[mira_talk] de novo assembly: boost::thread_resource_error
- From: vladimir mashanov <mashanovvlad@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 10 May 2011 08:59:44 -0400
Hi, Bastien
I am trying to run a de novo assembly of 1,866,192 454-reads
(1,029,483,065 bases) on a node with 50 Gb RAM. After about 30 min,
mira gets aborted with the following error (the bottom of the log
file):
'standard' exception occured (that's NOT normal):
boost::thread_resource_error
I would highly appreciate if you could tell me what I am doing wrong.
Here is my script to start mira:
--job=denovo,est,accurate,454 COMMON_SETTINGS -SK:mchr=4096
454_SETTINGS -LR:mxti=no -CL:cpat=no:qcmq=20:bsqc=yes -ED:ace=yes >&
lo
g_assembly.txt
Here is my complete log file:
This is MIRA V3.2.1 (production version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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Compiled by: bach
Sun Nov 28 00:49:16 CET 2010
On: Linux vKub90464 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
01:58:03 UTC 2009 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compilation 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-0-12.local
2.6.18-164.11.1.el5_lustre.1.8.2 #1 SMP Sat Jan 23 18:02:32 MST 2010
x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=cleaned_2_combined
--job=denovo,est,accurate,454 COMMON_SETTINGS -SK:mchr=4096
454_SETTINGS -LR:mxti=no -CL:cpat=no:qcmq=20:bsqc=yes -ED:ace=yes
Parameters parsed without error, perfect.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), 454 data
Used parameter settings:
General (-GE):
Project name in (proin) : cleaned_2_combined
Project name out (proout) : cleaned_2_combined
Number of threads (not) : 2
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[454] yes
Template insert size minimum (tismin) : [san] -1
[454] -1
Template insert size maximum (tismax) : [san] -1
[454] -1
Template partner build direction (tpbd) : [san] -1
[454] -1
Colour reads by hash frequency (crhf) : no
Load reads options (-LR):
Load sequence data (lsd) : [san] no
[454] yes
File type (ft) : [san] fasta
[454] fasta
External quality (eq) : from SCF (scf)
Ext. qual. override (eqo) : no
Discard reads on e.q. error (droeqe): no
Solexa scores in qual file (ssiqf) : no
FASTQ qual offset (fqqo) : [san] 0
[454] 0
Wants quality file (wqf) : [san] yes
[454] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[454] forward/reverse
(fr)
Merge with XML trace info (mxti) : [san] no
[454] no
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 5
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 3
Minimum read length (mrl) : [san] 80
[454] 40
Minimum reads per contig (mrpc) : [san] 2
[454] 2
Base default quality (bdq) : [san] 10
[454] 10
Enforce presence of qualities (epoq) : [san] yes
[454] yes
Automatic repeat detection (ard) : no
Coverage threshold (ardct) : [san] 2
[454] 2
Minimum length (ardml) : [san] 400
[454] 200
Grace length (ardgl) : [san] 40
[454] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [san] 1.5
[454] 1.5
Keep long repeats separated (klrs) : no
Spoiler detection (sd) : no
Last pass only (sdlpo) : yes
Use genomic pathfinder (ugpf) : no
Use emergency search stop (uess) : yes
ESS partner depth (esspd) : 500
Use emergency blacklist (uebl) : yes
Use max. contig build time (umcbt) : yes
Build time in seconds (bts) : 3600
Strain and backbone options (-SB):
Load straindata (lsd) : no
Assign default strain (ads) : [san] no
[454] no
Default strain name (dsn) : [san] StrainX
[454] StrainX
Load backbone (lb) : no
Start backbone usage in pass (sbuip) : 3
Backbone file type (bft) : fasta
Backbone base quality (bbq) : 30
Backbone strain name (bsn) : ReferenceStrain
Force for all (bsnffa) : no
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Also build new contigs (abnc) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [san] yes
[454] no
Read extension window length (rewl) : [san] 30
[454] 15
Read extension w. maxerrors (rewme) : [san] 2
[454] 2
First extension in pass (feip) : [san] 0
[454] 0
Last extension in pass (leip) : [san] 0
[454] 0
Clipping options (-CL):
Merge with SSAHA2/SMALT vector screen (msvs): [san] no
[454] no
Gap size (msvsgs) : [san] 10
[454] 8
Max front gap (msvsmfg) : [san] 60
[454] 8
Max end gap (msvsmeg) : [san] 120
[454] 12
Strict front clip (msvssfc) : [san] 0
[454] 0
Strict end clip (msvssec) : [san] 0
[454] 0
Possible vector leftover clip (pvlc) : [san] yes
[454] no
maximum len allowed (pvcmla) : [san] 18
[454] 18
