Banana Slug Genomics

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edser2:~> ./DiscovarDeNovo READS="frac:0.1,sample:18H::/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam+frac:0.1,sample:19M::/scratch/bananaSlugBAMS/SW019


_S1_L001_001.bam+frac:0.1,sample:19H::/scratch/bananaSlugBAMS/SW019_S2_L008_001.bam" OUT_DIR=/scratch/bananaSlugAssemblies/10run/


Performing re-exec to adjust stack size.





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


Mon Apr 27 22:01:35 2015 run on edser2, pid=31590 [Apr 10 2015 12:24:57 R52415 ]


DiscovarDeNovo                                                                 \


               READS="frac:0.1,sample:18H::/scratch/bananaSlugBAMS/SW018_S1_L0 \


               07_001.bam+frac:0.1,sample:19M::/scratch/bananaSlugBAMS/SW019_S \


               1_L001_001.bam+frac:0.1,sample:19H::/scratch/bananaSlugBAMS/SW0 \


               19_S2_L008_001.bam"                                             \


               OUT_DIR=/scratch/bananaSlugAssemblies/10run/


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





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 22:01:36 2015: finding input files


Mon Apr 27 22:01:36 2015: reading 3 files (which may take a while)


Mon Apr 27 22:01:36 2015: processing /scratch/bananaSlugBAMS/SW018_S1_L007_001.bam.


Mon Apr 27 22:01:36 2015: memory in use = 0.01 GB, peak = 0.01 GB


Mon Apr 27 22:24:52 2015: there are 28,603,868 reads of mean length 100


Mon Apr 27 22:24:52 2015: memory in use = 42.71 GB, peak = 43.92 GB


Mon Apr 27 22:25:28 2015: reads sorted


Mon Apr 27 22:25:28 2015: memory in use = 43.78 GB, peak = 43.92 GB


Mon Apr 27 22:27:33 2015: data stashed in output structures


Mon Apr 27 22:27:33 2015: memory in use = 2.64 GB, peak = 43.92 GB


Mon Apr 27 22:27:33 2015: processing /scratch/bananaSlugBAMS/SW019_S1_L001_001.bam.


Mon Apr 27 22:27:33 2015: memory in use = 2.64 GB, peak = 43.92 GB


Mon Apr 27 22:46:24 2015: there are 5,453,744 reads of mean length 301


Mon Apr 27 22:46:24 2015: memory in use = 18.61 GB, peak = 43.92 GB


Mon Apr 27 22:46:32 2015: reads sorted


Mon Apr 27 22:46:32 2015: memory in use = 18.81 GB, peak = 43.92 GB


Mon Apr 27 22:47:17 2015: data stashed in output structures


Mon Apr 27 22:47:17 2015: memory in use = 3.86 GB, peak = 43.92 GB


Mon Apr 27 22:47:17 2015: processing /scratch/bananaSlugBAMS/SW019_S2_L008_001.bam.


Mon Apr 27 22:47:17 2015: memory in use = 3.86 GB, peak = 43.92 GB


Mon Apr 27 23:02:58 2015: there are 19,727,231 reads of mean length 100


Mon Apr 27 23:02:58 2015: memory in use = 33.52 GB, peak = 43.92 GB


Mon Apr 27 23:03:22 2015: reads sorted


Mon Apr 27 23:03:22 2015: memory in use = 34.25 GB, peak = 43.92 GB


Mon Apr 27 23:04:52 2015: data stashed in output structures


Mon Apr 27 23:04:52 2015: memory in use = 5.65 GB, peak = 43.92 GB





INPUT FILES:


[1,type=frag,sample=18H,lib=1,frac=0.1]  /scratch/bananaSlugBAMS/SW018_S1_L007_001.bam


[2,type=frag,sample=19M,lib=1,frac=0.1]  /scratch/bananaSlugBAMS/SW019_S1_L001_001.bam


[3,type=frag,sample=19H,lib=1,frac=0.1]  /scratch/bananaSlugBAMS/SW019_S2_L008_001.bam





Mon Apr 27 23:04:52 2015: found 3 samples


Mon Apr 27 23:04:52 2015: starts = 0,28603868,34057612


Mon Apr 27 23:06:29 2015: using 53,784,844 reads


Mon Apr 27 23:06:29 2015: data extraction complete


1.08 hours used extracting reads


Mon Apr 27 23:06:31 2015: see total physical memory of 338,094,714,880 bytes


Mon Apr 27 23:06:31 2015: 52.59 bytes per read base, assuming max memory available


We need 1 passes.


