./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/ -------------------------------------------------------------------------------- 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 ==================================================================================== assembly has 2558 edges of mean length 151.654 contig line N50: 2,622 scaffold line N50: 2,622 total bases in 1 kb+ scaffolds: 75,233 total bases in 10 kb+ scaffolds: 10,572 There are 5,378,484 reads of mean length 119.4 and mean base quality 35.3. MPL1 = mean length of first read in pair up to first error = 2 (normal range is 175-225 for 250 base reads) Estimated chimera rate in read pairs (including mismapping) = 0.84%. genomic read coverage, using 1 kb+ scaffolds for genome size estimate: 8534.3 run started Sat Apr 25 18:46:06 2015, completed Sat Apr 25 20:30:57 2015 peak mem usage = 43.92 GB, total time = 1.75 hours final checksum = 1246515992559 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/ Sat Apr 25 20:30:57 2015: done