RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BzEclr/RM_746503.FriMay120959262023 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: 1683910766 Database = /dev/shm/rModeler.BzEclr/GCA_028501385.1_bRisTri1.mat.cur.20221130 - Sequences = 733 - Bases = 1268441171 - N50 = 127362208 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203666114-218212613 | [ 1 ] 189119616-203666114 | [ ] 174573118-189119616 | [ ] 160026620-174573118 | [ 1 ] 145480122-160026620 | [ ] 130933623-145480121 | [ ] 116387125-130933623 | [ 1 ] 101840627-116387125 | [ ] 87294129-101840627 | [ 1 ] 72747631-87294129 | [ 2 ] 58201132-72747630 | [ ] 43654634-58201132 | [ 3 ] 29108136-43654634 | [ 1 ] 14561638-29108136 | [ 6 ] 15140-14561638 |************************************************** [ 717 ] Storage Throughput = excellent ( 1160.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015994 bp ( 40010247 non ambiguous ) - Num Contigs Represented = 115 - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:32 (hh:mm:ss) Elapsed Time Round Time: 00:22:15 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2085 repeats masked totaling 766602 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030207 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10027995 bp After Masking: 8722783 bp Masked: 13.02 % -- Input Database Coverage: 10030207 bp out of 1268441171 bp ( 0.79 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:07:33 (hh:mm:ss) Elapsed Time, 827 HSPs Collected Number of families returned by RECON: 211 Round Time: 00:08:59 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6016 repeats masked totaling 2235977 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025859 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30022324 bp After Masking: 25283066 bp Masked: 15.79 % -- Input Database Coverage: 40056066 bp out of 1268441171 bp ( 3.16 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:35:12 (hh:mm:ss) Elapsed Time, 5843 HSPs Collected Number of families returned by RECON: 1164 Round Time: 00:39:31 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18804 repeats masked totaling 7003033 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90064148 bp Num Contigs Represented = 204 Non ambiguous bp: Initial: 90014370 bp After Masking: 75715924 bp Masked: 15.88 % -- Input Database Coverage: 130120214 bp out of 1268441171 bp ( 10.26 % ) Sampling Time: 00:10:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 03:49:35 (hh:mm:ss) Elapsed Time, 57057 HSPs Collected Number of families returned by RECON: 7124 Round Time: 04:34:03 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68108 repeats masked totaling 23993650 bp(s). - TE Masking time 00:03:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270103007 bp Num Contigs Represented = 382 Non ambiguous bp: Initial: 270008154 bp After Masking: 224113986 bp Masked: 17.00 % -- Input Database Coverage: 400223221 bp out of 1268441171 bp ( 31.55 % ) Sampling Time: 00:37:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23327865 Comparison Time: 29:03:05 (hh:mm:ss) Elapsed Time, 1302328 HSPs Collected Number of families returned by RECON: 43817 Round Time: 30:13:52 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatScout/RECON discovery complete: 383 families found Classification Time: 00:43:15 (hh:mm:ss) Elapsed Time Program Time: 36:41:55 (hh:mm:ss) Elapsed Time