RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7pZzS4/RM_3536850.ThuApr101843542025 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: 1744335833 Database = /dev/shm/rModeler.7pZzS4/GCA_965151615.1_bCygCol1.1 - Sequences = 603 - Bases = 1293538149 - N50 = 88185588 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197354426-211451100 | [ 1 ] 183257753-197354426 | [ ] 169161080-183257753 | [ ] 155064406-169161079 | [ 1 ] 140967733-155064406 | [ ] 126871060-140967733 | [ ] 112774386-126871059 | [ 1 ] 98677713-112774386 | [ ] 84581040-98677713 | [ 1 ] 70484366-84581039 | [ 1 ] 56387693-70484366 | [ 1 ] 42291020-56387693 | [ ] 28194346-42291019 | [ 3 ] 14097673-28194346 | [ 10 ] 1000-14097673 |************************************************** [ 584 ] Storage Throughput = excellent ( 1659.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035513 bp ( 40031313 non ambiguous ) - Num Contigs Represented = 132 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:57 (hh:mm:ss) Elapsed Time Round Time: 00:21:37 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1892 repeats masked totaling 928649 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037265 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 10036065 bp After Masking: 8317571 bp Masked: 17.12 % -- Input Database Coverage: 10037265 bp out of 1293538149 bp ( 0.78 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:31 (hh:mm:ss) Elapsed Time, 3987 HSPs Collected Number of families returned by RECON: 189 Round Time: 00:05:57 (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 : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5606 repeats masked totaling 2749572 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038091 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 30035091 bp After Masking: 24806116 bp Masked: 17.41 % -- Input Database Coverage: 40075356 bp out of 1293538149 bp ( 3.10 % ) Sampling Time: 00:07:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:16:29 (hh:mm:ss) Elapsed Time, 17765 HSPs Collected Number of families returned by RECON: 1292 Round Time: 00:24:21 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17612 repeats masked totaling 7919545 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026348 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 90018597 bp After Masking: 74953819 bp Masked: 16.74 % -- Input Database Coverage: 130101704 bp out of 1293538149 bp ( 10.06 % ) Sampling Time: 00:21:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 01:44:14 (hh:mm:ss) Elapsed Time, 85816 HSPs Collected Number of families returned by RECON: 8603 Round Time: 02:06:59 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62862 repeats masked totaling 26649193 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051292 bp Num Contigs Represented = 352 Non ambiguous bp: Initial: 270025370 bp After Masking: 220526633 bp Masked: 18.33 % -- Input Database Coverage: 400152996 bp out of 1293538149 bp ( 30.93 % ) Sampling Time: 01:09:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 12:38:33 (hh:mm:ss) Elapsed Time, 279562 HSPs Collected Number of families returned by RECON: 52338 Round Time: 14:04:16 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatScout/RECON discovery complete: 329 families found Classification Time: 00:14:56 (hh:mm:ss) Elapsed Time Program Time: 17:18:06 (hh:mm:ss) Elapsed Time