RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.eRoIQn/RM_190109.FriFeb71209412025 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: 1738958974 Database = /data/tmp/rModeler.eRoIQn/GCA_046129645.1_bCyaCrs1.hap2 - Sequences = 309 - Bases = 1195662530 - N50 = 76386218 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 147945309-158511236 | [ 1 ] 137379382-147945309 | [ ] 126813455-137379382 | [ ] 116247528-126813455 | [ 2 ] 105681601-116247528 | [ ] 95115674-105681601 | [ ] 84549747-95115674 | [ ] 73983820-84549747 | [ 2 ] 63417893-73983820 | [ 1 ] 52851966-63417893 | [ ] 42286039-52851966 | [ 1 ] 31720112-42286039 | [ 2 ] 21154185-31720112 | [ 5 ] 10588258-21154185 |* [ 8 ] 22331-10588258 |************************************************** [ 287 ] Storage Throughput = excellent ( 1481.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014611 bp ( 40013611 non ambiguous ) - Num Contigs Represented = 106 - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:22 (hh:mm:ss) Elapsed Time Round Time: 00:23:11 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3516 repeats masked totaling 1490068 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039653 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10039453 bp After Masking: 8197599 bp Masked: 18.35 % -- Input Database Coverage: 10039653 bp out of 1195662530 bp ( 0.84 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 56758 HSPs Collected Number of families returned by RECON: 217 Round Time: 00:04:44 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13399 repeats masked totaling 5450317 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014958 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 30014158 bp After Masking: 23671281 bp Masked: 21.13 % -- Input Database Coverage: 40054611 bp out of 1195662530 bp ( 3.35 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:14:49 (hh:mm:ss) Elapsed Time, 5218 HSPs Collected Number of families returned by RECON: 1253 Round Time: 00:17:48 (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 : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41501 repeats masked totaling 16534264 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008738 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 90002638 bp After Masking: 70835162 bp Masked: 21.30 % -- Input Database Coverage: 130063349 bp out of 1195662530 bp ( 10.88 % ) Sampling Time: 00:12:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:41:21 (hh:mm:ss) Elapsed Time, 46069 HSPs Collected Number of families returned by RECON: 8116 Round Time: 02:03:26 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131360 repeats masked totaling 53730561 bp(s). - TE Masking time 00:03:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017693 bp Num Contigs Represented = 235 Non ambiguous bp: Initial: 270003393 bp After Masking: 209007791 bp Masked: 22.59 % -- Input Database Coverage: 400081042 bp out of 1195662530 bp ( 33.46 % ) Sampling Time: 00:33:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 15:03:58 (hh:mm:ss) Elapsed Time, 236986 HSPs Collected Number of families returned by RECON: 54972 Round Time: 16:23:19 (hh:mm:ss) Elapsed Time : 277 families discovered. RepeatScout/RECON discovery complete: 502 families found Classification Time: 00:28:35 (hh:mm:ss) Elapsed Time Program Time: 19:41:03 (hh:mm:ss) Elapsed Time