Banana Slug Genomics

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./DiscovarDeNovo READS=frac:0.01::/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam+frac:0.01::/scratch/bananaSlugBAMS/SW019_S1_L001_001.


bam+frac:0.01:://scratch/bananaSlugBAMS/SW019_S2_L008_001.bam OUT_DIR=/soe/ceisenhart/discoOutput/


Performing re-exec to adjust stack size.





--------------------------------------------------------------------------------


Sat Apr 25 18:46:06 2015 run on edser2, pid=3465  [Apr 10 2015 12:24:57 R52415 ]


DiscovarDeNovo                                                                 \


               READS=frac:0.01::/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam+ \


               frac:0.01::/scratch/bananaSlugBAMS/SW019_S1_L001_001.bam+frac:0 \


               .01:://scratch/bananaSlugBAMS/SW019_S2_L008_001.bam             \


               OUT_DIR=/soe/ceisenhart/discoOutput/


--------------------------------------------------------------------------------





SYSTEM INFO


- OS: Linux :: 3.5.0-54-generic :: #81~precise1-Ubuntu SMP Tue Jul 15 04:02:22 UTC 2014


- node name: edser2


- hardware type: x86_64


- cache size: 30720 KB


- cpu MHz: 2699.924


- cpu model name: Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz


- physical memory: 314.88 GB





Omitting memory check.  If you run into problems with memory,


you might try rerunning with MEMORY_CHECK=True.





Sat Apr 25 18:46:06 2015: finding input files


Sat Apr 25 18:46:06 2015: reading 3 files (which may take a while)


Sat Apr 25 18:46:06 2015: processing /scratch/bananaSlugBAMS/SW018_S1_L007_001.bam.


Sat Apr 25 18:46:06 2015: memory in use = 0.01 GB, peak = 0.01 GB


Sat Apr 25 19:22:06 2015: there are 2,860,386 reads of mean length 100


Sat Apr 25 19:22:06 2015: memory in use = 42.71 GB, peak = 43.92 GB


Sat Apr 25 19:23:14 2015: reads sorted


Sat Apr 25 19:23:14 2015: memory in use = 43.78 GB, peak = 43.92 GB


Sat Apr 25 19:24:46 2015: data stashed in output structures


Sat Apr 25 19:24:46 2015: memory in use = 0.28 GB, peak = 43.92 GB


Sat Apr 25 19:24:46 2015: processing /scratch/bananaSlugBAMS/SW019_S1_L001_001.bam.


Sat Apr 25 19:24:46 2015: memory in use = 0.28 GB, peak = 43.92 GB


Sat Apr 25 19:57:41 2015: there are 545,374 reads of mean length 301


Sat Apr 25 19:57:41 2015: memory in use = 15.78 GB, peak = 43.92 GB


Sat Apr 25 19:57:54 2015: reads sorted


Sat Apr 25 19:57:54 2015: memory in use = 15.98 GB, peak = 43.92 GB


Sat Apr 25 19:58:26 2015: data stashed in output structures


Sat Apr 25 19:58:26 2015: memory in use = 0.40 GB, peak = 43.92 GB


Sat Apr 25 19:58:26 2015: processing //scratch/bananaSlugBAMS/SW019_S2_L008_001.bam.


Sat Apr 25 19:58:26 2015: memory in use = 0.40 GB, peak = 43.92 GB


Sat Apr 25 20:22:28 2015: there are 1,972,723 reads of mean length 100


Sat Apr 25 20:22:28 2015: memory in use = 30.00 GB, peak = 43.92 GB


INPUT FILES:


[1,type=frag,sample=C,lib=1,frac=0.01]  /scratch/bananaSlugBAMS/SW018_S1_L007_001.bam


[2,type=frag,sample=C,lib=1,frac=0.01]  /scratch/bananaSlugBAMS/SW019_S1_L001_001.bam


[3,type=frag,sample=C,lib=1,frac=0.01]  //scratch/bananaSlugBAMS/SW019_S2_L008_001.bam





Sat Apr 25 20:24:12 2015: found 1 samples


Sat Apr 25 20:24:12 2015: starts = 0


Sat Apr 25 20:24:32 2015: using 5,378,484 reads


Sat Apr 25 20:24:32 2015: data extraction complete


1.64 hours used extracting reads


Sat Apr 25 20:26:02 2015: see total physical memory of 338,094,714,880 bytes


Sat Apr 25 20:26:02 2015: 526.57 bytes per read base, assuming max memory available


We need 1 passes.


