RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.n2CUi4/RM_3164970.TueNov281233462023 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: 1701203626 Database = /dev/shm/rModeler.n2CUi4/GCF_030445035.1_mDasNov1.hap2 - Sequences = 539 - Bases = 3570966115 - N50 = 130203918 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195582549-209551734 | [ 2 ] 181613364-195582548 | [ 2 ] 167644179-181613363 | [ 2 ] 153674994-167644178 | [ ] 139705810-153674994 | [ 1 ] 125736625-139705809 | [ 5 ] 111767440-125736624 | [ 2 ] 97798255-111767439 | [ 3 ] 83829070-97798254 | [ 4 ] 69859886-83829070 | [ 2 ] 55890701-69859885 | [ 3 ] 41921516-55890700 | [ 5 ] 27952331-41921515 | [ 1 ] 13983146-27952330 | [ ] 13962-13983146 |************************************************** [ 507 ] Storage Throughput = excellent ( 1117.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40203661 bp ( 40018377 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:02:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:03 (hh:mm:ss) Elapsed Time Round Time: 00:25:43 (hh:mm:ss) Elapsed Time : 305 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13520 repeats masked totaling 4126875 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003361 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10003361 bp After Masking: 5754728 bp Masked: 42.47 % -- Input Database Coverage: 10003361 bp out of 3570966115 bp ( 0.28 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:38 (hh:mm:ss) Elapsed Time, 4269 HSPs Collected Number of families returned by RECON: 746 Round Time: 00:07:13 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42832 repeats masked totaling 13069333 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30200297 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30015013 bp After Masking: 16590872 bp Masked: 44.72 % -- Input Database Coverage: 40203658 bp out of 3570966115 bp ( 1.13 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:25:31 (hh:mm:ss) Elapsed Time, 20594 HSPs Collected Number of families returned by RECON: 2118 Round Time: 00:29:38 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136302 repeats masked totaling 41307534 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90243564 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90000819 bp After Masking: 47576777 bp Masked: 47.14 % -- Input Database Coverage: 130447222 bp out of 3570966115 bp ( 3.65 % ) Sampling Time: 00:10:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:23:30 (hh:mm:ss) Elapsed Time, 79369 HSPs Collected Number of families returned by RECON: 6921 Round Time: 02:36:22 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 436683 repeats masked totaling 132650706 bp(s). - TE Masking time 00:06:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270940307 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 270015024 bp After Masking: 134014735 bp Masked: 50.37 % -- Input Database Coverage: 401387529 bp out of 3570966115 bp ( 11.24 % ) Sampling Time: 00:34:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 15:50:44 (hh:mm:ss) Elapsed Time, 323461 HSPs Collected Number of families returned by RECON: 25825 Round Time: 16:42:15 (hh:mm:ss) Elapsed Time : 464 families discovered. RepeatScout/RECON discovery complete: 1007 families found Classification Time: 00:56:16 (hh:mm:ss) Elapsed Time Program Time: 21:17:27 (hh:mm:ss) Elapsed Time