d_tmp/527_int_clippings_t127.0.txt
527_assembly/527_d_tmp/527_int_clippings_t128.0.txt
527_assembly/527_d_tmp/527_int_clippings_t129.0.txt
527_assembly/527_d_tmp/527_int_clippings_t130.0.txt
527_assembly/527_d_tmp/527_int_clippings_t131.0.txt
527_assembly/527_d_tmp/527_int_clippings_t132.0.txt
527_assembly/527_d_tmp/527_int_clippings_t133.0.txt
527_assembly/527_d_tmp/527_int_clippings_t134.0.txt
527_assembly/527_d_tmp/527_int_clippings_t135.0.txt
527_assembly/527_d_tmp/527_int_clippings_t136.0.txt
527_assembly/527_d_tmp/527_int_clippings_t137.0.txt
527_assembly/527_d_tmp/527_int_clippings_t138.0.txt
527_assembly/527_d_tmp/527_int_clippings_t139.0.txt
527_assembly/527_d_tmp/527_int_clippings_t140.0.txt
527_assembly/527_d_tmp/527_int_clippings_t141.0.txt
527_assembly/527_d_tmp/527_int_clippings_t142.0.txt
527_assembly/527_d_tmp/527_int_clippings_t143.0.txt
527_assembly/527_d_tmp/527_int_clippings_t144.0.txt
527_assembly/527_d_tmp/527_int_clippings_t145.0.txt
527_assembly/527_d_tmp/527_int_clippings_t146.0.txt
527_assembly/527_d_tmp/527_int_clippings_t147.0.txt
527_assembly/527_d_tmp/527_int_clippings_t148.0.txt
527_assembly/527_d_tmp/527_int_clippings_t149.0.txt
527_assembly/527_d_tmp/527_int_clippings_t150.0.txt
527_assembly/527_d_tmp/527_int_clippings_t151.0.txt
527_assembly/527_d_tmp/527_int_clippings_t152.0.txt
527_assembly/527_d_tmp/527_int_clippings_t153.0.txt
527_assembly/527_d_tmp/527_int_clippings_t154.0.txt
527_assembly/527_d_tmp/527_int_clippings_t155.0.txt
527_assembly/527_d_tmp/527_int_clippings_t156.0.txt
527_assembly/527_d_tmp/527_int_clippings_t157.0.txt
527_assembly/527_d_tmp/527_int_clippings_t158.0.txt
527_assembly/527_d_tmp/527_int_clippings_t159.0.txt
527_assembly/527_d_tmp/527_int_clippings_t160.0.txt
527_assembly/527_d_tmp/527_int_clippings_t161.0.txt
527_assembly/527_d_tmp/527_int_clippings_t162.0.txt
527_assembly/527_d_tmp/527_int_clippings_t163.0.txt
527_assembly/527_d_tmp/527_int_clippings_t164.0.txt
527_assembly/527_d_tmp/527_int_clippings_t165.0.txt
527_assembly/527_d_tmp/527_int_clippings_t166.0.txt
527_assembly/527_d_tmp/527_int_clippings_t167.0.txt
527_assembly/527_d_tmp/527_int_clippings_t168.0.txt
527_assembly/527_d_tmp/527_int_clippings_t169.0.txt
527_assembly/527_d_tmp/527_int_clippings_t170.0.txt
527_assembly/527_d_tmp/527_int_clippings_t171.0.txt
527_assembly/527_d_tmp/527_int_clippings_t172.0.txt
527_assembly/527_d_tmp/527_int_clippings_t173.0.txt
527_assembly/527_d_tmp/527_int_clippings_t174.0.txt
527_assembly/527_d_tmp/527_int_clippings_t175.0.txt
527_assembly/527_d_tmp/527_int_clippings_t176.0.txt
527_assembly/527_d_tmp/527_int_clippings_t177.0.txt
527_assembly/527_d_tmp/527_int_clippings_t178.0.txt
527_assembly/527_d_tmp/527_int_clippings_t179.0.txt
527_assembly/527_d_tmp/527_int_clippings_t180.0.txt
527_assembly/527_d_tmp/527_int_clippings_t181.0.txt
527_assembly/527_d_tmp/527_int_clippings_t182.0.txt
