RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pooqKq/RM_640688.MonApr211259302025 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: 1745265570 Database = /dev/shm/rModeler.pooqKq/GCA_965194825.1_mBalPhy2.hap1.1 - Sequences = 2612 - Bases = 3442554901 - N50 = 112944795 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 184136623-197289168 | [ 1 ] 170984078-184136622 | [ 2 ] 157831534-170984078 | [ ] 144678989-157831533 | [ 3 ] 131526445-144678989 | [ 1 ] 118373900-131526444 | [ 2 ] 105221356-118373900 | [ 4 ] 92068811-105221355 | [ 4 ] 78916267-92068811 | [ 2 ] 65763722-78916266 | [ 1 ] 52611178-65763722 | [ 1 ] 39458633-52611177 | [ 1 ] 26306089-39458633 | [ ] 13153544-26306088 | [ 1 ] 1000-13153544 |************************************************** [ 2589 ] Storage Throughput = excellent ( 1801.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023431 bp ( 40021231 non ambiguous ) - Num Contigs Represented = 271 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:52 (hh:mm:ss) Elapsed Time Round Time: 00:17:20 (hh:mm:ss) Elapsed Time : 155 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 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8530 repeats masked totaling 3793914 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010102 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 10009502 bp After Masking: 5459465 bp Masked: 45.46 % -- Input Database Coverage: 10010102 bp out of 3442554901 bp ( 0.29 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 33184 HSPs Collected Number of families returned by RECON: 727 Round Time: 00:03:58 (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 : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28205 repeats masked totaling 11984017 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013249 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 30011649 bp After Masking: 15225027 bp Masked: 49.27 % -- Input Database Coverage: 40023351 bp out of 3442554901 bp ( 1.16 % ) Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:11:06 (hh:mm:ss) Elapsed Time, 91124 HSPs Collected Number of families returned by RECON: 1795 Round Time: 00:14:04 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93155 repeats masked totaling 36494855 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028265 bp Num Contigs Represented = 494 Non ambiguous bp: Initial: 90020465 bp After Masking: 44712430 bp Masked: 50.33 % -- Input Database Coverage: 130051616 bp out of 3442554901 bp ( 3.78 % ) Sampling Time: 00:07:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 01:03:04 (hh:mm:ss) Elapsed Time, 1119946 HSPs Collected Number of families returned by RECON: 6261 Round Time: 01:12:10 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 326165 repeats masked totaling 118282642 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040143 bp Num Contigs Represented = 1088 Non ambiguous bp: Initial: 270018943 bp After Masking: 126114132 bp Masked: 53.29 % -- Input Database Coverage: 400091759 bp out of 3442554901 bp ( 11.62 % ) Sampling Time: 00:23:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23409903 Comparison Time: 06:50:08 (hh:mm:ss) Elapsed Time, 4219015 HSPs Collected Number of families returned by RECON: 22863 Round Time: 07:21:57 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatScout/RECON discovery complete: 662 families found Classification Time: 00:16:18 (hh:mm:ss) Elapsed Time Program Time: 09:25:47 (hh:mm:ss) Elapsed Time