Expect 2750583 keys per batch.


Provide 5342050 keys per batch.


There were 192 buffer overflows.


We need 1 passes.


Expect 2750583 keys per batch.


Provide 5103062 keys per batch.


There were 192 buffer overflows.


Warning: HashSet initial size too small.


Mon Apr 27 23:36:51 2015: back from buildReadQGraph


memory in use = 13,995,552,768


checksum_60 = 759152776190314974


Mon Apr 27 23:37:57 2015: constructing places


Mon Apr 27 23:38:15 2015: sorting places


Mon Apr 27 23:41:26 2015: building all


Mon Apr 27 23:43:07 2015: calling LongReadsToPaths


Mon Apr 27 23:44:14 2015: writing


Mon Apr 27 23:44:21 2015: translating paths


Mon Apr 27 23:44:34 2015: final stage of path translation


Mon Apr 27 23:58:35 2015: writing paths


9.52 seconds used reloading assembly


Tue Apr 28 00:00:26 2015: start walking


memory in use = 7,987,261,440


Tue Apr 28 00:01:04 2015: start walking


memory in use = 7,825,833,984


1.21 minutes used cleaning 200-mer graph


55.5 minutes used in ReadQGrapher


5.96e-06 seconds used reloading reads


checksum_200 = 23687290918476347


1 peak mem usage = 151.05 GB


10.5 seconds used loading stuff


2 peak mem usage = 151.05 GB


launching gap assemblies, mem usage = 7,615,533,056


Tue Apr 28 00:02:26 2015: finding unsatisfieds


Tue Apr 28 00:02:27 2015: creating multiplicity map


Tue Apr 28 00:02:27 2015: economizing links


Tue Apr 28 00:02:27 2015: forming neighborhoods


Tue Apr 28 00:02:28 2015: forming initial clusters


Tue Apr 28 00:02:28 2015: start sort


0.086 seconds used sorting


Tue Apr 28 00:02:28 2015: merging clusters


xs.size( ) = 98897


7.32 seconds used merging


xs.size( ) = 16644


Tue Apr 28 00:02:36 2015: start overlap-based merging


Tue Apr 28 00:02:37 2015: start overlap-based merging


LR.size( ) = 15709


LR.size( ) = 7868


Tue Apr 28 00:03:02 2015: now processing 7868 blobs


Tue Apr 28 00:03:02 2015: memory in use = 7.22 GB, peak = 151.05 GB


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


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


10 minutes spent in local assemblies, memory in use = 7.40 GB, peak = 151.05 GB


Tue Apr 28 00:13:03 2015: patch reserving space


Tue Apr 28 00:13:03 2015: memory in use = 7.40 GB


0.39 seconds used patching, peak mem usage = 151.05 GB


new_stuff.size( ) = 51903


Tue Apr 28 00:13:13 2015: building hb2


5.14 seconds used in new stuff 1 test


memory in use now = 7,876,759,552


Warning: HashSet initial size too small.


Tue Apr 28 00:14:26 2015: back from buildBigKHBVFromReads


1.22 minutes used in new stuff 2 test


peak mem usage = 151.05 GB


11.8 seconds used in new stuff 5


Tue Apr 28 00:14:45 2015: finding interesting reads


Tue Apr 28 00:14:45 2015: memory in use = 7.29 GB, peak = 151.05 GB


Tue Apr 28 00:15:41 2015: building dictionary


Tue Apr 28 00:15:41 2015: memory in use = 7.30 GB, peak = 151.05 GB


Tue Apr 28 00:15:54 2015: reducing


Tue Apr 28 00:15:54 2015: memory in use = 13.40 GB, peak = 151.05 GB


We need 1 passes.