Quality clip (qc) : [san] no
[454] no
Minimum quality (qcmq) : [san] 20
[454] 20
Window length (qcwl) : [san] 30
[454] 30
Bad stretch quality clip (bsqc) : [san] yes
[454] yes
Minimum quality (bsqcmq) : [san] 20
[454] 5
Window length (bsqcwl) : [san] 30
[454] 20
Masked bases clip (mbc) : [san] yes
[454] yes
Gap size (mbcgs) : [san] 20
[454] 5
Max front gap (mbcmfg) : [san] 40
[454] 12
Max end gap (mbcmeg) : [san] 60
[454] 12
Lower case clip (lcc) : [san] no
[454] yes
Clip poly A/T at ends (cpat) : [san] no
[454] no
Keep poly-a signal (cpkps) : [san] no
[454] no
Minimum signal length (cpmsl) : [san] 12
[454] 12
Max errors allowed (cpmea) : [san] 1
[454] 1
Max gap from ends (cpmgfe) : [san] 9
[454] 20000
Ensure minimum left clip (emlc) : [san] yes
[454] no
Minimum left clip req. (mlcr) : [san] 25
[454] 4
Set minimum left clip to (smlc) : [san] 30
[454] 4
Ensure minimum right clip (emrc) : [san] no
[454] no
Minimum right clip req. (mrcr) : [san] 10
[454] 10
Set minimum right clip to (smrc) : [san] 20
[454] 15
Apply SKIM chimera detection clip (ascdc) : no
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : no
Bases per hash (pecbph) : 17
Handle Solexa GGCxG problem (pechsgp) : yes
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 2
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 21
Hash save stepping (hss) : 1
Percent required (pr) : [san] 70
[454] 80
Max hits per read (mhpr) : 30
Max megahub ratio (mmhr) : 0
Freq. est. min normal (fenn) : 0.4
Freq. est. max normal (fexn) : 1.6
Freq. est. repeat (fer) : 1.9
Freq. est. heavy repeat (fehr) : 8
Freq. est. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Repeat level in info file (rliif) : 6
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 4096
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[454] yes
Quick rule min len 1 (qrml1) : [san] 200
[454] 80
Quick rule min sim 1 (qrms1) : [san] 90
[454] 90
Quick rule min len 2 (qrml2) : [san] 100
[454] 60
Quick rule min sim 2 (qrms2) : [san] 95
[454] 95
Backbone quick overlap min len (bqoml) : [san] 150
[454] 80
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[454] 20
Bandwidth max (bmax) : [san] 130
[454] 80
Bandwidth min (bmin) : [san] 25
[454] 20
Minimum score (ms) : [san] 30
[454] 15
Minimum overlap (mo) : [san] 15
[454] 20
Minimum relative score in % (mrs) : [san] 70
[454] 80
Solexa_hack_max_errors (shme) : [san] 0
[454] 0
Extra gap penalty (egp) : [san] no
[454] yes
extra gap penalty level (egpl) : [san] low
[454] reject_codongaps
Max. egp in percent (megpp) : [san] 100
[454] 100
Contig parameters (-CO):
Name prefix (np) :
cleaned_2_combined
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[454] 15
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[454] 4
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[454] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[454] 25
End-read Marking Exclusion Area in bases (emea) : [san] 25
[454] 10
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[454] no
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[454] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[454] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[454] no
Merge short reads (msr) : [san] no
[454] no
Gap override ratio (gor) : [san] 66
[454] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[454] yes
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Misc (-MI):
Stop on NFS (sonfs) : yes
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 1000
Directories (-DI):
When loading EXP files :
When loading SCF files :
Top directory for writing files : cleaned_2_combined_assembly
For writing result files :
cleaned_2_combined_assembly/cleaned_2_combined_d_results
For writing result info files :
cleaned_2_combined_assembly/cleaned_2_combined_d_info
For writing log files :
cleaned_2_combined_assembly/cleaned_2_combined_d_log
Log redirected to (lrt) :
For writing checkpoint files :
cleaned_2_combined_assembly/cleaned_2_combined_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
cleaned_2_combined_in.sanger.fasta
[454]
cleaned_2_combined_in.454.fasta
When loading qualities from FASTA quality : [san]
cleaned_2_combined_in.sanger.fasta.qual
[454]
cleaned_2_combined_in.454.fasta.qual
When loading sequences from FASTQ : [san]
cleaned_2_combined_in.sanger.fastq
[454]
cleaned_2_combined_in.454.fastq
When loading project from CAF :
cleaned_2_combined_in.sanger.caf
When loading project from MAF (disabled) :
cleaned_2_combined_in.sanger.maf
When loading EXP fofn :
