RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bO61UU/RM_1016078.ThuFeb61846362025 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: 1738896395 Database = /dev/shm/rModeler.bO61UU/GCF_044704955.1_sPriJap1.hap1 - Sequences = 4318 - Bases = 5923069295 - N50 = 229984596 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 509820876-546236482 | [ 1 ] 473405271-509820876 | [ ] 436989665-473405270 | [ ] 400574060-436989665 | [ ] 364158455-400574060 | [ 1 ] 327742849-364158454 | [ 1 ] 291327244-327742849 | [ 2 ] 254911638-291327243 | [ 1 ] 218496033-254911638 | [ 5 ] 182080428-218496033 | [ 4 ] 145664822-182080427 | [ ] 109249217-145664822 | [ 3 ] 72833611-109249216 | [ 3 ] 36418006-72833611 | [ 5 ] 2401-36418006 |************************************************** [ 4292 ] Storage Throughput = excellent ( 1826.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017282 bp ( 40008082 non ambiguous ) - Num Contigs Represented = 152 - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:02 (hh:mm:ss) Elapsed Time Round Time: 00:15:21 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14939 repeats masked totaling 5830184 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004240 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 10002640 bp After Masking: 2415914 bp Masked: 75.85 % -- Input Database Coverage: 10004240 bp out of 5923069295 bp ( 0.17 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:30 (hh:mm:ss) Elapsed Time, 5475 HSPs Collected Number of families returned by RECON: 610 Round Time: 00:07:44 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48085 repeats masked totaling 18137577 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012962 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 30005362 bp After Masking: 7086501 bp Masked: 76.38 % -- Input Database Coverage: 40017202 bp out of 5923069295 bp ( 0.68 % ) Sampling Time: 00:14:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:08:59 (hh:mm:ss) Elapsed Time, 23061 HSPs Collected Number of families returned by RECON: 2087 Round Time: 00:23:47 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148538 repeats masked totaling 55357138 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020027 bp Num Contigs Represented = 264 Non ambiguous bp: Initial: 90002203 bp After Masking: 19979375 bp Masked: 77.80 % -- Input Database Coverage: 130037229 bp out of 5923069295 bp ( 2.20 % ) Sampling Time: 00:43:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 00:36:01 (hh:mm:ss) Elapsed Time, 124000 HSPs Collected Number of families returned by RECON: 5681 Round Time: 01:25:08 (hh:mm:ss) Elapsed Time : 266 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:54:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 474316 repeats masked totaling 172612340 bp(s). - TE Masking time 00:03:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059861 bp Num Contigs Represented = 616 Non ambiguous bp: Initial: 270007032 bp After Masking: 52431105 bp Masked: 80.58 % -- Input Database Coverage: 400097090 bp out of 5923069295 bp ( 6.75 % ) Sampling Time: 02:14:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23471526 Comparison Time: 03:15:24 (hh:mm:ss) Elapsed Time, 460207 HSPs Collected Number of families returned by RECON: 13956 Round Time: 05:35:09 (hh:mm:ss) Elapsed Time : 630 families discovered. RepeatScout/RECON discovery complete: 1574 families found Classification Time: 00:28:13 (hh:mm:ss) Elapsed Time Program Time: 08:15:22 (hh:mm:ss) Elapsed Time