RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ZZthPb/RM_1095096.WedNov130637542024 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: 1731508673 Database = /scratch/tmp/rModeler.ZZthPb/GCA_043290085.1_mRhyPet1.hap1 - Sequences = 469 - Bases = 5620370870 - N50 = 546821263 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 809192979-866991485 | [ 1 ] 751394473-809192978 | [ ] 693595968-751394473 | [ 1 ] 635797462-693595967 | [ ] 577998957-635797462 | [ 1 ] 520200451-577998956 | [ 2 ] 462401945-520200450 | [ 2 ] 404603440-462401945 | [ ] 346804934-404603439 | [ ] 289006429-346804934 | [ ] 231207923-289006428 | [ 3 ] 173409417-231207922 | [ 1 ] 115610912-173409417 | [ 2 ] 57812406-115610911 | [ ] 13901-57812406 |************************************************** [ 456 ] Storage Throughput = excellent ( 1461.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001369 bp ( 40000569 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:05:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:04:46 (hh:mm:ss) Elapsed Time Round Time: 00:15:46 (hh:mm:ss) Elapsed Time : 307 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25046 repeats masked totaling 6696516 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035892 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10035692 bp After Masking: 3225060 bp Masked: 67.86 % -- Input Database Coverage: 10035892 bp out of 5620370870 bp ( 0.18 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 4192 HSPs Collected Number of families returned by RECON: 439 Round Time: 00:04:43 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75791 repeats masked totaling 20836350 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005397 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30004797 bp After Masking: 8834092 bp Masked: 70.56 % -- Input Database Coverage: 40041289 bp out of 5620370870 bp ( 0.71 % ) Sampling Time: 00:04:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:10:09 (hh:mm:ss) Elapsed Time, 8558 HSPs Collected Number of families returned by RECON: 1076 Round Time: 00:15:19 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 231710 repeats masked totaling 62999337 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013260 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90010060 bp After Masking: 26027612 bp Masked: 71.08 % -- Input Database Coverage: 130054549 bp out of 5620370870 bp ( 2.31 % ) Sampling Time: 00:14:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 00:45:28 (hh:mm:ss) Elapsed Time, 65085 HSPs Collected Number of families returned by RECON: 3405 Round Time: 01:02:38 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:36:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 736330 repeats masked totaling 193424117 bp(s). - TE Masking time 00:02:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017958 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 270010358 bp After Masking: 73433043 bp Masked: 72.80 % -- Input Database Coverage: 400072507 bp out of 5620370870 bp ( 7.12 % ) Sampling Time: 00:44:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 04:39:35 (hh:mm:ss) Elapsed Time, 183571 HSPs Collected Number of families returned by RECON: 11517 Round Time: 05:27:58 (hh:mm:ss) Elapsed Time : 257 families discovered. RepeatScout/RECON discovery complete: 719 families found Classification Time: 00:13:32 (hh:mm:ss) Elapsed Time Program Time: 07:19:56 (hh:mm:ss) Elapsed Time