RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.P4esTD/RM_1495810.MonApr141230562025 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: 1744659054 Database = /dev/shm/rModeler.P4esTD/GCA_964205295.1_aBomVar4.paternal.1 - Sequences = 4757 - Bases = 9369791316 - N50 = 1144564707 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1321546500-1415942608 | [ 1 ] 1227150393-1321546500 | [ 1 ] 1132754286-1227150393 | [ 1 ] 1038358179-1132754286 | [ 1 ] 943962072-1038358179 | [ 2 ] 849565964-943962071 | [ ] 755169857-849565964 | [ ] 660773750-755169857 | [ ] 566377643-660773750 | [ ] 471981536-566377643 | [ 1 ] 377585428-471981535 | [ ] 283189321-377585428 | [ 1 ] 188793214-283189321 | [ 1 ] 94397107-188793214 | [ 3 ] 1000-94397107 |************************************************** [ 4745 ] Storage Throughput = excellent ( 1695.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012042 bp ( 40007842 non ambiguous ) - Num Contigs Represented = 117 - Sequence extraction : 00:09:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:38 (hh:mm:ss) Elapsed Time Round Time: 00:26:34 (hh:mm:ss) Elapsed Time : 642 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14737 repeats masked totaling 5469393 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041486 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10039686 bp After Masking: 3583551 bp Masked: 64.31 % -- Input Database Coverage: 10041486 bp out of 9369791316 bp ( 0.11 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:13 (hh:mm:ss) Elapsed Time, 10312 HSPs Collected Number of families returned by RECON: 1011 Round Time: 00:06:59 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46660 repeats masked totaling 16804536 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010476 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 30008076 bp After Masking: 10283012 bp Masked: 65.73 % -- Input Database Coverage: 40051962 bp out of 9369791316 bp ( 0.43 % ) Sampling Time: 00:10:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:11:40 (hh:mm:ss) Elapsed Time, 49637 HSPs Collected Number of families returned by RECON: 3558 Round Time: 00:22:31 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:21:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143122 repeats masked totaling 52968964 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024699 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 90014299 bp After Masking: 28464870 bp Masked: 68.38 % -- Input Database Coverage: 130076661 bp out of 9369791316 bp ( 1.39 % ) Sampling Time: 00:31:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 00:48:19 (hh:mm:ss) Elapsed Time, 275613 HSPs Collected Number of families returned by RECON: 10504 Round Time: 01:24:36 (hh:mm:ss) Elapsed Time : 332 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 481054 repeats masked totaling 169114542 bp(s). - TE Masking time 00:05:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270048626 bp Num Contigs Represented = 507 Non ambiguous bp: Initial: 270012426 bp After Masking: 74776041 bp Masked: 72.31 % -- Input Database Coverage: 400125287 bp out of 9369791316 bp ( 4.27 % ) Sampling Time: 01:36:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23103003 Comparison Time: 04:24:32 (hh:mm:ss) Elapsed Time, 1561806 HSPs Collected Number of families returned by RECON: 28400 Round Time: 06:22:46 (hh:mm:ss) Elapsed Time : 883 families discovered. RepeatScout/RECON discovery complete: 1959 families found Classification Time: 00:46:41 (hh:mm:ss) Elapsed Time Program Time: 09:30:07 (hh:mm:ss) Elapsed Time