RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.7rOGgF/RM_2155789.TueNov191120422024 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: 1732044041 Database = /scratch/tmp/rModeler.7rOGgF/GCA_964205295.1_aBomVar4.maternal.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 ( 1564.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028289 bp ( 40021889 non ambiguous ) - Num Contigs Represented = 90 - Sequence extraction : 00:10:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:22 (hh:mm:ss) Elapsed Time Round Time: 00:31:56 (hh:mm:ss) Elapsed Time : 693 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 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14790 repeats masked totaling 5636752 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032215 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10030415 bp After Masking: 3478936 bp Masked: 65.32 % -- Input Database Coverage: 10032215 bp out of 9369791316 bp ( 0.11 % ) Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:20 (hh:mm:ss) Elapsed Time, 6657 HSPs Collected Number of families returned by RECON: 1059 Round Time: 00:07:15 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:08:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44366 repeats masked totaling 16970372 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035994 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30031394 bp After Masking: 10268316 bp Masked: 65.81 % -- Input Database Coverage: 40068209 bp out of 9369791316 bp ( 0.43 % ) Sampling Time: 00:12:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:13:39 (hh:mm:ss) Elapsed Time, 54269 HSPs Collected Number of families returned by RECON: 3479 Round Time: 00:27:25 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:28:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138923 repeats masked totaling 52267559 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016229 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 90000815 bp After Masking: 28662606 bp Masked: 68.15 % -- Input Database Coverage: 130084438 bp out of 9369791316 bp ( 1.39 % ) Sampling Time: 00:41:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 01:07:22 (hh:mm:ss) Elapsed Time, 343083 HSPs Collected Number of families returned by RECON: 10136 Round Time: 01:54:12 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:22:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465269 repeats masked totaling 170054706 bp(s). - TE Masking time 00:08:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044278 bp Num Contigs Represented = 557 Non ambiguous bp: Initial: 270004551 bp After Masking: 74395208 bp Masked: 72.45 % -- Input Database Coverage: 400128716 bp out of 9369791316 bp ( 4.27 % ) Sampling Time: 01:59:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23198266 Comparison Time: 05:33:04 (hh:mm:ss) Elapsed Time, 1442479 HSPs Collected Number of families returned by RECON: 28260 Round Time: 07:52:37 (hh:mm:ss) Elapsed Time : 904 families discovered. RepeatScout/RECON discovery complete: 2027 families found Classification Time: 00:51:41 (hh:mm:ss) Elapsed Time Program Time: 11:45:06 (hh:mm:ss) Elapsed Time