Expect 274626 keys per batch.


Provide 610280 keys per batch.


We need 1 passes.


Expect 274626 keys per batch.


Provide 610280 keys per batch.


Warning: HashSet initial size too small.


Sat Apr 25 20:28:30 2015: back from buildReadQGraph


memory in use = 963,534,848


checksum_60 = 1766450764945282


Sat Apr 25 20:28:32 2015: constructing places


Sat Apr 25 20:28:33 2015: sorting places


Sat Apr 25 20:28:38 2015: building all


Sat Apr 25 20:28:41 2015: calling LongReadsToPaths


Sat Apr 25 20:28:46 2015: writing


Sat Apr 25 20:28:48 2015: translating paths


Sat Apr 25 20:28:48 2015: final stage of path translation


Sat Apr 25 20:29:00 2015: writing paths


2.03 seconds used reloading assembly


Sat Apr 25 20:29:09 2015: start walking


memory in use = 769,753,088


Sat Apr 25 20:29:10 2015: start walking


memory in use = 777,170,944


2.91 seconds used cleaning 200-mer graph


3.22 minutes used in ReadQGrapher


6.91e-06 seconds used reloading reads


checksum_200 = 77403320489521


1 peak mem usage = 43.92 GB


1.85 seconds used loading stuff


2 peak mem usage = 43.92 GB


launching gap assemblies, mem usage = 773,767,168


Sat Apr 25 20:29:18 2015: finding unsatisfieds


Sat Apr 25 20:29:18 2015: creating multiplicity map


Sat Apr 25 20:29:18 2015: economizing links


Sat Apr 25 20:29:18 2015: forming neighborhoods


Sat Apr 25 20:29:18 2015: forming initial clusters


Sat Apr 25 20:29:18 2015: start sort


0.0367 seconds used sorting


Sat Apr 25 20:29:18 2015: merging clusters


xs.size( ) = 3277


1.42 seconds used merging


xs.size( ) = 616


Sat Apr 25 20:29:19 2015: start overlap-based merging


Sat Apr 25 20:29:20 2015: start overlap-based merging


LR.size( ) = 606


LR.size( ) = 303


Sat Apr 25 20:29:21 2015: now processing 303 blobs


Sat Apr 25 20:29:21 2015: memory in use = 0.73 GB, peak = 43.92 GB


.......... .......... .......... .......... ..........


.......... .......... .......... .......... ..........


34.6 seconds spent in local assemblies, memory in use = 0.76 GB, peak = 43.92 GB


Sat Apr 25 20:29:56 2015: patch reserving space


Sat Apr 25 20:29:56 2015: memory in use = 0.76 GB


0.0911 seconds used patching, peak mem usage = 43.92 GB


new_stuff.size( ) = 3488


Sat Apr 25 20:29:56 2015: building hb2


0.185 seconds used in new stuff 1 test


memory in use now = 822,546,432


Sat Apr 25 20:30:02 2015: back from buildBigKHBVFromReads


6.06 seconds used in new stuff 2 test


peak mem usage = 43.92 GB


0.841 seconds used in new stuff 5


Sat Apr 25 20:30:04 2015: finding interesting reads


Sat Apr 25 20:30:04 2015: memory in use = 0.74 GB, peak = 43.92 GB


Sat Apr 25 20:30:06 2015: building dictionary


Sat Apr 25 20:30:06 2015: memory in use = 0.74 GB, peak = 43.92 GB


Sat Apr 25 20:30:06 2015: reducing


Sat Apr 25 20:30:06 2015: memory in use = 0.92 GB, peak = 43.92 GB


We need 1 passes.


