##### BRIEF SUMMARY OF INPUTS & OUTPUTS ###### Assembly_dir: /global/projectb/scratch/eugeneg/ASSEMBLY/Angomonas/k61.d8_2016-04-07_11h14m55s_minus-endosym_minus-phiX == Key Parameters == Library info: Name Insert_estimated Insert_calculated For_contigs? For_scaffolding?(round) For_gap-closure? FIVH 478 477 y 1 y MATE4 5500 5041 n 2 n MATE3 8500 7744 n 3 n Mer_size: 61 Min_depth: 8 Diploid mode: 1 Diploid_depth_threshold: 66 == Input Data Summary == lib estNumReads readLen estTotalSeq qAvg [ min - max ] pctQ20Bases estQ20Depth FIVH 23140000 250.0 5.8Gb 33.6 [ 0 - 40 ] 88.60% 256.3 MATE4 2440000 75.0 0.2Gb 34.9 [ 0 - 38 ] 95.46% 8.7 MATE3 21660000 75.0 1.6Gb 36.0 [ 0 - 38 ] 97.76% 79.4 == Assembly Stats === Description cnt total min max N50 stats ------------------------------------------------------------------------------ Final Scaffolds 5800 32.3Mb 1.0Kb 956.9Kb 53 > 122.9Kb totalling 16.3Mb Final Contigs 7276 30.6Mb 0.1Kb 205.8Kb 569 > 9.2Kb totalling 15.3Mb Starting UUtigs 518238 60.8Mb 0.1Kb 33.8Kb 133706 > 0.1Kb totalling 30.4Mb ##### RUN PROGRESS REPORT ###### Number of restarts: 3 Number of resumes: 0 Failed stages: 2016/04/13 12:54:48 meraculous.pl main:: 768> Stage meraculous_merblast failed (245.915202 seconds) 2016/04/13 15:23:10 meraculous.pl main:: 768> Stage meraculous_merblast failed (135.07787 seconds) -----JOB SETS Total number of jobs: Total number of job sets: 0 Number of successful job sets: 28 Number of incomplete or failed job sets: 0 Time spent in successful job sets: 9802.44 s Time spent in incomplete or failed job sets: 0 s -----CLUSTER SUBMISSIONS Number of submitted task arrays: 30 Number of failed qsub submissions: 0 -----STAGES STAGE TIME_IN_STAGE(s) PROC_TIME_SUM(s) PROC_TIME_MAX(s) PROC_TIME_SUM-MAX(s) PROC_MEM_MAX(kb) meraculous_import 0 78 42 78 8004 meraculous_mercount 0 1394 316 415 6008700 meraculous_mergraph 0 994 292 292 2534268 meraculous_ufx 0 532 190 190 4696 meraculous_contigs 0 136 136 136 2000332 meraculous_bubble 2391 682 229 459 2328536 meraculous_merblast 2018 632 228 592 1926928 meraculous_ono 4687 741 157 693 3122072 meraculous_gap_closure 1139 1896 396 427 1905428 meraculous_final_results 7 0 0 0 0 ##### INTERMEDIATE RESULTS SUMMARY ####### -----MERCOUNTS: Total 61-mers (over 8x) : 6628325900 Total unique sequeces (over 8x) : 62028974 Weighted average 61-mer depth : 106.858544847123 -----MERGRAPH: Mers read in: 104282676 Mers meeting the depth cutoff: 62692584 Mers used in the mer graph: 62692556 Mers excluded: 28 -----CONTIGING: Main genome contig total: 518238 Main genome contig sequence total: 60.8 MB (-> 0.0% gap) Main genome contig N/L50: 133706/121 -----BUBBLE-TIGGING: Total complete bubbles (non-bubble uutig on both ends) : 58250 Total diplotigs: 9560 Total isotigs: 31158 Total blessed paths: 19120 Main genome contig total: 50278 Main genome contig sequence total: 37.6 MB (-> 0.0% gap) Main genome contig N/L50: 5236/2.0 KB -----LIBRARY MAPPING ANALYSIS: Gap-splinting: total_mapped hits_omitted(rate) total_splints 13587671 3833709(.282) 838291 Gap-spanning: library total_mapped hits_omitted(rate) total_spans FIVH 13587671 3553800(.261) 1088392 MATE4 1254595 461685(.367) 93300 MATE3 10678836 3533685(.330) 294459 Mapped reads omitted for following reasons: library truncated singleton minlen FIVH 1770774 1783026 0 MATE4 68478 385446 0 MATE3 778580 2716744 0 -----SCAFFOLDING: round avg_span_gap total_links anomalous_links anomaly_rate avg_scf_gap best_minLinks_cutoff scaffold_N50 1 114.866 1062971 5760 0 64.3065 3 5836 2 2433.29 84931 3207 .03 173.574 6 20315 3 2995.98 81278 4364 .05 205.302 3 66060 -----GAP CLOSING: Gap-filling reads: 2254359 Gaps closed: 10482 Gaps failed to close: 1062 Efficiency of gap closure: .90 ##### FINAL SCAFFOLDS ( filtered for 1kb+) ####### Main genome scaffold total: 5800 Main genome contig total: 7276 Main genome scaffold sequence total: 32.3 MB Main genome contig sequence total: 30.6 MB (-> 5.3% gap) Main genome scaffold N/L50: 53/122.9 KB Main genome contig N/L50: 569/9.2 KB Number of scaffolds > 50 KB: 71 % main genome in scaffolds > 50 KB: 55.1% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- --------- ------- ----------- ----------- -------- All 5,800 7,276 32,331,251 30,602,520 94.65% 1 kb 5,800 7,276 32,331,251 30,602,520 94.65% 2.5 kb 1,887 3,192 26,066,674 24,360,114 93.45% 5 kb 462 1,727 21,214,996 19,511,816 91.97% 10 kb 140 1,279 19,137,357 17,528,865 91.60% 25 kb 90 1,187 18,435,648 16,914,890 91.75% 50 kb 71 1,076 17,814,966 16,454,829 92.37% 100 kb 59 982 16,956,957 15,724,925 92.73% 250 kb 32 703 12,659,849 11,791,290 93.14% 500 kb 7 220 4,333,755 4,098,998 94.58% 1 mb 0 0 0 0 0.00%