Banana Slug Genomics

edser2:~> ./DiscovarDeNovo READS=“frac:0.05,sample:18H::/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam+frac:0.05,sample:19M::/sc

ratch/bananaSlugBAMS/SW019_S1_L001_001.bam+frac:0.05,sample:19H::/scratch/bananaSlugBAMS/SW019_S2_L008_001.bam” OUT_DIR=/scratc

h/bananaSlugAssemblies

Performing re-exec to adjust stack size.

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Mon Apr 27 19:16:20 2015 run on edser2, pid=21615 [Apr 10 2015 12:24:57 R52415 ]

DiscovarDeNovo \

             READS="frac:0.05,sample:18H::/scratch/bananaSlugBAMS/SW018_S1_L \

             007_001.bam+frac:0.05,sample:19M::/scratch/bananaSlugBAMS/SW019 \

             _S1_L001_001.bam+frac:0.05,sample:19H::/scratch/bananaSlugBAMS/ \

             SW019_S2_L008_001.bam" OUT_DIR=/scratch/bananaSlugAssemblies

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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.

Mon Apr 27 19:16:20 2015: finding input files

Mon Apr 27 19:16:20 2015: reading 3 files (which may take a while)

Mon Apr 27 19:16:20 2015: processing /scratch/bananaSlugBAMS/SW018_S1_L007_001.bam.

Mon Apr 27 19:16:20 2015: memory in use = 0.01 GB, peak = 0.01 GB

Mon Apr 27 19:40:42 2015: there are 14,301,934 reads of mean length 100

Mon Apr 27 19:40:42 2015: memory in use = 42.71 GB, peak = 43.92 GB

Mon Apr 27 19:41:21 2015: reads sorted

Mon Apr 27 19:41:21 2015: memory in use = 43.78 GB, peak = 43.92 GB

Mon Apr 27 19:43:16 2015: data stashed in output structures

Mon Apr 27 19:43:16 2015: memory in use = 1.33 GB, peak = 43.92 GB

Mon Apr 27 19:43:16 2015: processing /scratch/bananaSlugBAMS/SW019_S1_L001_001.bam.

Mon Apr 27 19:43:16 2015: memory in use = 1.33 GB, peak = 43.92 GB

Mon Apr 27 20:02:13 2015: there are 2,726,872 reads of mean length 301

Mon Apr 27 20:02:13 2015: memory in use = 17.50 GB, peak = 43.92 GB

Mon Apr 27 20:02:19 2015: reads sorted

Mon Apr 27 20:02:20 2015: memory in use = 17.70 GB, peak = 43.92 GB

Mon Apr 27 20:02:59 2015: data stashed in output structures

Mon Apr 27 20:02:59 2015: memory in use = 1.94 GB, peak = 43.92 GB

Mon Apr 27 20:02:59 2015: processing /scratch/bananaSlugBAMS/SW019_S2_L008_001.bam.

Mon Apr 27 20:02:59 2015: memory in use = 1.94 GB, peak = 43.92 GB

Mon Apr 27 20:18:24 2015: there are 9,863,615 reads of mean length 100

Mon Apr 27 20:18:24 2015: memory in use = 31.60 GB, peak = 43.92 GB

Mon Apr 27 20:18:49 2015: reads sorted

Mon Apr 27 20:18:49 2015: memory in use = 32.34 GB, peak = 43.92 GB

Mon Apr 27 20:20:10 2015: data stashed in output structures

Mon Apr 27 20:20:10 2015: memory in use = 2.84 GB, peak = 43.92 GB

INPUT FILES:

[1,type=frag,sample=18H,lib=1,frac=0.05] /scratch/bananaSlugBAMS/SW018_S1_L007_001.bam

[2,type=frag,sample=19M,lib=1,frac=0.05] /scratch/bananaSlugBAMS/SW019_S1_L001_001.bam

[3,type=frag,sample=19H,lib=1,frac=0.05] /scratch/bananaSlugBAMS/SW019_S2_L008_001.bam

Mon Apr 27 20:20:10 2015: found 3 samples

Mon Apr 27 20:20:10 2015: starts = 0,14301934,17028806

Mon Apr 27 20:20:59 2015: using 26,892,422 reads

Mon Apr 27 20:20:59 2015: data extraction complete

1.08 hours used extracting reads

Mon Apr 27 20:21:00 2015: see total physical memory of 338,094,714,880 bytes

Mon Apr 27 20:21:00 2015: 104.30 bytes per read base, assuming max memory available

We need 1 passes.

Expect 1374449 keys per batch.

Provide 3054330 keys per batch.

We need 1 passes.

Expect 1374449 keys per batch.

Provide 3054330 keys per batch.

