RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.8Px56W/RM_1049373.FriApr110704272025 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: 1744380266 Database = /data/tmp/rModeler.8Px56W/GCA_965113315.1_rPodVau1.hap1.1 - Sequences = 285 - Bases = 1614928384 - N50 = 108032231 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 132442826-141902957 | [ 2 ] 122982696-132442826 | [ 1 ] 113522565-122982695 | [ 1 ] 104062435-113522565 | [ 2 ] 94602304-104062434 | [ 2 ] 85142174-94602304 | [ ] 75682043-85142173 | [ 2 ] 66221913-75682043 | [ 1 ] 56761782-66221912 | [ 2 ] 47301652-56761782 | [ 3 ] 37841521-47301651 | [ 3 ] 28381391-37841521 | [ ] 18921260-28381390 | [ ] 9461130-18921260 | [ 1 ] 1000-9461130 |************************************************** [ 265 ] Storage Throughput = excellent ( 1814.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024475 bp ( 40020275 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:30 (hh:mm:ss) Elapsed Time Round Time: 00:12:58 (hh:mm:ss) Elapsed Time : 535 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 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16286 repeats masked totaling 3264009 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031917 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10030717 bp After Masking: 6078062 bp Masked: 39.41 % -- Input Database Coverage: 10031917 bp out of 1614928384 bp ( 0.62 % ) Sampling Time: 00:02:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 8390 HSPs Collected Number of families returned by RECON: 1199 Round Time: 00:05:34 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52102 repeats masked totaling 10126287 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032558 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30029358 bp After Masking: 17795815 bp Masked: 40.74 % -- Input Database Coverage: 40064475 bp out of 1614928384 bp ( 2.48 % ) Sampling Time: 00:06:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:14:15 (hh:mm:ss) Elapsed Time, 46621 HSPs Collected Number of families returned by RECON: 4169 Round Time: 00:21:39 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 171008 repeats masked totaling 32902433 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033259 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90023059 bp After Masking: 51890854 bp Masked: 42.36 % -- Input Database Coverage: 130097734 bp out of 1614928384 bp ( 8.06 % ) Sampling Time: 00:13:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:25:59 (hh:mm:ss) Elapsed Time, 173908 HSPs Collected Number of families returned by RECON: 12943 Round Time: 01:44:38 (hh:mm:ss) Elapsed Time : 412 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 571112 repeats masked totaling 109573021 bp(s). - TE Masking time 00:05:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062350 bp Num Contigs Represented = 109 Non ambiguous bp: Initial: 270026267 bp After Masking: 146016296 bp Masked: 45.93 % -- Input Database Coverage: 400160084 bp out of 1614928384 bp ( 24.78 % ) Sampling Time: 00:45:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 09:14:42 (hh:mm:ss) Elapsed Time, 494085 HSPs Collected Number of families returned by RECON: 45049 Round Time: 10:28:25 (hh:mm:ss) Elapsed Time : 1014 families discovered. RepeatScout/RECON discovery complete: 2102 families found Classification Time: 00:37:40 (hh:mm:ss) Elapsed Time Program Time: 13:30:54 (hh:mm:ss) Elapsed Time