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contributors:team_5:50perrun

Performing re-exec to adjust stack size.


Sun May 03 14:50:05 2015 run on campusrocks2-0-1, pid=55420 [Apr 4 2015 20:59:59 R52415 ]

DiscovarDeNovo \

             READS="frac:0.5,sample:19::/campusdata/BME235/Spring2015Data/ba \
             ms/SW019_adapterTrimmed_dupRemoved_150424.bam+frac:0.5,sample:1 \
             8::/campusdata/BME235/Spring2015Data/bams/SW018_adapterTrimmed_ \
             dupRemoved_150424.bam"                                          \
             OUT_DIR=/campusdata/rcalef/0.5_dataDDN_150501 NUM_THREADS=50    \
             MAX_MEM_GB=220 MEMORY_CHECK=True

SYSTEM INFO

- OS: Linux :: 2.6.32-220.13.1.el6.x86_64 :: #1 SMP Tue Apr 17 23:56:34 BST 2012

- node name: campusrocks2-0-1.local

- hardware type: x86_64

- cache size: 2048 KB

- cpu MHz: 2400.084

- cpu model name: AMD Opteron™ Processor 6278

- physical memory: 252.39 GB

MEMORY CHECK (typically takes several minutes; could cause

machine to become sluggish or result in this job being killed)

- Apparently able to allocate 100% of nominally available memory.

- Can access at least 220 GB.

Sun May 03 14:50:28 2015: finding input files

Sun May 03 14:50:28 2015: reading 2 files (which may take a while)

Sun May 03 14:50:28 2015: processing /campusdata/BME235/Spring2015Data/bams/SW019_adapterTrimmed_dupRemoved_150424.bam.

Sun May 03 14:50:28 2015: memory in use = 0.01 GB, peak = 0.01 GB

Sun May 03 15:13:28 2015: there are 124,970,747 reads of mean length 143

Sun May 03 15:13:28 2015: memory in use = 72.40 GB, peak = 74.21 GB

Sun May 03 15:13:49 2015: reads sorted

Sun May 03 15:13:49 2015: memory in use = 73.34 GB, peak = 74.21 GB

Sun May 03 15:16:17 2015: data stashed in output structures

Sun May 03 15:16:17 2015: memory in use = 12.77 GB, peak = 74.21 GB

Sun May 03 15:16:17 2015: processing /campusdata/BME235/Spring2015Data/bams/SW018_adapterTrimmed_dupRemoved_150424.bam.

Sun May 03 15:16:17 2015: memory in use = 12.77 GB, peak = 74.21 GB

Sun May 03 15:33:24 2015: there are 138,864,653 reads of mean length 99

Sun May 03 15:33:24 2015: memory in use = 62.37 GB, peak = 74.21 GB

Sun May 03 15:33:46 2015: reads sorted

Sun May 03 15:33:46 2015: memory in use = 63.42 GB, peak = 74.21 GB

Sun May 03 15:36:32 2015: data stashed in output structures

Sun May 03 15:36:32 2015: memory in use = 26.67 GB, peak = 74.21 GB

INPUT FILES:

[1,type=frag,sample=19,lib=1,frac=0.5] /campusdata/BME235/Spring2015Data/bams/SW019_adapterTrimmed_dupRemoved_150424.bam

[2,type=frag,sample=18,lib=1,frac=0.5] /campusdata/BME235/Spring2015Data/bams/SW018_adapterTrimmed_dupRemoved_150424.bam

Sun May 03 15:36:32 2015: found 2 samples

Sun May 03 15:36:32 2015: starts = 0,124970748

Sun May 03 15:45:17 2015: using 263,835,402 reads

Sun May 03 15:45:17 2015: data extraction complete

54.8 minutes used extracting reads

Sun May 03 15:52:15 2015: see total physical memory of 270,999,298,048 bytes

Sun May 03 15:52:15 2015: see user-imposed limit on memory of 236,223,201,280 bytes

Sun May 03 15:52:15 2015: 8.96 bytes per read base, assuming max memory available

We need 4 passes.