527_assembly/527_d_tmp/527_int_clippings_t183.0.txt
527_assembly/527_d_tmp/527_int_clippings_t184.0.txt
527_assembly/527_d_tmp/527_int_clippings_t185.0.txt
527_assembly/527_d_tmp/527_int_clippings_t186.0.txt
527_assembly/527_d_tmp/527_int_clippings_t187.0.txt
527_assembly/527_d_tmp/527_int_clippings_t188.0.txt
527_assembly/527_d_tmp/527_int_clippings_t189.0.txt
527_assembly/527_d_tmp/527_int_clippings_t190.0.txt
527_assembly/527_d_tmp/527_int_clippings_t191.0.txt
527_assembly/527_d_tmp/527_int_clippings_t192.0.txt
527_assembly/527_d_tmp/527_int_clippings_t193.0.txt
527_assembly/527_d_tmp/527_int_clippings_t194.0.txt
527_assembly/527_d_tmp/527_int_clippings_t195.0.txt
527_assembly/527_d_tmp/527_int_clippings_t196.0.txt
527_assembly/527_d_tmp/527_int_clippings_t197.0.txt
527_assembly/527_d_tmp/527_int_clippings_t198.0.txt
527_assembly/527_d_tmp/527_int_clippings_t199.0.txt
527_assembly/527_d_tmp/527_int_clippings_t200.0.txt
527_assembly/527_d_tmp/527_int_clippings_t201.0.txt
527_assembly/527_d_tmp/527_int_clippings_t202.0.txt
527_assembly/527_d_tmp/527_int_clippings_t203.0.txt
527_assembly/527_d_tmp/527_int_clippings_t204.0.txt
527_assembly/527_d_tmp/527_int_clippings_t205.0.txt
527_assembly/527_d_tmp/527_int_clippings_t206.0.txt
527_assembly/527_d_tmp/527_int_clippings_t207.0.txt
527_assembly/527_d_tmp/527_int_clippings_t208.0.txt
527_assembly/527_d_tmp/527_int_clippings_t209.0.txt
527_assembly/527_d_tmp/527_int_clippings_t210.0.txt
527_assembly/527_d_tmp/527_int_clippings_t211.0.txt
527_assembly/527_d_tmp/527_int_clippings_t212.0.txt
527_assembly/527_d_tmp/527_int_clippings_t213.0.txt
527_assembly/527_d_tmp/527_int_clippings_t214.0.txt
527_assembly/527_d_tmp/527_int_clippings_t215.0.txt
527_assembly/527_d_tmp/527_int_clippings_t216.0.txt
527_assembly/527_d_tmp/527_int_clippings_t217.0.txt
527_assembly/527_d_tmp/527_int_clippings_t218.0.txt
527_assembly/527_d_tmp/527_int_clippings_t219.0.txt
527_assembly/527_d_tmp/527_int_clippings_t220.0.txt
527_assembly/527_d_tmp/527_int_clippings_t221.0.txt
527_assembly/527_d_tmp/527_int_clippings_t222.0.txt
527_assembly/527_d_tmp/527_int_clippings_t223.0.txt
527_assembly/527_d_tmp/527_int_clippings_t224.0.txt
527_assembly/527_d_tmp/527_int_clippings_t225.0.txt
527_assembly/527_d_tmp/527_int_clippings_t226.0.txt
527_assembly/527_d_tmp/527_int_clippings_t227.0.txt
527_assembly/527_d_tmp/527_int_clippings_t228.0.txt
527_assembly/527_d_tmp/527_int_clippings_t229.0.txt
527_assembly/527_d_tmp/527_int_clippings_t230.0.txt
527_assembly/527_d_tmp/527_int_clippings_t231.0.txt
527_assembly/527_d_tmp/527_int_clippings_t232.0.txt
527_assembly/527_d_tmp/527_int_clippings_t233.0.txt
527_assembly/527_d_tmp/527_int_clippings_t234.0.txt
527_assembly/527_d_tmp/527_int_clippings_t235.0.txt
527_assembly/527_d_tmp/527_int_clippings_t236.0.txt
527_assembly/527_d_tmp/527_int_clippings_t237.0.txt
527_assembly/527_d_tmp/527_int_clippings_t238.0.txt
527_assembly/527_d_tmp/527_int_clippings_t239.0.txt
