Banana Slug Genomics

./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/

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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

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