RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Gkd0pI/RM_26389.SatNov252138152023 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: 1700977093 Database = /dev/shm/rModeler.Gkd0pI/GCA_007364235.1_fArcCen1_v1.h - Sequences = 9292 - Bases = 1034011644 - N50 = 457146 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 2853032-3056767 | [ 3 ] 2649298-2853032 | [ ] 2445564-2649298 | [ 3 ] 2241830-2445564 | [ 5 ] 2038096-2241830 | [ 8 ] 1834362-2038096 | [ 8 ] 1630628-1834362 | [ 12 ] 1426894-1630628 | [ 18 ] 1223160-1426894 | [ 34 ] 1019426-1223160 | [ 63 ] 815692-1019426 | [ 101 ] 611958-815692 | [ 143 ] 408224-611958 |* [ 268 ] 204490-408224 |*** [ 524 ] 756-204490 |************************************************** [ 8102 ] Storage Throughput = excellent ( 1161.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008832 bp ( 40008832 non ambiguous ) - Num Contigs Represented = 935 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:05 (hh:mm:ss) Elapsed Time Round Time: 00:26:32 (hh:mm:ss) Elapsed Time : 575 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11085 repeats masked totaling 2452998 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000689 bp Num Contigs Represented = 264 Non ambiguous bp: Initial: 10000689 bp After Masking: 7401312 bp Masked: 25.99 % -- Input Database Coverage: 10000689 bp out of 1034011644 bp ( 0.97 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42486 Comparison Time: 00:07:16 (hh:mm:ss) Elapsed Time, 5841 HSPs Collected Number of families returned by RECON: 1236 Round Time: 00:08:22 (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 : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34565 repeats masked totaling 7391592 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008096 bp Num Contigs Represented = 738 Non ambiguous bp: Initial: 30008096 bp After Masking: 22210997 bp Masked: 25.98 % -- Input Database Coverage: 40008785 bp out of 1034011644 bp ( 3.87 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 376278 Comparison Time: 00:37:40 (hh:mm:ss) Elapsed Time, 40455 HSPs Collected Number of families returned by RECON: 4749 Round Time: 00:41:13 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112496 repeats masked totaling 23750534 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019966 bp Num Contigs Represented = 1796 Non ambiguous bp: Initial: 90013230 bp After Masking: 64887023 bp Masked: 27.91 % -- Input Database Coverage: 130028751 bp out of 1034011644 bp ( 12.58 % ) Sampling Time: 00:06:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3412578 Comparison Time: 04:12:36 (hh:mm:ss) Elapsed Time, 246722 HSPs Collected Number of families returned by RECON: 16629 Round Time: 04:32:29 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 390429 repeats masked totaling 83505196 bp(s). - TE Masking time 00:13:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270124425 bp Num Contigs Represented = 3926 Non ambiguous bp: Initial: 270039997 bp After Masking: 182739208 bp Masked: 32.33 % -- Input Database Coverage: 400153176 bp out of 1034011644 bp ( 38.70 % ) Sampling Time: 00:24:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31525770 Comparison Time: 31:54:39 (hh:mm:ss) Elapsed Time, 725667 HSPs Collected Number of families returned by RECON: 57916 Round Time: 34:16:31 (hh:mm:ss) Elapsed Time : 1069 families discovered. RepeatScout/RECON discovery complete: 2171 families found Classification Time: 02:47:37 (hh:mm:ss) Elapsed Time Program Time: 42:52:44 (hh:mm:ss) Elapsed Time