RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mi7VOy/RM_27638.TueDec50326112023 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: 1701775565 Database = /dev/shm/rModeler.mi7VOy/GCA_031468805.1_bMorBas2.hap1 - Sequences = 829 - Bases = 1381630140 - N50 = 85498604 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 158969366-170323554 | [ 1 ] 147615178-158969365 | [ ] 136260991-147615178 | [ ] 124906803-136260990 | [ 1 ] 113552616-124906803 | [ 1 ] 102198428-113552615 | [ ] 90844241-102198428 | [ ] 79490053-90844240 | [ 3 ] 68135866-79490053 | [ ] 56781678-68135865 | [ 1 ] 45427491-56781678 | [ 2 ] 34073303-45427490 | [ 2 ] 22719116-34073303 | [ 6 ] 11364928-22719115 | [ 4 ] 10741-11364928 |************************************************** [ 808 ] Storage Throughput = excellent ( 1109.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025972 bp ( 40024372 non ambiguous ) - Num Contigs Represented = 127 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:22 (hh:mm:ss) Elapsed Time Round Time: 00:43:54 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1108 repeats masked totaling 868491 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002417 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10002217 bp After Masking: 8745064 bp Masked: 12.57 % -- Input Database Coverage: 10002417 bp out of 1381630140 bp ( 0.72 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:45 (hh:mm:ss) Elapsed Time, 614 HSPs Collected Number of families returned by RECON: 254 Round Time: 00:07:53 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3393 repeats masked totaling 2493857 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023475 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 30022075 bp After Masking: 26224801 bp Masked: 12.65 % -- Input Database Coverage: 40025892 bp out of 1381630140 bp ( 2.90 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:34:25 (hh:mm:ss) Elapsed Time, 6259 HSPs Collected Number of families returned by RECON: 1378 Round Time: 00:42:35 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12300 repeats masked totaling 7683129 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043641 bp Num Contigs Represented = 200 Non ambiguous bp: Initial: 90039641 bp After Masking: 77655847 bp Masked: 13.75 % -- Input Database Coverage: 130069533 bp out of 1381630140 bp ( 9.41 % ) Sampling Time: 00:17:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 04:21:23 (hh:mm:ss) Elapsed Time, 69496 HSPs Collected Number of families returned by RECON: 7852 Round Time: 06:02:19 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50065 repeats masked totaling 34813902 bp(s). - TE Masking time 00:09:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018000 bp Num Contigs Represented = 374 Non ambiguous bp: Initial: 270007000 bp After Masking: 222302414 bp Masked: 17.67 % -- Input Database Coverage: 400087533 bp out of 1381630140 bp ( 28.96 % ) Sampling Time: 00:57:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23218705 Comparison Time: 34:51:47 (hh:mm:ss) Elapsed Time, 170448 HSPs Collected Number of families returned by RECON: 50227 Round Time: 36:41:08 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatScout/RECON discovery complete: 339 families found Classification Time: 01:00:03 (hh:mm:ss) Elapsed Time Program Time: 45:17:52 (hh:mm:ss) Elapsed Time