RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wLqKKN/RM_1642339.SatApr190623172025 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: 1745068997 Database = /dev/shm/rModeler.wLqKKN/GCF_036169615.1_bHelExo1.hap1 - Sequences = 131 - Bases = 1049650714 - N50 = 115481020 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185011529-198225612 | [ 1 ] 171797446-185011528 | [ ] 158583364-171797446 | [ ] 145369281-158583363 | [ 1 ] 132155199-145369281 | [ ] 118941116-132155198 | [ ] 105727034-118941116 | [ 1 ] 92512951-105727033 | [ ] 79298869-92512951 | [ ] 66084786-79298868 | [ 1 ] 52870704-66084786 | [ ] 39656621-52870703 | [ 2 ] 26442539-39656621 |* [ 3 ] 13228456-26442538 |***** [ 12 ] 14374-13228456 |************************************************* [ 110 ] Storage Throughput = excellent ( 1776.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005339 bp ( 40001839 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:22 (hh:mm:ss) Elapsed Time Round Time: 00:10:21 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2725 repeats masked totaling 739704 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010283 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10009283 bp After Masking: 8993282 bp Masked: 10.15 % -- Input Database Coverage: 10010283 bp out of 1049650714 bp ( 0.95 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 596 HSPs Collected Number of families returned by RECON: 270 Round Time: 00:03:50 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8123 repeats masked totaling 2143418 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034976 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30032476 bp After Masking: 27213641 bp Masked: 9.39 % -- Input Database Coverage: 40045259 bp out of 1049650714 bp ( 3.82 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:16:06 (hh:mm:ss) Elapsed Time, 7052 HSPs Collected Number of families returned by RECON: 1893 Round Time: 00:17:54 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24174 repeats masked totaling 6182591 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041189 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90033550 bp After Masking: 82351575 bp Masked: 8.53 % -- Input Database Coverage: 130086448 bp out of 1049650714 bp ( 12.39 % ) Sampling Time: 00:04:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:52:43 (hh:mm:ss) Elapsed Time, 45473 HSPs Collected Number of families returned by RECON: 12316 Round Time: 01:58:55 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87743 repeats masked totaling 22029256 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270048025 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270028924 bp After Masking: 243184315 bp Masked: 9.94 % -- Input Database Coverage: 400134473 bp out of 1049650714 bp ( 38.12 % ) Sampling Time: 00:16:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 14:16:46 (hh:mm:ss) Elapsed Time, 235326 HSPs Collected Number of families returned by RECON: 81156 Round Time: 15:04:07 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatScout/RECON discovery complete: 388 families found Classification Time: 00:11:15 (hh:mm:ss) Elapsed Time Program Time: 17:46:22 (hh:mm:ss) Elapsed Time