Mon Apr 27 20:31:03 2015: back from buildReadQGraph

memory in use = 5,837,869,056

checksum_60 = 228984253420209548

Mon Apr 27 20:31:25 2015: constructing places

Mon Apr 27 20:31:31 2015: sorting places

Mon Apr 27 20:32:32 2015: building all

Mon Apr 27 20:33:11 2015: calling LongReadsToPaths

Mon Apr 27 20:33:34 2015: writing

Mon Apr 27 20:33:37 2015: translating paths

Mon Apr 27 20:33:41 2015: final stage of path translation

Mon Apr 27 20:37:46 2015: writing paths

4.51 seconds used reloading assembly

Mon Apr 27 20:38:32 2015: start walking

memory in use = 3,881,275,392

Mon Apr 27 20:38:44 2015: start walking

memory in use = 3,905,556,480

21.1 seconds used cleaning 200-mer graph

18.1 minutes used in ReadQGrapher

5.01e-06 seconds used reloading reads

checksum_200 = 2464942371563220

1 peak mem usage = 78.10 GB

4.52 seconds used loading stuff

2 peak mem usage = 78.10 GB

launching gap assemblies, mem usage = 3,768,946,688

Mon Apr 27 20:39:15 2015: finding unsatisfieds

Mon Apr 27 20:39:16 2015: creating multiplicity map

Mon Apr 27 20:39:16 2015: economizing links

Mon Apr 27 20:39:16 2015: forming neighborhoods

Mon Apr 27 20:39:16 2015: forming initial clusters

Mon Apr 27 20:39:16 2015: start sort

0.0509 seconds used sorting

Mon Apr 27 20:39:16 2015: merging clusters

xs.size( ) = 33377

2.92 seconds used merging

xs.size( ) = 5156

Mon Apr 27 20:39:19 2015: start overlap-based merging

Mon Apr 27 20:39:20 2015: start overlap-based merging

LR.size( ) = 4784

LR.size( ) = 2404

Mon Apr 27 20:39:25 2015: now processing 2404 blobs

Mon Apr 27 20:39:25 2015: memory in use = 3.55 GB, peak = 78.10 GB

………. ………. ………. ………. ……….

………. ………. ………. ………. ……….

4.13 minutes spent in local assemblies, memory in use = 3.64 GB, peak = 78.10 GB

Mon Apr 27 20:43:33 2015: patch reserving space

Mon Apr 27 20:43:33 2015: memory in use = 3.64 GB

0.159 seconds used patching, peak mem usage = 78.10 GB

new_stuff.size( ) = 25139

Mon Apr 27 20:43:35 2015: building hb2

1.57 seconds used in new stuff 1 test

memory in use now = 3,913,150,464

Mon Apr 27 20:44:02 2015: back from buildBigKHBVFromReads

26.4 seconds used in new stuff 2 test

peak mem usage = 78.10 GB

4.07 seconds used in new stuff 5

Mon Apr 27 20:44:09 2015: finding interesting reads

Mon Apr 27 20:44:09 2015: memory in use = 3.61 GB, peak = 78.10 GB

Mon Apr 27 20:44:18 2015: building dictionary

Mon Apr 27 20:44:18 2015: memory in use = 3.61 GB, peak = 78.10 GB

Mon Apr 27 20:44:22 2015: reducing

Mon Apr 27 20:44:22 2015: memory in use = 5.10 GB, peak = 78.10 GB

We need 1 passes.

Expect 12921 keys per batch.

Provide 100000 keys per batch.

Mon Apr 27 20:44:28 2015: kmerizing

Mon Apr 27 20:44:28 2015: memory in use = 5.21 GB, peak = 78.10 GB

We need 1 passes.

Expect 25094 keys per batch.

Provide 100000 keys per batch.

Mon Apr 27 20:44:32 2015: cleaning

Mon Apr 27 20:44:32 2015: memory in use = 5.21 GB, peak = 78.10 GB

Mon Apr 27 20:44:35 2015: finding uniquely aligning edges

Mon Apr 27 20:44:35 2015: memory in use = 5.21 GB, peak = 78.10 GB

1.1 minutes used in new phase

hb.N( ) = 369790, hb.EdgeObjectCount( ) = 246052

945 paths improved by rerouting

Sum(invalid) = 375, npids = 13446211

153 edges tamped down

Mon Apr 27 20:45:13 2015: checking involution

Mon Apr 27 20:45:13 2015: done

WARNING: 125 suspicious read-paths.

Sum(invalid) = 261, npids = 13446211

84 edges tamped down

Mon Apr 27 20:45:47 2015: making paths index for pull apart

Mon Apr 27 20:45:50 2015: pulling apart repeats

0.0133 seconds used separating paths 1

1.08 seconds used in fixing mToLeft, mToRight, and mEdgeToPathIds

Mon Apr 27 20:45:52 2015: there were 88 repeats pulled apart.

Mon Apr 27 20:45:52 2015: there were 700 read paths removed during separation.

Mon Apr 27 20:45:53 2015: improving paths

Mon Apr 27 20:46:22 2015: done

21368 paths extended

Mon Apr 27 20:46:45 2015: start degloop

Mon Apr 27 20:46:45 2015: creating path index

Mon Apr 27 20:46:49 2015: starting loop

Mon Apr 27 20:46:51 2015: degloop complete

Mon Apr 27 20:46:58 2015: unwinding three-edge plasmids

Mon Apr 27 20:46:58 2015: removing small components

Mon Apr 27 20:47:14 2015: writing a.fin files

Mon Apr 27 20:47:37 2015: determining candidates

Mon Apr 27 20:47:37 2015: determining candidates

Mon Apr 27 20:47:37 2015: determining candidates

CN fraction good = 0.22

Mon Apr 27 20:47:41 2015: deleting 0 gaps and adding 0 gaps to force symmetry

Mon Apr 27 20:47:44 2015: done making gaps, time used = 4.16 seconds

Mon Apr 27 20:47:55 2015: determining candidates

Mon Apr 27 20:47:55 2015: determining candidates

Mon Apr 27 20:47:55 2015: determining candidates

0.0732 seconds using setting up final fasta

0.381 seconds using printing final fasta