RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Provw8/RM_3071073.FriAug211559532026 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1787353192 Database = /dev/shm/rModeler.Provw8/GCA_054083975.1_aFejLim2.hap1 - Sequences = 628 - Bases = 3519779937 - N50 = 391817772 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 512611157-549225634 | [ 1 ] 475996680-512611156 | [ ] 439382203-475996679 | [ 1 ] 402767726-439382202 | [ ] 366153250-402767726 | [ 2 ] 329538773-366153249 | [ 1 ] 292924296-329538772 | [ ] 256309819-292924295 | [ ] 219695342-256309818 | [ ] 183080866-219695342 | [ 3 ] 146466389-183080865 | [ 3 ] 109851912-146466388 | [ 2 ] 73237435-109851911 | [ ] 36622958-73237434 | [ ] 8482-36622958 |************************************************** [ 615 ] Storage Throughput = excellent ( 1670.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025611 bp ( 40022711 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 765 raw families identified - RepeatScout: Running filtering stage.. 663 families remaining - RepeatScout: 00:05:09 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 639 families... 00:07:25 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 12 satellite(s), 249 contained, found in 00:00:06 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:06 (hh:mm:ss) Elapsed Time Round Time: 00:15:09 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21666 repeats masked totaling 4077607 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005690 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10005190 bp After Masking: 4918901 bp Masked: 50.84 % -- Input Database Coverage: 10005690 bp out of 3519779937 bp ( 0.28 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:08 (hh:mm:ss) Elapsed Time, 310055 HSPs Collected Number of families returned by RECON: 1661 Round Time: 00:09:50 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67516 repeats masked totaling 13907370 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019841 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30017441 bp After Masking: 12711356 bp Masked: 57.65 % -- Input Database Coverage: 40025531 bp out of 3519779937 bp ( 1.14 % ) Sampling Time: 00:06:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:14:34 (hh:mm:ss) Elapsed Time, 81719 HSPs Collected Number of families returned by RECON: 4290 Round Time: 00:22:43 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 223943 repeats masked totaling 45206820 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016578 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90009378 bp After Masking: 34736866 bp Masked: 61.41 % -- Input Database Coverage: 130042109 bp out of 3519779937 bp ( 3.69 % ) Sampling Time: 00:15:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:07:58 (hh:mm:ss) Elapsed Time, 268496 HSPs Collected Number of families returned by RECON: 10595 Round Time: 01:28:49 (hh:mm:ss) Elapsed Time : 513 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 778178 repeats masked totaling 150912158 bp(s). - TE Masking time 00:07:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027302 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 270002610 bp After Masking: 90172552 bp Masked: 66.60 % -- Input Database Coverage: 400069411 bp out of 3519779937 bp ( 11.37 % ) Sampling Time: 00:49:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 06:28:18 (hh:mm:ss) Elapsed Time, 629186 HSPs Collected Number of families returned by RECON: 26308 Round Time: 07:36:39 (hh:mm:ss) Elapsed Time : 1273 families discovered. RepeatScout/RECON discovery complete: 2380 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Provw8/RM_3071073.FriAug211559532026 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:03:38 (hh:mm:ss) Elapsed Time Program Time: 09:56:48 (hh:mm:ss) Elapsed Time