cleaned_2_combined_in.sanger.fofn
When loading project from PHD :
cleaned_2_combined_in.phd.1
When loading strain data :
cleaned_2_combined_straindata_in.txt
When loading XML trace info files : [san]
cleaned_2_combined_traceinfo_in.sanger.xml
[454]
cleaned_2_combined_traceinfo_in.454.xml
When loading SSAHA2 vector screen results :
cleaned_2_combined_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
cleaned_2_combined_smaltvectorscreen_in.txt
When loading backbone from MAF :
cleaned_2_combined_backbone_in.maf
When loading backbone from CAF :
cleaned_2_combined_backbone_in.caf
When loading backbone from GenBank :
cleaned_2_combined_backbone_in.gbf
When loading backbone from FASTA :
cleaned_2_combined_backbone_in.fasta
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[454] no
Save tagged singlets in project (stsip) : [san] yes
[454] yes
Remove rollover logs (rrol) : yes
Remove log directory (rld) : 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) : yes
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : no
Saved as wiggle (orw) : no
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 : cleaned_2_combined_out.caf
MAF : cleaned_2_combined_out.maf
FASTA : cleaned_2_combined_out.unpadded.fasta
FASTA quality : cleaned_2_combined_out.unpadded.fasta.qual
FASTA (padded) : cleaned_2_combined_out.padded.fasta
FASTA qual.(pad): cleaned_2_combined_out.padded.fasta.qual
GAP4 (directory): cleaned_2_combined_out.gap4da
ACE : cleaned_2_combined_out.ace
HTML : cleaned_2_combined_out.html
Simple text : cleaned_2_combined_out.txt
TCS overview : cleaned_2_combined_out.tcs
Wiggle : cleaned_2_combined_out.wig
------------------------------------------------------------------------------
Creating directory cleaned_2_combined_assembly ... done.
Creating directory
cleaned_2_combined_assembly/cleaned_2_combined_d_log ... done.
Creating directory
cleaned_2_combined_assembly/cleaned_2_combined_d_results ... done.
Creating directory
cleaned_2_combined_assembly/cleaned_2_combined_d_info ... done.
Creating directory
cleaned_2_combined_assembly/cleaned_2_combined_d_chkpt ... done.
Log directory is not on a NFS mount, good.
Localtime: Tue May 10 08:09:57 2011
Loading data (454) from FASTA files,
Localtime: Tue May 10 08:09:57 2011
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Found 1866192 sequences.
Localtime: Tue May 10 08:10:59 2011
454 will load 1866192 reads.
Longest Sanger: 0
Longest 454: 1099
Longest PacBio: 0
Longest Solexa: 0
Longest Solid: 0
Longest overall: 1099
Total reads to load: 1866192
Reserving space for reads (this may take a while)
Reserved space for 1866202 reads.
Loading data (454) from FASTA files,
Localtime: Tue May 10 08:10:59 2011
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Found 1866192 sequences.
Localtime: Tue May 10 08:12:00 2011
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Localtime: Tue May 10 08:13:40 2011
rnm size: 0
Loading quality data from FASTA quality file
cleaned_2_combined_in.454.fasta.qual:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Localtime: Tue May 10 08:17:41 2011
Done.
Loaded 1866192 reads with 1029483065 raw bases.
1866192 reads have quality accounted for.
Loaded 1866192 454 reads.
Total reads loaded: 1866192
Checking reads for trace data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
No SCF data present in any read, automatic contig editing for Sanger
data is now switched off.
1866192 reads with valid data for assembly.
Localtime: Tue May 10 08:17:46 2011
Generated 1866192 unique template ids for 1866192 valid reads.
No useful template information found, template routines will not be used.
Localtime: Tue May 10 08:17:53 2011
Generated 0 unique strain ids for 1866192 reads.
Strain "default" has 1866192 reads.
Have read pool with 1866192 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 0 1866192 0 0 0
Reads wo qual 0 0 0 0 0
Used reads 0 1866192 0 0 0
Avg tot rlen 0 551 0 0 0
Avg rlen used 0 551 0 0 0
With strain 0 0 0 0 0
W/o clips 0 1866192 0 0 0
===========================================================================
Starting clips: done.
Performing search for bad sequence quality ... done.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 0 1866192 0 0 0
Reads wo qual 0 0 0 0 0
Used reads 0 1843257 0 0 0
Avg tot rlen 0 551 0 0 0
Avg rlen used 0 301 0 0 0
With strain 0 0 0 0 0
W/o clips 0 59160 0 0 0
===========================================================================
Log directory is not on a NFS mount, good.
