RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.KtuAPw/RM_3527120.TueSep21230192025 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: 1756841418 Database = /dev/shm/rModeler.KtuAPw/GCA_018852615.3_hg002v1.1.mat - Sequences = 24 - Bases = 3051529554 Storage Throughput = excellent ( 1160.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40560879 bp ( 40022503 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 195 raw families identified - RepeatScout: Running filtering stage.. 176 families remaining - RepeatScout: 00:07:34 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 171 families... 00:02:52 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 89 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:11:33 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4416 repeats masked totaling 1754636 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080184 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000184 bp After Masking: 7568606 bp Masked: 24.32 % -- Input Database Coverage: 10080184 bp out of 3051529554 bp ( 0.33 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 01:02:27 (hh:mm:ss) Elapsed Time, 13926830 HSPs Collected Number of families returned by RECON: 2478 Round Time: 06:56:57 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35756 repeats masked totaling 9513965 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30480615 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30022239 bp After Masking: 18702058 bp Masked: 37.71 % -- Input Database Coverage: 40560799 bp out of 3051529554 bp ( 1.33 % ) Sampling Time: 00:06:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:32:42 (hh:mm:ss) Elapsed Time, 58134 HSPs Collected Number of families returned by RECON: 2482 Round Time: 00:40:45 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127990 repeats masked totaling 33912347 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90802065 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90002008 bp After Masking: 50530945 bp Masked: 43.86 % -- Input Database Coverage: 131362864 bp out of 3051529554 bp ( 4.30 % ) Sampling Time: 00:22:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 03:12:14 (hh:mm:ss) Elapsed Time, 69294 HSPs Collected Number of families returned by RECON: 5750 Round Time: 03:37:21 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 421122 repeats masked totaling 107670454 bp(s). - TE Masking time 00:10:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271591505 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270031404 bp After Masking: 144355529 bp Masked: 46.54 % -- Input Database Coverage: 402954369 bp out of 3051529554 bp ( 13.20 % ) Sampling Time: 01:07:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 23:28:02 (hh:mm:ss) Elapsed Time, 210427 HSPs Collected Number of families returned by RECON: 22211 Round Time: 25:08:38 (hh:mm:ss) Elapsed Time : 285 families discovered. RepeatScout/RECON discovery complete: 644 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.KtuAPw/RM_3527120.TueSep21230192025 # 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: 00:03:56 (hh:mm:ss) Elapsed Time Program Time: 36:39:10 (hh:mm:ss) Elapsed Time