RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.sgi4xY/RM_2018379.SunApr131724252025 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: 1744590264 Database = /data/tmp/rModeler.sgi4xY/GCA_045363895.1_fPriTyp1.hap1 - Sequences = 283 - Bases = 1147302341 - N50 = 50144621 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52576437-56331368 | [ 4 ] 48821506-52576436 |* [ 7 ] 45066575-48821505 |* [ 6 ] 41311644-45066574 | [ 2 ] 37556713-41311643 | [ 2 ] 33801782-37556712 | [ 2 ] 30046851-33801781 | [ ] 26291920-30046850 | [ 1 ] 22536989-26291919 | [ ] 18782058-22536988 | [ ] 15027127-18782057 | [ ] 11272196-15027126 | [ ] 7517265-11272195 | [ ] 3762334-7517264 | [ ] 7404-3762334 |************************************************** [ 259 ] Storage Throughput = excellent ( 1595.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030131 bp ( 40029531 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:50 (hh:mm:ss) Elapsed Time Round Time: 00:12:26 (hh:mm:ss) Elapsed Time : 1376 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23693 repeats masked totaling 3086897 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003279 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10003079 bp After Masking: 6641686 bp Masked: 33.60 % -- Input Database Coverage: 10003279 bp out of 1147302341 bp ( 0.87 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:35 (hh:mm:ss) Elapsed Time, 34990 HSPs Collected Number of families returned by RECON: 2009 Round Time: 00:04:34 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74220 repeats masked totaling 9706608 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026772 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30026372 bp After Masking: 19616382 bp Masked: 34.67 % -- Input Database Coverage: 40030051 bp out of 1147302341 bp ( 3.49 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:16:52 (hh:mm:ss) Elapsed Time, 99039 HSPs Collected Number of families returned by RECON: 6454 Round Time: 00:20:40 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:55 (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... 235650 repeats masked totaling 31195648 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008169 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90007569 bp After Masking: 56396351 bp Masked: 37.34 % -- Input Database Coverage: 130038220 bp out of 1147302341 bp ( 11.33 % ) Sampling Time: 00:06:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:42:55 (hh:mm:ss) Elapsed Time, 463404 HSPs Collected Number of families returned by RECON: 18352 Round Time: 01:59:48 (hh:mm:ss) Elapsed Time : 857 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 815893 repeats masked totaling 112714161 bp(s). - TE Masking time 00:09:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012952 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 270009452 bp After Masking: 149769676 bp Masked: 44.53 % -- Input Database Coverage: 400051172 bp out of 1147302341 bp ( 34.87 % ) Sampling Time: 00:23:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 11:24:27 (hh:mm:ss) Elapsed Time, 936036 HSPs Collected Number of families returned by RECON: 52968 Round Time: 12:30:03 (hh:mm:ss) Elapsed Time : 1677 families discovered. RepeatScout/RECON discovery complete: 4173 families found Classification Time: 01:18:40 (hh:mm:ss) Elapsed Time Program Time: 16:26:11 (hh:mm:ss) Elapsed Time