RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zcumQj/RM_2733.MonDec42342552023 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: 1701762174 Database = /dev/shm/rModeler.zcumQj/GCF_011762595.1_mTurTru1.mat.Y - Sequences = 362 - Bases = 2378522213 - N50 = 114015307 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 171493422-183742880 | [ 2 ] 159243964-171493421 | [ 1 ] 146994507-159243964 | [ ] 134745049-146994506 | [ 2 ] 122495592-134745049 | [ 1 ] 110246134-122495591 | [ 2 ] 97996677-110246134 | [ 4 ] 85747219-97996676 | [ 4 ] 73497762-85747219 | [ 3 ] 61248304-73497761 | [ ] 48998847-61248304 | [ 2 ] 36749389-48998846 | [ ] 24499932-36749389 | [ 1 ] 12250474-24499931 | [ ] 1017-12250474 |************************************************** [ 340 ] Storage Throughput = excellent ( 1146.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40100663 bp ( 40015751 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:43 (hh:mm:ss) Elapsed Time Round Time: 00:28:45 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9102 repeats masked totaling 2577793 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022252 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10022252 bp After Masking: 7361167 bp Masked: 26.55 % -- Input Database Coverage: 10022252 bp out of 2378522213 bp ( 0.42 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 12910 HSPs Collected Number of families returned by RECON: 943 Round Time: 00:09:42 (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 : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31609 repeats masked totaling 9058903 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30118406 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30033494 bp After Masking: 20780222 bp Masked: 30.81 % -- Input Database Coverage: 40140658 bp out of 2378522213 bp ( 1.69 % ) Sampling Time: 00:06:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:30:31 (hh:mm:ss) Elapsed Time, 27087 HSPs Collected Number of families returned by RECON: 2578 Round Time: 00:37:20 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104484 repeats masked totaling 29334189 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90331050 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90037199 bp After Masking: 60247648 bp Masked: 33.09 % -- Input Database Coverage: 130471708 bp out of 2378522213 bp ( 5.49 % ) Sampling Time: 00:16:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 03:11:42 (hh:mm:ss) Elapsed Time, 92734 HSPs Collected Number of families returned by RECON: 9344 Round Time: 03:31:47 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 360269 repeats masked totaling 97578027 bp(s). - TE Masking time 00:04:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270733769 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 270017443 bp After Masking: 170917303 bp Masked: 36.70 % -- Input Database Coverage: 401205477 bp out of 2378522213 bp ( 16.87 % ) Sampling Time: 00:40:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 21:58:50 (hh:mm:ss) Elapsed Time, 208820 HSPs Collected Number of families returned by RECON: 36379 Round Time: 23:21:07 (hh:mm:ss) Elapsed Time : 401 families discovered. RepeatScout/RECON discovery complete: 887 families found Classification Time: 00:35:33 (hh:mm:ss) Elapsed Time Program Time: 28:44:14 (hh:mm:ss) Elapsed Time