RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.moHY31/RM_1288556.MonSep81131442025 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: 1757356303 Database = /dev/shm/rModeler.moHY31/GCA_000441875.1_Bgt_70_1 - Sequences = 90458 - Bases = 76521554 - N50 = 1746 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31292-33513 | [ 1 ] 29071-31291 | [ ] 26850-29070 | [ 2 ] 24629-26849 | [ 5 ] 22408-24628 | [ 5 ] 20187-22407 | [ 13 ] 17966-20186 | [ 34 ] 15746-17966 | [ 60 ] 13525-15745 | [ 107 ] 11304-13524 | [ 223 ] 9083-11303 | [ 375 ] 6862-9082 | [ 689 ] 4641-6861 | [ 1218 ] 2420-4640 |* [ 3142 ] 200-2420 |************************************************** [ 84584 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = excellent ( 1647.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40100754 bp ( 40000145 non ambiguous ) - Num Contigs Represented = 47580 - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 1337 raw families identified - RepeatScout: Running filtering stage.. 1332 families remaining - RepeatScout: 00:01:56 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 1300 families... 00:02:30 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 220 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:04:35 (hh:mm:ss) Elapsed Time : 1080 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29400 repeats masked totaling 5248332 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026603 bp Num Contigs Represented = 12190 Non ambiguous bp: Initial: 10001223 bp After Masking: 4764930 bp Masked: 52.36 % -- Input Database Coverage: 10026603 bp out of 76521554 bp ( 13.10 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 74291955 Comparison Time: 00:45:30 (hh:mm:ss) Elapsed Time, 213433 HSPs Collected Number of families returned by RECON: 1246 Round Time: 00:48:53 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93416 repeats masked totaling 16850119 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30075237 bp Num Contigs Represented = 35393 Non ambiguous bp: Initial: 30000008 bp After Masking: 13200901 bp Masked: 56.00 % -- Input Database Coverage: 40101840 bp out of 76521554 bp ( 52.41 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 626314528 Comparison Time: 02:19:32 (hh:mm:ss) Elapsed Time, 36535 HSPs Collected Number of families returned by RECON: 2853 Round Time: 02:20:50 (hh:mm:ss) Elapsed Time : 99 families discovered. - Increasing sample size to include end piece now = 126494951 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 126494951 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117802 repeats masked totaling 21357474 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 36419486 bp Num Contigs Represented = 42875 Non ambiguous bp: Initial: 36330365 bp After Masking: 15034842 bp Masked: 58.62 % -- Input Database Coverage: 76521326 bp out of 76521554 bp ( 100.00 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 919111375 Comparison Time: 02:53:57 (hh:mm:ss) Elapsed Time, 36234 HSPs Collected Number of families returned by RECON: 3352 Round Time: 02:55:29 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatScout/RECON discovery complete: 1315 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.moHY31/RM_1288556.MonSep81131442025 # 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: 00:01:33 (hh:mm:ss) Elapsed Time Program Time: 06:11:20 (hh:mm:ss) Elapsed Time