RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.35FmWa/RM_2047081.FriJul181029412025 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: 1752859781 Database = /dev/shm/rModeler.35FmWa/GCA_046126825.1_rDibSmi1.hap2 - Sequences = 720 - Bases = 1821555219 - N50 = 134480062 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 233885664-250591293 | [ 1 ] 217180035-233885664 | [ ] 200474406-217180035 | [ ] 183768777-200474406 | [ 1 ] 167063148-183768777 | [ 1 ] 150357519-167063148 | [ ] 133651890-150357519 | [ 2 ] 116946261-133651890 | [ 3 ] 100240632-116946261 | [ ] 83535003-100240632 | [ 1 ] 66829374-83535003 | [ 1 ] 50123745-66829374 | [ 3 ] 33418116-50123745 | [ 4 ] 16712487-33418116 | [ ] 6858-16712487 |************************************************** [ 703 ] Storage Throughput = excellent ( 1195.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007891 bp ( 40007291 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:21 (hh:mm:ss) Elapsed Time Round Time: 00:37:34 (hh:mm:ss) Elapsed Time : 791 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18902 repeats masked totaling 4285303 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023079 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10023079 bp After Masking: 5413797 bp Masked: 45.99 % -- Input Database Coverage: 10023079 bp out of 1821555219 bp ( 0.55 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:13 (hh:mm:ss) Elapsed Time, 9131 HSPs Collected Number of families returned by RECON: 1419 Round Time: 00:06:50 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60878 repeats masked totaling 13294309 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024732 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30024132 bp After Masking: 15855240 bp Masked: 47.19 % -- Input Database Coverage: 40047811 bp out of 1821555219 bp ( 2.20 % ) Sampling Time: 00:06:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:21:22 (hh:mm:ss) Elapsed Time, 57376 HSPs Collected Number of families returned by RECON: 4538 Round Time: 00:29:44 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 198551 repeats masked totaling 42830523 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008222 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90007022 bp After Masking: 44643127 bp Masked: 50.40 % -- Input Database Coverage: 130056033 bp out of 1821555219 bp ( 7.14 % ) Sampling Time: 00:20:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 02:19:05 (hh:mm:ss) Elapsed Time, 240290 HSPs Collected Number of families returned by RECON: 12359 Round Time: 02:49:16 (hh:mm:ss) Elapsed Time : 445 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 663038 repeats masked totaling 141411379 bp(s). - TE Masking time 00:12:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032945 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 270027145 bp After Masking: 122018642 bp Masked: 54.81 % -- Input Database Coverage: 400088978 bp out of 1821555219 bp ( 21.96 % ) Sampling Time: 00:58:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23103003 Comparison Time: 16:38:01 (hh:mm:ss) Elapsed Time, 577526 HSPs Collected Number of families returned by RECON: 36145 Round Time: 18:39:10 (hh:mm:ss) Elapsed Time : 1119 families discovered. RepeatScout/RECON discovery complete: 2507 families found Classification Time: 01:22:38 (hh:mm:ss) Elapsed Time Program Time: 24:05:12 (hh:mm:ss) Elapsed Time