Banana Slug Genomics

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
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(tm) 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
Banana Slug Genomics

User Tools

Site Tools

Page Tools