Expect 1429 keys per batch.


Provide 100000 keys per batch.


Sat Apr 25 20:30:09 2015: kmerizing


Sat Apr 25 20:30:09 2015: memory in use = 0.93 GB, peak = 43.92 GB


We need 1 passes.


Expect 2945 keys per batch.


Provide 100000 keys per batch.


Sat Apr 25 20:30:12 2015: cleaning


Sat Apr 25 20:30:12 2015: memory in use = 0.93 GB, peak = 43.92 GB


Sat Apr 25 20:30:12 2015: finding uniquely aligning edges


Sat Apr 25 20:30:12 2015: memory in use = 0.93 GB, peak = 43.92 GB


17.1 seconds used in new phase


hb.N( ) = 41338, hb.EdgeObjectCount( ) = 28850


122 paths improved by rerouting


Sum(invalid) = 49, npids = 2689242


10 edges tamped down


Sat Apr 25 20:30:19 2015: checking involution


Sat Apr 25 20:30:19 2015: done


WARNING: 4 suspicious read-paths.


Sum(invalid) = 34, npids = 2689242


12 edges tamped down


Sat Apr 25 20:30:26 2015: making paths index for pull apart


Sat Apr 25 20:30:27 2015: pulling apart repeats


0.00239 seconds used separating paths 1


0.183 seconds used in fixing mToLeft, mToRight, and mEdgeToPathIds


Sat Apr 25 20:30:27 2015: there were 14 repeats pulled apart.


Sat Apr 25 20:30:27 2015: there were 371 read paths removed during separation.


Sat Apr 25 20:30:27 2015: improving paths


Sat Apr 25 20:30:34 2015: done


4349 paths extended


Sat Apr 25 20:30:38 2015: start degloop


Sat Apr 25 20:30:38 2015: creating path index


Sat Apr 25 20:30:39 2015: starting loop


Sat Apr 25 20:30:39 2015: degloop complete


Sat Apr 25 20:30:40 2015: unwinding three-edge plasmids


Sat Apr 25 20:30:40 2015: removing small components


Sat Apr 25 20:30:43 2015: writing a.fin files


Sat Apr 25 20:30:48 2015: determining candidates


CN fraction good = 0.33


Sat Apr 25 20:30:49 2015: deleting 0 gaps and adding 0 gaps to force symmetry


Sat Apr 25 20:30:50 2015: done making gaps, time used = 1.78 seconds


Sat Apr 25 20:30:52 2015: determining candidates


0.0209 seconds using setting up final fasta


0.0553 seconds using printing final fasta





====================================================================================





assembly has 2558 edges of mean length 151.654


contig line N50: 2,622


scaffold line N50: 2,622


total bases in 1 kb+ scaffolds: 75,233


total bases in 10 kb+ scaffolds: 10,572


There are 5,378,484 reads of mean length 119.4 and mean base quality 35.3.


MPL1 = mean length of first read in pair up to first error = 2


(normal range is 175-225 for 250 base reads)


Estimated chimera rate in read pairs (including mismapping) = 0.84%.


genomic read coverage, using 1 kb+ scaffolds for genome size estimate: 8534.3





run started Sat Apr 25 18:46:06 2015, completed Sat Apr 25 20:30:57 2015


peak mem usage = 43.92 GB, total time = 1.75 hours


final checksum = 1246515992559





DiscovarDeNovo READS=frac:0.01::/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam+frac:0.01::/scratch/bananaSlugBAMS/SW019_S1_L001_001.bam+frac:0.01:://scratch/bananaSlugBAMS/SW019_S2_L008_001.bam OUT_DIR=/soe/ceisenhart/discoOutput/





Sat Apr 25 20:30:57 2015: done
Banana Slug Genomics

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