Expect 2578518 keys per batch.

Provide 3243760 keys per batch.

We need 5 passes.

Expect 2062814 keys per batch.

Provide 2387988 keys per batch.

Sun May 03 16:51:17 2015: back from buildReadQGraph

memory in use = 57,726,877,696

checksum_60 = 1091042242363737796

Sun May 03 16:53:37 2015: constructing places

Sun May 03 16:54:01 2015: sorting places

Sun May 03 17:00:11 2015: building all

Sun May 03 17:06:25 2015: calling LongReadsToPaths

Warning: HashSet initial size too small.

Sun May 03 17:09:17 2015: writing

Sun May 03 17:10:16 2015: translating paths

Sun May 03 17:10:28 2015: final stage of path translation

Sun May 03 17:29:36 2015: writing paths

56.1 seconds used reloading assembly

Sun May 03 17:43:11 2015: start walking

memory in use = 36,509,278,208

Sun May 03 17:44:23 2015: start walking

memory in use = 36,612,886,528

2.86 minutes used cleaning 200-mer graph

1.97 hours used in ReadQGrapher

6.2e-06 seconds used reloading reads

checksum_200 = 529403660712473571

1 peak mem usage = 140.27 GB

3.66 minutes used loading stuff

2 peak mem usage = 140.27 GB

launching gap assemblies, mem usage = 35,265,961,984

Sun May 03 17:54:38 2015: finding unsatisfieds

Sun May 03 17:54:45 2015: creating multiplicity map

Sun May 03 17:54:47 2015: economizing links

Sun May 03 17:54:47 2015: forming neighborhoods

Sun May 03 17:54:47 2015: forming initial clusters

Sun May 03 17:55:04 2015: start sort

0.688 seconds used sorting

Sun May 03 17:55:05 2015: merging clusters

xs.size( ) = 2689147

2.77 minutes used merging

xs.size( ) = 2235783

Sun May 03 17:58:12 2015: start overlap-based merging

Sun May 03 17:59:11 2015: start overlap-based merging

LR.size( ) = 2219803

LR.size( ) = 1109905

Sun May 03 18:03:02 2015: now processing 1109905 blobs

Sun May 03 18:03:03 2015: memory in use = 36.20 GB, peak = 140.27 GB

………. ………. ………. ………. ……….

………. ………. ………. ………. ……….

4.17 hours spent in local assemblies, memory in use = 39.19 GB, peak = 140.27 GB

Sun May 03 22:13:21 2015: patch reserving space

Sun May 03 22:13:21 2015: memory in use = 39.20 GB

25.2 seconds used patching, peak mem usage = 140.27 GB

new_stuff.size( ) = 2202589

Sun May 03 22:14:27 2015: building hb2

22.1 seconds used in new stuff 1 test

memory in use now = 37,405,421,568

Warning: HashSet initial size too small.

Warning: HashSet initial size too small.

Sun May 03 22:19:13 2015: back from buildBigKHBVFromReads

4.77 minutes used in new stuff 2 test

peak mem usage = 140.27 GB

26.2 seconds used in new stuff 5

Sun May 03 22:20:12 2015: finding interesting reads

Sun May 03 22:20:12 2015: memory in use = 32.74 GB, peak = 140.27 GB

Sun May 03 22:20:24 2015: building dictionary

Sun May 03 22:20:24 2015: memory in use = 33.02 GB, peak = 140.27 GB

Sun May 03 22:27:44 2015: reducing

Sun May 03 22:27:44 2015: memory in use = 140.68 GB, peak = 140.27 GB

We need 1 passes.

Expect 1066152 keys per batch.

Provide 1508583 keys per batch.