Localtime: Tue May 10 08:18:36 2011
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%] tcmalloc: large alloc 1607274496
bytes == 0x29c9fd000 @
done
Localtime: Tue May 10 08:22:01 2011
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%] tcmalloc: large alloc 1723363328
bytes == 0x2fd154000 @
Localtime: Tue May 10 08:29:06 2011
Hash statistics:
=========================================================
Measured avg. frequency coverage: 6
Deduced thresholds:
-------------------
Min normal cov: 2.4
Max normal cov: 9.6
Repeat cov: 11.4
Heavy cov: 48
Crazy cov: 120
Mask cov: 600
Repeat ratio histogram:
-----------------------
0 40901238
1 48998876
2 8509488
3 3303460
4 1743874
5 1046978
6 676522
7 472766
8 347306
9 265714
10 200774
11 157332
12 127002
13 103788
14 84410
15 72892
16 62040
17 53860
18 46066
19 40986
20 36016
21 33216
22 30366
23 27544
24 22930
25 22524
26 18764
27 17424
28 16546
29 15046
30 13620
31 12276
32 11462
33 10512
34 10120
35 9150
36 8588
37 7844
38 7452
39 6258
40 6076
41 5524
42 5362
43 4870
44 4726
45 4352
46 4118
47 3600
48 3282
49 3006
50 3176
51 2918
52 2680
53 2486
54 2314
55 2002
56 1894
57 2050
58 2038
59 2128
60 1650
61 1510
62 1624
63 1476
64 1560
65 1516
66 1614
67 1498
68 1374
69 1392
70 1222
71 1050
72 1086
73 1256
74 1118
75 1064
76 1180
77 1154
78 1190
79 994
80 998
81 850
82 752
83 826
84 736
85 700
86 716
87 784
88 642
89 660
90 614
91 644
92 636
93 514
94 512
95 548
96 472
97 482
98 450
99 490
100 560
101 586
102 544
103 352
104 312
105 354
106 348
107 304
108 342
109 298
110 366
111 298
112 354
113 246
114 272
115 264
116 356
117 348
118 308
119 262
120 240
121 178
122 268
123 302
124 272
125 236
126 274
127 310
128 290
129 284
130 226
131 252
132 248
133 286
134 300
135 310
136 250
137 288
138 250
139 224
140 216
141 168
142 218
143 204
144 196
145 164
146 184
147 210
148 202
149 148
150 192
151 186
152 138
153 148
154 130
155 88
156 120
157 126
158 114
159 100
160 120
161 82
162 116
163 110
164 112
165 142
166 152
167 178
168 130
169 196
170 144
171 172
172 142
173 128
174 146
175 212
176 170
177 140
178 158
179 174
180 172
181 170
182 154
183 134
184 136
185 140
186 162
187 160
188 162
189 158
190 140
191 188
192 198
193 156
194 102
195 96
196 132
197 128
198 132
199 110
200 136
201 128
202 122
203 142
204 144
205 128
206 126
207 124
208 120
209 122
210 170
211 128
212 122
213 106
214 112
215 126
216 110
217 116
218 132
219 154
220 128
221 144
222 134
223 140
224 138
225 120
226 120
227 104
228 124
229 104
230 138
231 138
232 156
233 142
234 150
235 84
236 106
237 102
238 78
239 80
240 96
241 98
242 116
243 68
244 102
245 104
246 120
247 138
248 122
249 96
250 92
251 104
252 94
253 110
254 96
255 112
256 124
257 68
258 78
259 100
260 50
261 66
262 98
263 102
264 78
265 80
266 72
267 92
268 108
269 82
270 72
271 132
272 104
273 68
274 80
275 106
276 90
277 102
278 124
279 118
280 84
281 66
282 58
283 76
284 74
285 78
286 88
287 110
288 106
289 86
290 106
291 94
292 102
293 100
294 98
295 88
296 92
297 112
298 80
299 80
300 78
301 90
302 62
303 74
304 74
305 50
306 72
307 54
308 56
309 66
310 52
311 74
312 90
313 86
314 106
315 66
316 100
317 72
318 62
319 70
320 84
321 64
322 48
323 44
324 38
325 56
326 50
327 62
328 56
329 66
330 56
331 58
332 58
333 56
334 42
335 40
336 78
337 52
338 48
339 28
340 56
341 46
342 72
343 38
344 70
345 56
346 82
347 52
348 50
349 48
350 48
