RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.RuY2We/RM_3094773.MonAug241905532026 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: 1787623552 Database = /data/tmp/rModeler.RuY2We/GCA_056363955.1_mPteMes1.pri - Sequences = 27 - Bases = 2137861399 Storage Throughput = good ( 757.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038612 bp ( 40038412 non ambiguous ) - Num Contigs Represented = 22 - 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.. : 151 raw families identified - RepeatScout: Running filtering stage.. 144 families remaining - RepeatScout: 00:03:00 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 140 families... 00:11:57 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 3 satellite(s), 65 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:17:31 (hh:mm:ss) Elapsed Time : 72 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 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5867 repeats masked totaling 2140900 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035255 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10035255 bp After Masking: 7847135 bp Masked: 21.80 % -- Input Database Coverage: 10035255 bp out of 2137861399 bp ( 0.47 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:42 (hh:mm:ss) Elapsed Time, 22390 HSPs Collected Number of families returned by RECON: 1095 Round Time: 00:10:14 (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 : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25073 repeats masked totaling 7729463 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003355 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30003155 bp After Masking: 22169704 bp Masked: 26.11 % -- Input Database Coverage: 40038610 bp out of 2137861399 bp ( 1.87 % ) Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:21 (hh:mm:ss) Elapsed Time, 28715 HSPs Collected Number of families returned by RECON: 2117 Round Time: 00:36:30 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87940 repeats masked totaling 27309853 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90001191 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90000791 bp After Masking: 62387069 bp Masked: 30.68 % -- Input Database Coverage: 130039801 bp out of 2137861399 bp ( 6.08 % ) Sampling Time: 00:09:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:50:22 (hh:mm:ss) Elapsed Time, 70625 HSPs Collected Number of families returned by RECON: 6489 Round Time: 03:08:58 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 303508 repeats masked totaling 88438072 bp(s). - TE Masking time 00:07:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040616 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270039416 bp After Masking: 180627004 bp Masked: 33.11 % -- Input Database Coverage: 400080417 bp out of 2137861399 bp ( 18.71 % ) Sampling Time: 00:34:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 20:50:54 (hh:mm:ss) Elapsed Time, 192126 HSPs Collected Number of families returned by RECON: 28748 Round Time: 22:08:44 (hh:mm:ss) Elapsed Time : 297 families discovered. RepeatScout/RECON discovery complete: 593 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.RuY2We/RM_3094773.MonAug241905532026 # 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: 00:04:03 (hh:mm:ss) Elapsed Time Program Time: 26:26:00 (hh:mm:ss) Elapsed Time