Expect 57267 keys per batch.


Provide 143166 keys per batch.


Tue Apr 28 00:16:18 2015: kmerizing


Tue Apr 28 00:16:18 2015: memory in use = 13.88 GB, peak = 151.05 GB


We need 1 passes.


Expect 77877 keys per batch.


Provide 194692 keys per batch.


Tue Apr 28 00:16:29 2015: cleaning


Tue Apr 28 00:16:29 2015: memory in use = 13.88 GB, peak = 151.05 GB


Tue Apr 28 00:16:42 2015: finding uniquely aligning edges


Tue Apr 28 00:16:42 2015: memory in use = 13.88 GB, peak = 151.05 GB


3.89 minutes used in new phase


hb.N( ) = 1180208, hb.EdgeObjectCount( ) = 741914


1867 paths improved by rerouting


Sum(invalid) = 898, npids = 26892422


271 edges tamped down


Tue Apr 28 00:18:34 2015: checking involution


Tue Apr 28 00:18:34 2015: done


WARNING: 235 suspicious read-paths.


Sum(invalid) = 564, npids = 26892422


216 edges tamped down


Tue Apr 28 00:19:44 2015: making paths index for pull apart


Tue Apr 28 00:19:48 2015: pulling apart repeats


0.0336 seconds used separating paths 1


2.87 seconds used in fixing mToLeft, mToRight, and mEdgeToPathIds


Tue Apr 28 00:19:54 2015: there were 234 repeats pulled apart.


Tue Apr 28 00:19:54 2015: there were 2055 read paths removed during separation.


Tue Apr 28 00:19:56 2015: improving paths


Tue Apr 28 00:21:03 2015: done


44210 paths extended


Tue Apr 28 00:21:50 2015: start degloop


Tue Apr 28 00:21:50 2015: creating path index


Tue Apr 28 00:21:59 2015: starting loop


Tue Apr 28 00:22:02 2015: degloop complete


Tue Apr 28 00:22:19 2015: unwinding three-edge plasmids


Tue Apr 28 00:22:20 2015: removing small components


Tue Apr 28 00:22:54 2015: writing a.fin files


Tue Apr 28 00:23:48 2015: determining candidates


Tue Apr 28 00:23:48 2015: determining candidates


Tue Apr 28 00:23:48 2015: determining candidates


CN fraction good = 0.18


/bin/sh: 1: set: Illegal option -o pipefail


Tue Apr 28 00:24:04 2015: deleting 0 gaps and adding 0 gaps to force symmetry


Tue Apr 28 00:24:11 2015: done making gaps, time used = 9.07 seconds


Tue Apr 28 00:24:35 2015: determining candidates


Tue Apr 28 00:24:35 2015: determining candidates


Tue Apr 28 00:24:35 2015: determining candidates


0.204 seconds using setting up final fasta


0.833 seconds using printing final fasta





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





assembly has 38195 edges of mean length 187.611


contig line N50: 2,563


scaffold line N50: 2,563


total bases in 1 kb+ scaffolds: 1,476,875


total bases in 10 kb+ scaffolds: 168,543


There are 53,784,844 reads of mean length 119.5 and mean base quality 35.4.


MPL1 = mean length of first read in pair up to first error = 3


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


Estimated chimera rate in read pairs (including mismapping) = 5.92%.





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: 4353.3





run started Mon Apr 27 22:01:35 2015, completed Tue Apr 28 00:25:19 2015


peak mem usage = 151.05 GB, total time = 2.4 hours


final checksum = 376448268699082





DiscovarDeNovo READS="frac:0.1,sample:18H::/scratch/bananaSlugBAMS/SW018_S1_L007_001.bam+frac:0.1,sample:19M::/scratch/bananaSlugBAMS/SW019_S1_L001_001.bam+frac:0.1,sample:19H::/scratch/bananaSlugBAMS/SW019_S2_L008_001.bam" OUT_DIR=/scratch/bananaSlugAssemblies/10run/





Tue Apr 28 00:25:20 2015: done
Banana Slug Genomics

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