351 56
352 50
353 66
354 52
355 60
356 42
357 48
358 36
359 28
360 24
361 20
362 58
363 38
364 68
365 36
366 60
367 48
368 56
369 48
370 52
371 52
372 42
373 42
374 32
375 44
376 54
377 36
378 50
379 42
380 44
381 40
382 58
383 28
384 40
385 30
386 32
387 52
388 38
389 16
390 26
391 42
392 32
393 28
394 38
395 24
396 44
397 46
398 46
399 26
400 38
401 36
402 30
403 18
404 44
405 36
406 32
407 34
408 38
409 48
410 34
411 44
412 38
413 30
414 28
415 32
416 40
417 18
418 44
419 50
420 56
421 34
422 32
423 50
424 42
425 38
426 52
427 44
428 36
429 38
430 30
431 36
432 24
433 62
434 42
435 36
436 22
437 24
438 22
439 28
440 36
441 24
442 22
443 30
444 20
445 54
446 26
447 44
448 36
449 28
450 38
451 48
452 30
453 20
454 14
455 54
456 48
457 40
458 34
459 32
460 34
461 10
462 20
463 26
464 42
465 32
466 30
467 10
468 18
469 26
470 14
471 26
472 30
473 10
474 18
475 6
476 4
477 8
478 6
479 12
480 10
481 14
482 30
483 16
484 22
485 12
486 20
487 10
488 14
489 8
490 12
491 18
492 10
493 4
494 10
495 16
496 16
497 18
498 16
499 16
500 20
501 14
502 20
503 16
504 18
505 16
506 16
507 20
508 6
509 12
510 18
511 4
512 8
513 22
514 20
515 16
516 18
517 14
518 14
519 18
520 18
521 20
522 20
523 26
524 16
525 18
526 12
527 16
528 16
529 10
530 20
531 20
532 6
533 26
534 10
535 8
536 14
537 12
538 14
539 28
540 20
541 16
542 14
543 16
544 8
545 12
546 4
547 6
548 4
549 4
550 16
551 10
552 8
553 14
554 4
555 16
556 10
557 28
558 20
559 10
560 4
561 4
562 10
563 8
564 8
565 12
566 8
567 12
568 24
569 12
570 12
571 12
572 12
573 22
574 20
575 16
576 22
577 8
578 2
579 14
580 12
581 10
582 16
583 14
584 8
585 16
586 14
587 14
588 14
589 16
590 10
591 6
593 10
594 8
595 12
596 22
597 18
598 14
599 22
600 16
601 18
602 16
603 26
604 18
605 28
606 20
607 30
608 18
609 36
610 10
611 32
612 16
613 20
614 34
615 18
616 18
617 8
618 22
619 14
620 24
621 20
622 16
623 8
624 12
625 14
626 10
627 26
628 24
629 30
630 24
631 32
632 26
633 22
634 24
635 20
636 8
637 24
638 16
639 16
640 18
641 26
642 14
643 26
644 14
645 16
646 12
647 4
648 4
649 20
650 20
651 14
652 18
653 10
654 16
655 10
656 8
657 12
658 14
659 14
660 8
661 4
662 16
663 10
664 16
665 12
666 2
667 14
668 4
669 8
670 16
671 12
672 10
673 10
674 22
675 10
676 10
677 18
678 12
679 8
680 14
681 16
682 8
683 16
684 18
685 14
686 26
687 20
688 20
689 12
690 18
691 16
692 12
693 22
694 16
695 14
696 10
697 12
698 12
699 22
700 10
701 18
702 4
703 12
704 14
705 6
706 4
707 12
708 4
709 16
710 12
711 10
712 16
713 14
714 14
715 4
716 8
717 14
718 2
719 12
720 2
721 14
722 4
723 6
724 8
725 4
726 16
727 12
728 12
729 10
730 16
731 18
732 4
733 14
734 12
735 8
736 12
737 14
738 8
739 4
740 4
741 14
742 20
743 18
744 10
745 12
746 20
747 18
748 10
749 22
750 18
751 10
752 24
753 10
754 10
755 12
756 16
757 28
758 14
759 4
760 14
761 8
762 6
763 14
764 6
765 12
766 8
767 14
768 12
769 8
770 6
771 6
772 10
773 2
774 8
775 8
776 10
777 8
778 24
779 16
780 14
781 30
782 16
783 10
784 16
785 14
786 6
787 8
788 16
789 16
790 10
791 10
792 4
793 10
794 6
795 6
796 8
797 4
798 8
799 2
800 8
801 10
802 8
803 14
804 4
805 6
806 10
807 12
808 6
810 16
811 12
812 6
813 12
814 12
815 14
816 16
817 8
818 4
819 8
820 6
821 8
822 6
823 10
824 2
826 2
827 16
828 12
829 4
830 4
831 10
832 6
833 12
834 8
835 6
836 8
837 6
839 6
840 12
841 4
842 8
843 2
844 12
846 4
847 6
848 4
849 4
855 2
856 4
857 8
858 18
