RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6DCmZo/RM_456102.MonNov271105562023 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: 1701111955 Database = /dev/shm/rModeler.6DCmZo/GCF_030684315.1_sSteTig4.hap1 - Sequences = 835 - Bases = 3198515386 - N50 = 79394055 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 181115602-194051863 | [ 1 ] 168179341-181115601 | [ ] 155243081-168179341 | [ 1 ] 142306820-155243080 | [ ] 129370560-142306820 | [ 3 ] 116434299-129370559 | [ ] 103498039-116434299 | [ 3 ] 90561778-103498038 | [ 3 ] 77625518-90561778 | [ 3 ] 64689257-77625517 | [ 2 ] 51752997-64689257 | [ 8 ] 38816736-51752996 | [ 8 ] 25880476-38816736 | [ 6 ] 12944215-25880475 | [ 9 ] 7955-12944215 |************************************************** [ 788 ] Storage Throughput = excellent ( 1264.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40220194 bp ( 40029658 non ambiguous ) - Num Contigs Represented = 119 - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:16 (hh:mm:ss) Elapsed Time Round Time: 00:27:02 (hh:mm:ss) Elapsed Time : 383 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19417 repeats masked totaling 4624162 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022638 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 10004063 bp After Masking: 4469381 bp Masked: 55.32 % -- Input Database Coverage: 10022638 bp out of 3198515386 bp ( 0.31 % ) Sampling Time: 00:06:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 6582 HSPs Collected Number of families returned by RECON: 787 Round Time: 00:12:59 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59996 repeats masked totaling 14367030 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30197522 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 30025561 bp After Masking: 13120170 bp Masked: 56.30 % -- Input Database Coverage: 40220160 bp out of 3198515386 bp ( 1.26 % ) Sampling Time: 00:16:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:21:58 (hh:mm:ss) Elapsed Time, 30426 HSPs Collected Number of families returned by RECON: 2630 Round Time: 00:42:47 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:49:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 193293 repeats masked totaling 45739980 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90415721 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 90038838 bp After Masking: 36404120 bp Masked: 59.57 % -- Input Database Coverage: 130635881 bp out of 3198515386 bp ( 4.08 % ) Sampling Time: 00:55:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 01:57:06 (hh:mm:ss) Elapsed Time, 93245 HSPs Collected Number of families returned by RECON: 6659 Round Time: 02:55:50 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:24:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 618658 repeats masked totaling 146233562 bp(s). - TE Masking time 00:09:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271162428 bp Num Contigs Represented = 299 Non ambiguous bp: Initial: 270020447 bp After Masking: 100304101 bp Masked: 62.85 % -- Input Database Coverage: 401798309 bp out of 3198515386 bp ( 12.56 % ) Sampling Time: 02:44:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 13:36:21 (hh:mm:ss) Elapsed Time, 326445 HSPs Collected Number of families returned by RECON: 20217 Round Time: 16:36:10 (hh:mm:ss) Elapsed Time : 600 families discovered. RepeatScout/RECON discovery complete: 1274 families found Classification Time: 00:53:32 (hh:mm:ss) Elapsed Time Program Time: 21:48:20 (hh:mm:ss) Elapsed Time