This is an old revision of the document!
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. -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- 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 ==================================================================================== assembly has 18224 edges of mean length 171.617 contig line N50: 2,067 scaffold line N50: 2,067 total bases in 1 kb+ scaffolds: 592,685 total bases in 10 kb+ scaffolds: 11,088 There are 26,892,422 reads of mean length 120.5 and mean base quality 35.4. 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) = 1.43%. genomic read coverage, using 1 kb+ scaffolds for genome size estimate: 5469.5 run started Mon Apr 27 19:16:20 2015, completed Mon Apr 27 20:48:14 2015 peak mem usage = 78.10 GB, total time = 1.53 hours final checksum = 60623142131077 DiscovarDeNovo READS="frac:0.05,sample:18H::/scratch/bananaSlugBAMS/SW018_S1_L007_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 Mon Apr 27 20:48:14 2015: done
