RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.eiCoGR/RM_3577510.SatJan112346172025 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: 1736667976 Database = /data/tmp/rModeler.eiCoGR/GCA_019425755.1_ASM1942575v1 - Sequences = 625 - Bases = 370913848 - N50 = 21703505 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32280743-34586494 | [ 1 ] 29974992-32280742 | [ ] 27669241-29974991 | [ 1 ] 25363490-27669240 | [ 1 ] 23057740-25363490 | [ 1 ] 20751989-23057739 | [ 7 ] 18446238-20751988 | [ 2 ] 16140487-18446237 | [ 1 ] 13834736-16140486 | [ 2 ] 11528986-13834736 | [ 1 ] 9223235-11528985 | [ ] 6917484-9223234 | [ ] 4611733-6917483 | [ ] 2305982-4611732 | [ ] 232-2305982 |************************************************** [ 608 ] Storage Throughput = excellent ( 1735.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40055537 bp ( 40039497 non ambiguous ) - Num Contigs Represented = 85 - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:42 (hh:mm:ss) Elapsed Time Round Time: 00:11:33 (hh:mm:ss) Elapsed Time : 879 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15749 repeats masked totaling 3971925 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021031 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10019234 bp After Masking: 5886909 bp Masked: 41.24 % -- Input Database Coverage: 10021031 bp out of 370913848 bp ( 2.70 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 56599 HSPs Collected Number of families returned by RECON: 1455 Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50263 repeats masked totaling 12544395 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034427 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30020184 bp After Masking: 17037564 bp Masked: 43.25 % -- Input Database Coverage: 40055458 bp out of 370913848 bp ( 10.80 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 312445 Comparison Time: 00:13:25 (hh:mm:ss) Elapsed Time, 47253 HSPs Collected Number of families returned by RECON: 4666 Round Time: 00:16:01 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157819 repeats masked totaling 39413146 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90057611 bp Num Contigs Represented = 162 Non ambiguous bp: Initial: 90025968 bp After Masking: 49267494 bp Masked: 45.27 % -- Input Database Coverage: 130113069 bp out of 370913848 bp ( 35.08 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2790703 Comparison Time: 01:16:52 (hh:mm:ss) Elapsed Time, 291254 HSPs Collected Number of families returned by RECON: 15997 Round Time: 01:28:43 (hh:mm:ss) Elapsed Time : 455 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 470133 repeats masked totaling 119462488 bp(s). - TE Masking time 00:09:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 240800457 bp Num Contigs Represented = 418 Non ambiguous bp: Initial: 240709845 bp After Masking: 117756454 bp Masked: 51.08 % -- Input Database Coverage: 370913526 bp out of 370913848 bp ( 100.00 % ) Sampling Time: 00:21:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 20094630 Comparison Time: 06:38:22 (hh:mm:ss) Elapsed Time, 784551 HSPs Collected Number of families returned by RECON: 46924 Round Time: 07:23:11 (hh:mm:ss) Elapsed Time : 1027 families discovered. RepeatScout/RECON discovery complete: 2486 families found Classification Time: 00:53:11 (hh:mm:ss) Elapsed Time Program Time: 10:16:26 (hh:mm:ss) Elapsed Time