RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fW4VsI/RM_843758.TueMar120159042024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1710233943 Database = /dev/shm/rModeler.fW4VsI/GCA_031001765.1_BBF_mMolAlv_v1 - Sequences = 187 - Bases = 2395140990 - N50 = 114136598 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 252928096-270994318 | [ 1 ] 234861875-252928096 | [ ] 216795654-234861875 | [ ] 198729433-216795654 | [ ] 180663212-198729433 | [ ] 162596990-180663211 | [ ] 144530769-162596990 | [ 1 ] 126464548-144530769 | [ 2 ] 108398327-126464548 |** [ 8 ] 90332106-108398327 | [ 3 ] 72265884-90332105 | [ 2 ] 54199663-72265884 |* [ 4 ] 36133442-54199663 | [ ] 18067221-36133442 | [ 1 ] 1000-18067221 |************************************************** [ 165 ] Storage Throughput = excellent ( 1171.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029615 bp ( 40025215 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:29 (hh:mm:ss) Elapsed Time Round Time: 00:24:12 (hh:mm:ss) Elapsed Time : 184 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9985 repeats masked totaling 2857800 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020758 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10019558 bp After Masking: 7038833 bp Masked: 29.75 % -- Input Database Coverage: 10020758 bp out of 2395140990 bp ( 0.42 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:47 (hh:mm:ss) Elapsed Time, 5524 HSPs Collected Number of families returned by RECON: 828 Round Time: 00:07:28 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34770 repeats masked totaling 9186004 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008856 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30005656 bp After Masking: 20470715 bp Masked: 31.78 % -- Input Database Coverage: 40029614 bp out of 2395140990 bp ( 1.67 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:28:19 (hh:mm:ss) Elapsed Time, 34685 HSPs Collected Number of families returned by RECON: 2213 Round Time: 00:33:21 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110677 repeats masked totaling 29882507 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040324 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90030885 bp After Masking: 59044290 bp Masked: 34.42 % -- Input Database Coverage: 130069938 bp out of 2395140990 bp ( 5.43 % ) Sampling Time: 00:10:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:46:14 (hh:mm:ss) Elapsed Time, 136661 HSPs Collected Number of families returned by RECON: 7202 Round Time: 03:00:19 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 377279 repeats masked totaling 96932126 bp(s). - TE Masking time 00:04:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059302 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 270032102 bp After Masking: 169688856 bp Masked: 37.16 % -- Input Database Coverage: 400129240 bp out of 2395140990 bp ( 16.71 % ) Sampling Time: 00:39:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 21:48:01 (hh:mm:ss) Elapsed Time, 643777 HSPs Collected Number of families returned by RECON: 31839 Round Time: 22:45:57 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 765 families found Classification Time: 00:30:29 (hh:mm:ss) Elapsed Time Program Time: 27:21:46 (hh:mm:ss) Elapsed Time