527_assembly/527_d_tmp/527_int_clippings_t240.0.txt
527_assembly/527_d_tmp/527_int_clippings_t241.0.txt
527_assembly/527_d_tmp/527_int_clippings_t242.0.txt
527_assembly/527_d_tmp/527_int_clippings_t243.0.txt
527_assembly/527_d_tmp/527_int_clippings_t244.0.txt
527_assembly/527_d_tmp/527_int_clippings_t245.0.txt
527_assembly/527_d_tmp/527_int_clippings_t246.0.txt
527_assembly/527_d_tmp/527_int_clippings_t247.0.txt
527_assembly/527_d_tmp/527_int_clippings_t248.0.txt
527_assembly/527_d_tmp/527_int_clippings_t249.0.txt
527_assembly/527_d_tmp/527_int_clippings_t250.0.txt
527_assembly/527_d_tmp/527_int_clippings_t251.0.txt
527_assembly/527_d_tmp/527_int_clippings_t252.0.txt
527_assembly/527_d_tmp/527_int_clippings_t253.0.txt
527_assembly/527_d_tmp/527_int_clippings_t254.0.txt
527_assembly/527_d_tmp/527_int_clippings_t255.0.txt
Post-load clips:
Localtime: Thu Jul 17 11:23:54 2014
Writing temporary hstat files:
freemem: 1197448802304
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: Thu Jul 17 11:23:54 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jul 17 11:23:54 2014
clean up temporary stat files...Localtime: Thu Jul 17 11:23:54 2014
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Thu Jul 17 11:23:54 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
CLIP MSG: Adaptor right found: 371417
===========================================================================
Pool statistics:
Backbones: 1 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 9812455 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 9437445 0
Avg tot rlen 0 0 0 0 0 0 100 0
Avg rlen used 0 0 0 0 0 0 99 0
W/o clips 0 0 0 0 0 0 9413435 0
Solexa total bases: 981245500 used bases in used reads: 943034343
===========================================================================
-AL:shme is < 0, automatically determining optimal value.
set -AL:shme 15
-SB:brl is 0, automatically determining optimal value.
brl: 230
-SB:bro is 0, automatically determining optimal value.
bro: 115
Adding rails: length 230 and overlap 115
makeIntelligentConsensus() complete calc .. mict_fin 1320356
mict_pre 473
mict_shadow 17461
mict_fallout 2804774
mict_newin 2717043
mict_helper1 4003352
mict_newin 2717043
mict_restofloop 2984841
mict_totalloop 23305971
done.
NC_009617_bb first rail: rr_####9812456####
NC_009617_bb last rail: rr_####9864632####
Sorting reads ... done.
===========================================================================
Pool statistics:
Backbones: 1 Backbone rails: 52177
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 9812455 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 9437445 0
Avg tot rlen 0 0 0 0 0 0 100 0
Avg rlen used 0 0 0 0 0 0 99 0
W/o clips 0 0 0 0 0 0 9413435 0
Solexa total bases: 981245500 used bases in used reads: 943034343
===========================================================================
Tmp directory is not on a NFS mount, good.
