RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.otFJcq/RM_2115058.SunJul201432392025 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: 1753047159 Database = /dev/shm/rModeler.otFJcq/GCA_965153305.1_rPodTil1.hap2.1 - Sequences = 306 - Bases = 1382196565 - N50 = 98439720 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 126217391-135232848 | [ 1 ] 117201934-126217390 | [ 2 ] 108186478-117201934 | [ ] 99171021-108186477 | [ 1 ] 90155565-99171021 | [ 3 ] 81140108-90155564 | [ 1 ] 72124652-81140108 | [ 2 ] 63109195-72124651 | [ 1 ] 54093739-63109195 | [ 2 ] 45078282-54093738 | [ 1 ] 36062826-45078282 | [ 3 ] 27047369-36062825 | [ ] 18031913-27047369 | [ ] 9016456-18031912 | [ ] 1000-9016456 |************************************************** [ 289 ] Storage Throughput = excellent ( 1343.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032965 bp ( 40027365 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:47 (hh:mm:ss) Elapsed Time Round Time: 00:12:41 (hh:mm:ss) Elapsed Time : 576 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18215 repeats masked totaling 2991358 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035198 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10033598 bp After Masking: 6772690 bp Masked: 32.50 % -- Input Database Coverage: 10035198 bp out of 1382196565 bp ( 0.73 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:46 (hh:mm:ss) Elapsed Time, 9753 HSPs Collected Number of families returned by RECON: 1284 Round Time: 00:03:24 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59204 repeats masked totaling 9602270 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037772 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30033772 bp After Masking: 19719211 bp Masked: 34.34 % -- Input Database Coverage: 40072970 bp out of 1382196565 bp ( 2.90 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:11:15 (hh:mm:ss) Elapsed Time, 45981 HSPs Collected Number of families returned by RECON: 4482 Round Time: 00:13:13 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189847 repeats masked totaling 30540939 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031480 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90017880 bp After Masking: 56255897 bp Masked: 37.51 % -- Input Database Coverage: 130104450 bp out of 1382196565 bp ( 9.41 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 01:02:39 (hh:mm:ss) Elapsed Time, 181540 HSPs Collected Number of families returned by RECON: 13748 Round Time: 01:10:29 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 631623 repeats masked totaling 101401386 bp(s). - TE Masking time 00:02:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270048148 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270008946 bp After Masking: 159653652 bp Masked: 40.87 % -- Input Database Coverage: 400152598 bp out of 1382196565 bp ( 28.95 % ) Sampling Time: 00:13:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 07:18:11 (hh:mm:ss) Elapsed Time, 469528 HSPs Collected Number of families returned by RECON: 49655 Round Time: 07:56:15 (hh:mm:ss) Elapsed Time : 1025 families discovered. RepeatScout/RECON discovery complete: 2177 families found Classification Time: 00:29:57 (hh:mm:ss) Elapsed Time Program Time: 10:05:59 (hh:mm:ss) Elapsed Time