RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QUK7MG/RM_10995.ThuNov301915022023 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: 1701400501 Database = /dev/shm/rModeler.QUK7MG/GCA_030014385.1_fTriRos1.hap1 - Sequences = 349 - Bases = 1045025885 - N50 = 40889004 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 81571129-87397567 | [ 1 ] 75744691-81571128 | [ ] 69918253-75744690 | [ ] 64091815-69918252 | [ 1 ] 58265378-64091815 | [ ] 52438940-58265377 | [ 4 ] 46612502-52438939 | [ ] 40786064-46612501 | [ 3 ] 34959626-40786063 | [ 5 ] 29133189-34959626 | [ 5 ] 23306751-29133188 | [ 1 ] 17480313-23306750 | [ 6 ] 11653875-17480312 | [ 1 ] 5827437-11653874 | [ ] 1000-5827437 |************************************************** [ 322 ] Storage Throughput = excellent ( 1122.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022549 bp ( 40021349 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:46 (hh:mm:ss) Elapsed Time Round Time: 00:28:17 (hh:mm:ss) Elapsed Time : 703 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19191 repeats masked totaling 4260427 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012978 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10012778 bp After Masking: 4901470 bp Masked: 51.05 % -- Input Database Coverage: 10012978 bp out of 1045025885 bp ( 0.96 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:31 (hh:mm:ss) Elapsed Time, 10370 HSPs Collected Number of families returned by RECON: 1005 Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 16 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 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58588 repeats masked totaling 12506662 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009559 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30008559 bp After Masking: 15246896 bp Masked: 49.19 % -- Input Database Coverage: 40022537 bp out of 1045025885 bp ( 3.83 % ) Sampling Time: 00:06:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:04 (hh:mm:ss) Elapsed Time, 32645 HSPs Collected Number of families returned by RECON: 3804 Round Time: 00:35:05 (hh:mm:ss) Elapsed Time : 78 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 00:20:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189297 repeats masked totaling 39497952 bp(s). - TE Masking time 00:02:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018331 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 90015731 bp After Masking: 43534293 bp Masked: 51.64 % -- Input Database Coverage: 130040868 bp out of 1045025885 bp ( 12.44 % ) Sampling Time: 00:25:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:37:38 (hh:mm:ss) Elapsed Time, 206130 HSPs Collected Number of families returned by RECON: 11863 Round Time: 03:12:05 (hh:mm:ss) Elapsed Time : 392 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 629501 repeats masked totaling 127831115 bp(s). - TE Masking time 00:12:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020348 bp Num Contigs Represented = 166 Non ambiguous bp: Initial: 270009467 bp After Masking: 121899967 bp Masked: 54.85 % -- Input Database Coverage: 400061216 bp out of 1045025885 bp ( 38.28 % ) Sampling Time: 01:11:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 20:17:55 (hh:mm:ss) Elapsed Time, 556979 HSPs Collected Number of families returned by RECON: 37267 Round Time: 22:24:24 (hh:mm:ss) Elapsed Time : 938 families discovered. RepeatScout/RECON discovery complete: 2127 families found Classification Time: 01:37:00 (hh:mm:ss) Elapsed Time Program Time: 28:26:01 (hh:mm:ss) Elapsed Time