859 4
860 10
861 2
862 4
863 4
864 2
865 2
866 2
867 4
868 6
869 8
870 2
871 6
872 4
873 6
874 6
875 4
876 6
877 4
878 4
879 6
880 8
881 2
883 6
884 6
885 2
886 2
888 4
889 8
890 8
891 6
892 12
893 6
894 10
895 4
896 8
898 2
899 6
900 10
901 14
902 10
903 4
904 10
905 14
906 2
907 4
908 4
909 10
910 4
911 6
912 2
913 4
914 2
915 8
916 6
917 14
918 2
919 4
920 4
921 6
922 8
923 6
924 12
925 8
926 12
927 12
928 18
929 12
930 8
931 6
932 6
933 12
934 8
935 8
936 4
937 8
938 6
940 8
941 4
943 6
944 10
945 10
946 8
947 6
948 4
949 12
950 14
951 10
952 10
953 6
954 10
955 8
956 6
957 4
959 4
960 4
961 10
962 4
963 12
964 12
965 4
966 10
967 4
968 6
969 4
970 4
971 4
972 4
973 10
974 2
975 2
976 8
977 6
978 10
979 8
980 2
981 12
983 16
984 2
985 4
986 4
987 4
988 8
989 6
990 4
991 14
992 4
993 6
994 12
995 10
996 8
997 4
998 4
999 4
1000 10
1001 6
1002 8
1003 16
1004 10
1005 10
1006 4
1007 8
1008 8
1009 12
1010 12
1011 4
1012 6
1013 6
1014 8
1015 10
1016 12
1017 4
1018 8
1019 8
1020 8
1021 6
1022 4
1024 2
1025 4
1026 8
1027 4
1028 10
1029 10
1030 8
1031 4
1032 4
1033 14
1034 10
1035 8
1036 8
1037 26
1038 16
1039 8
1040 14
1041 6
1042 6
1043 4
1044 4
1045 14
1046 8
1047 14
1048 12
1049 4
1050 8
1051 14
1052 6
1053 8
1054 6
1055 14
1056 6
1057 6
1058 12
1059 6
1061 16
1062 2
1063 6
1064 8
1065 12
1066 6
1067 6
1068 8
1069 14
1070 6
1071 12
1072 8
1073 8
1074 2
1075 8
1076 8
1077 2
1078 4
1079 4
1080 14
1082 8
1083 2
1084 10
1085 4
1086 10
1087 8
1088 8
1089 8
1090 8
1091 2
1092 10
1093 8
1094 10
1095 4
1096 6
1097 6
1098 6
1100 2
1101 8
1102 10
1103 6
1104 2
1105 2
1107 2
1108 4
1109 2
1110 2
1111 2
1112 10
1113 4
1114 2
1115 2
1116 4
1117 2
1118 4
1119 2
1120 4
1121 4
1122 10
1123 10
1124 6
1125 4
1126 8
1127 6
1128 4
1129 6
1130 6
1131 4
1132 4
1133 2
1134 8
1135 4
1136 4
1137 2
1138 2
1139 2
1140 4
1141 8
1142 2
1143 2
1144 2
1145 6
1147 6
1148 8
1149 4
1150 8
1151 6
1152 8
1154 2
1155 2
1156 2
1157 4
1158 4
1159 10
1160 12
1161 4
1162 6
1163 4
1164 2
1165 4
1166 4
1168 4
1170 6
1171 4
1172 6
1173 2
1174 6
1176 2
1177 4
1178 14
1179 8
1180 2
1181 8
1182 6
1183 8
1185 2
1186 10
1187 8
1188 8
1189 6
1190 4
1191 6
1192 8
1193 18
1194 4
1195 6
1196 14
1197 6
1198 4
1199 8
1200 2
1201 2
1202 6
1203 4
1206 6
1210 4
1211 6
1212 2
1213 8
1214 6
1215 2
1217 4
1218 4
1219 12
1220 6
1221 6
1222 6
1223 12
1224 6
1225 4
1226 8
1227 10
1228 8
1229 4
1230 12
1231 4
1233 14
1234 8
1236 8
1237 6
1240 8
1241 8
1242 4
1243 2
1244 12
1245 2
1246 6
1247 10
1248 4
1249 2
1250 8
1251 8
1253 2
1255 4
1257 4
1258 2
1259 2
1260 4
1261 2
1262 10
1263 6
1264 2
1265 10
1266 6
1267 8
1268 6
1269 4
1271 8
1272 2
1273 2
1274 4
1275 8
1276 2
1277 8
1278 4
1279 12
1280 8
1281 2
1282 6
1283 2
1284 6
1285 4
1286 10
1287 2
1288 8
1289 6
1290 8
1291 2
1292 2
1293 8
1294 4
1295 4
1296 4
1297 4
1298 2
1299 2
1300 6
1301 6
1302 4
1303 8
1304 4
1305 2
1306 4
1308 6
1309 4
1310 8
1311 2
1312 8
1313 4
1314 8
1315 10
1316 14
1317 10
1318 6
1319 6
1320 6
1321 10
1322 4
1323 8
1324 2
1325 6
1326 4
1328 4
1329 2
1330 2
1331 2
1332 2
1333 6
1334 4
1335 2
1336 2
1337 2
1338 2
1340 4
1343 2
1345 2
1346 2
1350 6
1352 2
1353 4
1354 6
1355 4
1356 10
1357 2
1359 2
1360 2
1362 2
1364 8
1365 2
1368 6
1369 2
1371 2
1373 2
1374 4
1375 2
1376 6
1377 2
1378 2
1380 4
1381 4
1382 6
1383 10
1384 8
1385 6
1386 4
1387 4
1388 8
1389 8
1390 2
1391 2
1392 2
1393 4
1394 6
1395 4
1396 4
1397 4