Sun May 03 22:37:47 2015: kmerizing

Sun May 03 22:37:47 2015: memory in use = 171.42 GB, peak = 220.11 GB

We need 1 passes.

Expect 695406 keys per batch.

Provide 1398894 keys per batch.

There were 209 buffer overflows.

Sun May 03 22:39:04 2015: cleaning

Sun May 03 22:39:04 2015: memory in use = 171.43 GB, peak = 220.11 GB

Sun May 03 22:40:21 2015: finding uniquely aligning edges

Sun May 03 22:40:21 2015: memory in use = 171.44 GB, peak = 220.11 GB

28.2 minutes used in new phase

hb.N( ) = 8067352, hb.EdgeObjectCount( ) = 4464217

26257 paths improved by rerouting

Sum(invalid) = 19494, npids = 131917701

691 edges tamped down

Sun May 03 22:47:10 2015: checking involution

Sun May 03 22:47:10 2015: done

WARNING: 684 suspicious read-paths.

Sum(invalid) = 2233, npids = 131917701

677 edges tamped down

Sun May 03 22:51:06 2015: making paths index for pull apart

Sun May 03 22:51:14 2015: pulling apart repeats

0.0117 seconds used separating paths 1

5.41 seconds used in fixing mToLeft, mToRight, and mEdgeToPathIds

Sun May 03 22:51:28 2015: there were 95 repeats pulled apart.

Sun May 03 22:51:28 2015: there were 8121 read paths removed during separation.

Sun May 03 22:51:33 2015: improving paths

Sun May 03 22:59:39 2015: done

5684 paths extended

Sun May 03 23:02:40 2015: start degloop

Sun May 03 23:02:40 2015: creating path index

Sun May 03 23:02:51 2015: starting loop

Sun May 03 23:02:51 2015: degloop complete

Sun May 03 23:03:22 2015: unwinding three-edge plasmids

Sun May 03 23:03:24 2015: removing small components

Sun May 03 23:04:54 2015: writing a.fin files

Sun May 03 23:13:51 2015: determining candidates

Sun May 03 23:13:52 2015: determining candidates

CN fraction good = 0.33

Sun May 03 23:14:34 2015: deleting 0 gaps and adding 0 gaps to force symmetry

Sun May 03 23:14:54 2015: done making gaps, time used = 30.6 seconds

Sun May 03 23:16:10 2015: determining candidates

Sun May 03 23:16:11 2015: determining candidates

1.7 seconds using setting up final fasta

12.5 seconds using printing final fasta

assembly has 273653 edges of mean length 807.36

contig line N50: 1,489

scaffold line N50: 1,489

total bases in 1 kb+ scaffolds: 101,397,871

total bases in 10 kb+ scaffolds: 151,417

There are 263,835,402 reads of mean length 100.0 and mean base quality 36.7.

MPL1 = mean length of first read in pair up to first error = 7

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

Estimated chimera rate in read pairs (including mismapping) = 21.08%.

WARNING: based on the observed chimera rate, it looks like something may be

very wrong with your input data.

genomic read coverage, using 1 kb+ scaffolds for genome size estimate: 260.2

run started Sun May 03 14:50:05 2015, completed Sun May 03 23:21:47 2015

peak mem usage = 220.11 GB, total time = 8.53 hours

final checksum = 63450798033837183

DiscovarDeNovo READS=“frac:0.5,sample:19::/campusdata/BME235/Spring2015Data/bams/SW019_adapterTrimmed_dupRemoved_150424.bam+frac:0.5,sample:18::/campusdata/BME235/Spring2015Data/bams/SW018_adapterTrimmed_dupRemoved_150424.bam” OUT_DIR=/campusdata/rcalef/0.5_dataDDN_150501 NUM_THREADS=50 MAX_MEM_GB=220 MEMORY_CHECK=True

Sun May 03 23:21:48 2015: done

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contributors/team_5/50perrun.txt · Last modified: 2015/09/02 09:22 by ceisenhart