PRED MAXTID 9812455
Hash analysis for proposed cutbacks:Localtime: Thu Jul 17 11:33:05 2014
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: Thu Jul 17 11:44:01 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jul 17 12:00:24 2014
clean up temporary stat files...Localtime: Thu Jul 17 12:00:24 2014
Raw MHI: 15359864
Raw avg. freq. : 99
HSS 21266280 HSST: 19139652
Localtime: Thu Jul 17 12:00:42 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 99
Corrected avg. raw frequency coverage: 99
Final average frequency: 99
Deduced thresholds:
-------------------
Min normal cov: 39.6
Max normal cov: 158.4
Repeat cov: 188.1
Heavy cov: 792
Crazy cov: 1980
Mask cov: 9900
Repeat ratio histogram:
-----------------------
0 9065454
1 11833974
2 304112
3 22472
4 10000
5 7816
6 4568
7 3494
8 3268
9 2406
10 2346
11 2328
12 1564
13 816
14 728
15 438
16 184
17 206
18 54
19 12
20 26
21 12
22 2
=========================================================
Assigning statistics values:
Localtime: Thu Jul 17 12:00:43 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Thu Jul 17 12:09:38 2014
Detected probable higher coverage in Illumina genome project, setting:
-CL:pmkfr=2
Localtime: Thu Jul 17 12:09:38 2014
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 376228
Num reads cliped right: 523245
Num reads completely killed: 68356
Total bases clipped : 22349535
Clipping dubious poly-base stretches at end of reads ... Hash analysis for
proposed cutbacks:Localtime: Thu Jul 17 12:10:50 2014
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: Thu Jul 17 12:20:36 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jul 17 12:38:26 2014
clean up temporary stat files...Localtime: Thu Jul 17 12:38:26 2014
Raw MHI: 13890443
Raw avg. freq. : 99
HSS 19726590 HSST: 17753931
Localtime: Thu Jul 17 12:38:51 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 99
Corrected avg. raw frequency coverage: 99
Final average frequency: 99
Deduced thresholds:
-------------------
Min normal cov: 39.6
Max normal cov: 158.4
Repeat cov: 188.1
Heavy cov: 792
Crazy cov: 1980
Mask cov: 9900
Repeat ratio histogram:
-----------------------
0 7526068
1 11833856
2 303938
3 22470
4 9990
5 7830
6 4554
7 3498
8 3282
9 2410
10 2330
11 2324
12 1566
13 812
14 730
15 438
16 182
17 206
18 54
19 12
20 26
21 12
22 2
=========================================================
Assigning statistics values:
Localtime: Thu Jul 17 12:38:52 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Thu Jul 17 12:39:36 2014
Localtime: Thu Jul 17 12:39:36 2014
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 19521
Num reads cliped right: 25556
Num reads completely killed: 7918
Total bases clipped : 1000261
Clipping dubious poly-base stretches at end of reads ...
===========================================================================
Pool statistics:
Backbones: 1 Backbone rails: 52177
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 9812455 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 9365901 0
Avg tot rlen 0 0 0 0 0 0 100 0
Avg rlen used 0 0 0 0 0 0 98 0
W/o clips 0 0 0 0 0 0 8552480 0
Solexa total bases: 981245500 used bases in used reads: 919662342
===========================================================================
Performing snapshot 1
Localtime: Thu Jul 17 12:40:33 2014
Creating directory 527_assembly/527_d_chkpt ... done.