1398 4
1399 4
1400 2
1401 2
1404 4
1405 4
1406 4
1408 2
1409 4
1413 4
1414 4
1415 2
1416 2
1418 2
1420 2
1423 2
1425 4
1426 2
1427 8
1428 2
1429 4
1432 2
1433 2
1434 6
1436 2
1437 4
1438 2
1439 2
1441 2
1443 2
1445 2
1447 2
1450 2
1454 2
1457 2
1458 2
1459 2
1460 2
1461 2
1464 2
1465 8
1466 4
1468 6
1469 2
1470 4
1471 2
1472 2
1473 2
1475 2
1477 8
1479 2
1480 2
1481 8
1483 6
1484 2
1485 2
1486 2
1487 4
1488 2
1489 2
1490 2
1492 2
1493 4
1494 2
1495 2
1496 4
1497 4
1501 2
1505 2
1508 2
1511 2
1512 4
1513 2
1515 2
1519 2
1520 2
1521 2
1522 6
1523 4
1524 2
1525 2
1527 4
1529 4
1535 8
1538 2
1539 2
1542 2
1543 2
1544 4
1545 6
1546 2
1547 2
1548 2
1549 2
1550 2
1551 2
1555 2
1556 2
1557 2
1558 4
1560 2
1561 2
1562 2
1563 4
1565 8
1568 6
1569 2
1570 2
1571 8
1572 2
1576 4
1578 2
1579 2
1580 2
1581 2
1582 2
1584 4
1586 2
1588 6
1590 2
1593 2
1597 4
1600 2
1601 2
1603 2
1610 2
1614 2
1619 2
1622 2
1624 4
1625 2
1638 4
1642 2
1643 2
1645 2
1651 2
1653 2
1654 2
1655 2
1658 2
1659 4
1660 2
1663 6
1665 6
1668 2
1670 2
1671 2
1677 2
1679 4
1686 2
1690 4
1693 4
1695 2
1698 2
1701 2
1702 4
1704 2
1714 2
1725 2
1726 2
1728 2
1732 2
1737 2
1740 2
1741 2
1742 2
1743 2
1744 4
1745 2
1746 6
1747 8
1748 6
1749 4
1750 6
1751 2
1752 4
1753 2
1754 4
1755 4
1756 2
1757 6
1758 8
1759 2
1760 4
1761 4
1763 2
1765 2
1766 2
1767 2
1770 6
1771 2
1772 2
1773 4
1776 2
1777 2
1781 2
1782 4
1786 2
1787 2
1788 6
1789 2
1790 4
1792 2
1795 8
1796 2
1797 2
1798 4
1802 6
1803 2
1807 2
1808 2
1810 2
1812 4
1813 4
1814 2
1815 4
1816 10
1817 2
1818 2
1820 2
1821 6
1822 2
1825 2
1828 4
1829 4
1833 4
1836 2
1837 2
1838 4
1839 10
1840 2
1843 4
1845 2
1847 2
1848 4
1849 12
1850 6
1851 4
1853 6
1854 6
1855 2
1857 6
1858 6
1859 2
1860 2
1861 2
1862 2
1863 2
1864 2
1865 2
1867 6
1868 2
1872 2
1873 2
1874 2
1875 6
1876 2
1878 4
1879 4
1880 4
1881 4
1882 4
1883 4
1886 2
1889 2
1890 2
1891 4
1893 6
1894 2
1896 2
1898 2
1900 2
1901 4
1904 2
1906 2
1909 2
1911 4
1912 2
1916 6
1918 2
1919 4
1920 2
1921 2
1922 2
1925 2
1926 6
1927 2
1929 4
1931 6
1932 2
1933 2
1934 2
1935 8
1936 2
1937 2
1938 4
1939 2
1940 4
1942 2
1944 2
1947 2
1949 2
1951 2
1953 4
1956 4
1957 6
1959 2
1960 4
1965 2
1967 2
1968 2
1969 2
1970 2
1971 2
1974 2
1976 2
1978 2
1982 4
1983 2
1984 2
1985 2
1987 2
1988 2
1989 2
1991 2
1992 4
1993 4
1994 2
1995 4
1997 4
1998 4
1999 4
2000 4
2001 4
2002 2
2003 2
2004 2
2005 2
2006 2
2007 6
2010 2
2012 4
2013 4
2014 6
2017 2
2022 4
2026 2
2027 4
2028 2
2029 2
2030 2
2031 2
2034 2
2035 2
2036 2
2037 4
2038 2
2041 4
2042 8
2043 2
2044 2
2045 2
2047 4
2048 4
2049 10
2050 2
2051 4
2052 2
2053 4
2054 2
2055 4
2056 2
2057 4
2058 2
2059 6
2061 2
2062 4
2064 2
2067 2
2070 2
2075 4
2078 2
2083 2
2087 2
2104 2
2105 4
2108 2
2120 2
2141 4
2149 2
2151 2
2155 2
2159 2
2177 2
2184 2
2189 2
2190 2
2192 2
2193 4
2194 4
2196 2
2197 2
2198 2
2201 2
2202 2
2204 2
2211 2
2215 2
2217 2
2226 2
2227 2
2230 2
2233 2
2241 2
2249 2
2265 2
2266 2
=========================================================
Assigning statistics values:
Localtime: Tue May 10 08:30:27 2011
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Localtime: Tue May 10 08:38:43 2011
clean up temporary stat files...Localtime: Tue May 10 08:39:18 2011
Writing read repeat info to:
cleaned_2_combined_assembly/cleaned_2_combined_d_info/cleaned_2_combined_info_readrepeats.lst
... 235758 sequences with 436089 masked stretches.
