RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TwQEhx/RM_129568.TueApr20134492024 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: 1712046889 Database = /dev/shm/rModeler.TwQEhx/GCF_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 = good ( 816.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020244 bp ( 40017844 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:54 (hh:mm:ss) Elapsed Time Round Time: 00:24:17 (hh:mm:ss) Elapsed Time : 708 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 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19770 repeats masked totaling 4075537 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024998 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10024198 bp After Masking: 5083965 bp Masked: 49.28 % -- Input Database Coverage: 10024998 bp out of 1045025885 bp ( 0.96 % ) Sampling Time: 00:02:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:16 (hh:mm:ss) Elapsed Time, 5825 HSPs Collected Number of families returned by RECON: 1036 Round Time: 00:08:24 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60553 repeats masked totaling 12726834 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035180 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30033580 bp After Masking: 14812703 bp Masked: 50.68 % -- Input Database Coverage: 40060178 bp out of 1045025885 bp ( 3.83 % ) Sampling Time: 00:08:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:24:09 (hh:mm:ss) Elapsed Time, 30805 HSPs Collected Number of families returned by RECON: 3490 Round Time: 00:33:51 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 194217 repeats masked totaling 38721629 bp(s). - TE Masking time 00:02:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034457 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 90030857 bp After Masking: 44279984 bp Masked: 50.82 % -- Input Database Coverage: 130094635 bp out of 1045025885 bp ( 12.45 % ) Sampling Time: 00:25:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 02:23:45 (hh:mm:ss) Elapsed Time, 215122 HSPs Collected Number of families returned by RECON: 11863 Round Time: 03:03:45 (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 : 00:05:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:58:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 654668 repeats masked totaling 128329802 bp(s). - TE Masking time 00:10:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037924 bp Num Contigs Represented = 179 Non ambiguous bp: Initial: 270030324 bp After Masking: 120693736 bp Masked: 55.30 % -- Input Database Coverage: 400132559 bp out of 1045025885 bp ( 38.29 % ) Sampling Time: 01:14:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 16:21:15 (hh:mm:ss) Elapsed Time, 672223 HSPs Collected Number of families returned by RECON: 36647 Round Time: 18:15:03 (hh:mm:ss) Elapsed Time : 939 families discovered. RepeatScout/RECON discovery complete: 2140 families found Classification Time: 01:29:02 (hh:mm:ss) Elapsed Time Program Time: 23:54:22 (hh:mm:ss) Elapsed Time