Localtime: Thu Jul 17 12:46:30 2014
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 8686
Pid: 8686
PPid: 8685
TracerPid: 0
Uid: 3143 3143 3143 3143
Gid: 3143 3143 3143 3143
Utrace: 0
FDSize: 512
Groups: 3143
VmPeak: 15086060 kB
VmSize: 14339132 kB
VmLck: 0 kB
VmHWM: 14078724 kB
VmRSS: 14062240 kB
VmData: 14333208 kB
VmStk: 88 kB
VmExe: 5792 kB
VmLib: 0 kB
VmPTE: 27588 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/16538231
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000001000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff,ffffffff
Cpus_allowed_list: 0-383
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,ffffffff,ffffffff
Mems_allowed_list: 0-63
voluntary_ctxt_switches: 554999
nonvoluntary_ctxt_switches: 4747
--------------------------------------------------------------------------------
Pass: 1 / 1
===========================================================================
Pool statistics:
Backbones: 1 Backbone rails: 52177
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 9812455 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 9365901 0
Avg tot rlen 0 0 0 0 0 0 100 0
Avg rlen used 0 0 0 0 0 0 98 0
W/o clips 0 0 0 0 0 0 8552480 0
Solexa total bases: 981245500 used bases in used reads: 919662342
===========================================================================
Localtime: Thu Jul 17 12:46:46 2014
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: Thu Jul 17 12:58:28 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jul 17 12:58:28 2014
clean up temporary stat files...Localtime: Thu Jul 17 12:58:28 2014
Raw MHI: 769339
Raw avg. freq. : 2658
HSS 935436 HSST: 841893
Localtime: Thu Jul 17 12:58:29 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 2658
Corrected avg. raw frequency coverage: 2658
Final average frequency: 2658
Deduced thresholds:
-------------------
Min normal cov: 1063.2
Max normal cov: 4252.8
Repeat cov: 5050.2
Heavy cov: 21264
Crazy cov: 53160
Mask cov: 265800
Repeat ratio histogram:
-----------------------
0 635733
1 192255
2 53145
3 23444
4 10805
5 5843
6 3765
7 2923
8 2136
9 1495
10 1025
11 637
12 438
13 292
14 208
15 133
16 93
17 117
18 91
19 122
20 113
21 99
22 87
23 114
24 72
25 66
26 42
27 33
28 18
29 23
30 22
31 12
32 8
33 9
34 12
35 2
36 4
=========================================================
Assigning statistics values:
Localtime: Thu Jul 17 12:58:29 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Thu Jul 17 12:58:44 2014
Buntifying reads (this may take a while) ... done.
Adding fork tags (this may take a while) ... done.
Writing read repeat info to: 527_assembly/527_d_info/527_info_readrepeats.lst
... 244 sequences with 528 masked stretches.
AS_resumeasembly 0
AS_resumeisok 0
fileExists(527_assembly/527_d_tmp/527_signal_findpossibleoverlaps_pass.1.ok) 0
Localtime: Thu Jul 17 13:00:11 2014
Searching for possible overlaps (only against backbone, the progress bar will
be skewed):
Localtime: Thu Jul 17 13:00:11 2014
Now running threaded and partitioned skimmer with 63 partitions in 256 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
truncating 527_assembly/527_d_tmp/527_int_posmatchf_pass.1.bin
truncated 527_assembly/527_d_tmp/527_int_posmatchf_pass.1.bin from 8557763328
to 7896138792
truncating 527_assembly/527_d_tmp/527_int_posmatchc_pass.1.bin
truncated 527_assembly/527_d_tmp/527_int_posmatchc_pass.1.bin from 8448112872
to 7834898856
Hits chosen: 1310919804
Localtime: Thu Jul 17 13:27:11 2014
Total megahubs: 0
Localtime: Thu Jul 17 13:27:11 2014
Backbone SW checks forward:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Had to recalculate 326851516 skims (out of 329005783) with Smith-Waterman.
Localtime: Thu Jul 17 17:08:04 2014
Backbone SW checks reverse:
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* File not found: 527_assembly/527_d_tmp/527_int_posmatchc_pass.1.bin *
********************************************************************************
->Thrown: void Assembly::rnpskmbs_helper(const string & filename, const int32
version, const int8 direction)
->Caught: void Assembly::recalcNonPerfectSkimMappingsBySW(int32 version)
Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /home/a-m/cmendezg
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, wrapped MIRA process aborted.
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