Localtime: Tue May 10 08:39:23 2011
Searching for possible overlaps:
Localtime: Tue May 10 08:39:23 2011
Now running threaded and partitioned skimmer with 38 partitions in 2 threads:
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 66003152 kB
MemFree: 40817652 kB
Buffers: 162996 kB
Cached: 8683844 kB
SwapCached: 0 kB
Active: 22936340 kB
Inactive: 792228 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 66003152 kB
LowFree: 40817652 kB
SwapTotal: 1052248 kB
SwapFree: 1052248 kB
Dirty: 2236 kB
Writeback: 0 kB
AnonPages: 14881612 kB
Mapped: 19224 kB
Slab: 1371068 kB
PageTables: 34784 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 34053824 kB
Committed_AS: 15133900 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 1944 kB
VmallocChunk: 34359736395 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 78%
Tgid: 15755
Pid: 15755
PPid: 15753
TracerPid: 0
Uid: 1087 1087 1087 1087
Gid: 1090 1090 1090 1090
FDSize: 256
Groups: 1065 1090
VmPeak: 14138820 kB
VmSize: 14136772 kB
VmLck: 0 kB
VmHWM: 14100196 kB
VmRSS: 14098940 kB
VmData: 14131924 kB
VmStk: 84 kB
VmExe: 4728 kB
VmLib: 0 kB
VmPTE: 27580 kB
StaBrk: 05a06000 kB
Brk: 36405b000 kB
StaStk: 7fffb2d660e0 kB
Threads: 1
SigQ: 0/532480
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,0000ffff
Mems_allowed: 00000000,000000ff
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 1866192 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 9785362448 (9.1 GiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 1866192 7 MiB 0 B 0 B
AS_skim_edges: 0 24 B 0 B 0 B
AS_adsfacts: 0 24 B 0 B 0 B
AS_confirmed_edges: 0 24 B 0 B 0 B
AS_permanent_overlap_bans: 0 85 MiB 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: 1866192 7 MiB 0 B 0 B
AS_clipright: 1866192 7 MiB 0 B 0 B
AS_used_ids: 1866192 2 MiB 0 B 0 B
AS_multicopies: 0 2 MiB 2 MiB 0 B
AS_hasmcoverlaps: 0 2 MiB 2 MiB 0 B
AS_maxcoveragereached: 1866192 7 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 1866192 2 MiB 0 B 0 B
AS_isdebris: 1866192 2 MiB 0 B 0 B
AS_needalloverlaps: 1866192 2 MiB 48 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 7 MiB 7 MiB 0 B
AS_probablermbsnotok: 0 7 MiB 7 MiB 0 B
AS_weakrmbsnotok: 0 7 MiB 7 MiB 0 B
AS_readmaytakeskim: 0 40 B 0 B 0 B
AS_skimstaken: 0 40 B 0 B 0 B
AS_numskimoverlaps: 0 24 B 0 B 0 B
AS_numleftextendskims: 0 24 B 0 B 0 B
AS_rightextendskims: 0 24 B 0 B 0 B
AS_skimleftextendratio: 0 24 B 0 B 0 B
AS_skimrightextendratio: 0 24 B 0 B 0 B
AS_usedlogfiles: 8 272 B 0 B 0 B
Total: 9938391272 (9.3 GiB)
================================================================================
Dynamic allocs: 0
Align allocs: 0
A 'standard' exception occured (that's NOT normal):
boost::thread_resource_error
If the cause is not immediatly obvious, please contact: bach@xxxxxxxxxxxx
For general help, you will probably get a quicker response on the
MIRA talk mailing list
than if you mailed the author directly.
To report bugs or ask for features, please use the new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.
Thank you,
Vladimir
--
Vladimir Mashanov, PhD
Universidad de Puerto Rico
Faculdad de Ciencias Naturales
Departamento de Biologia
JGD Building, #220
PO Box 70377, UPR Station
Rio Piedras, PR 00936-8377
email: mashanovvlad@xxxxxxxxxxxxxx;
vladimir.mashanov@xxxxxxxxx
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