RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Sjiafk/RM_1489.FriJul51541022024 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: 1720219261 Database = /dev/shm/rModeler.Sjiafk/GCF_000735185.1_NC01 - Sequences = 38657 - Bases = 636613682 - N50 = 218610 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 26876910-28796675 | [ 2 ] 24957145-26876910 | [ 1 ] 23037380-24957145 | [ ] 21117615-23037380 | [ ] 19197850-21117615 | [ ] 17278085-19197850 | [ ] 15358320-17278085 | [ 1 ] 13438555-15358320 | [ ] 11518790-13438555 | [ ] 9599025-11518790 | [ 1 ] 7679260-9599025 | [ ] 5759495-7679260 | [ ] 3839730-5759495 | [ 1 ] 1919965-3839730 | [ 4 ] 200-1919965 |************************************************** [ 38647 ] Storage Throughput = excellent ( 1035.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40900285 bp ( 40039270 non ambiguous ) - Num Contigs Represented = 2811 - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:47 (hh:mm:ss) Elapsed Time Round Time: 00:24:32 (hh:mm:ss) Elapsed Time : 744 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 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10374 repeats masked totaling 1791240 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10210767 bp Num Contigs Represented = 671 Non ambiguous bp: Initial: 10019195 bp After Masking: 7992465 bp Masked: 20.23 % -- Input Database Coverage: 10210767 bp out of 636613682 bp ( 1.60 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 263175 Comparison Time: 00:07:07 (hh:mm:ss) Elapsed Time, 6528 HSPs Collected Number of families returned by RECON: 1145 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 9 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 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31772 repeats masked totaling 5371738 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30689466 bp Num Contigs Represented = 2188 Non ambiguous bp: Initial: 30020023 bp After Masking: 23906283 bp Masked: 20.37 % -- Input Database Coverage: 40900233 bp out of 636613682 bp ( 6.42 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2907666 Comparison Time: 00:36:46 (hh:mm:ss) Elapsed Time, 29742 HSPs Collected Number of families returned by RECON: 3987 Round Time: 00:40:07 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101236 repeats masked totaling 16953967 bp(s). - TE Masking time 00:02:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91852246 bp Num Contigs Represented = 6205 Non ambiguous bp: Initial: 90001176 bp After Masking: 70711421 bp Masked: 21.43 % -- Input Database Coverage: 132752479 bp out of 636613682 bp ( 20.85 % ) Sampling Time: 00:06:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25300941 Comparison Time: 04:03:14 (hh:mm:ss) Elapsed Time, 219420 HSPs Collected Number of families returned by RECON: 14839 Round Time: 04:20:26 (hh:mm:ss) Elapsed Time : 487 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 364912 repeats masked totaling 62403717 bp(s). - TE Masking time 00:11:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275704949 bp Num Contigs Represented = 17326 Non ambiguous bp: Initial: 270037647 bp After Masking: 200903424 bp Masked: 25.60 % -- Input Database Coverage: 408457428 bp out of 636613682 bp ( 64.16 % ) Sampling Time: 00:23:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 220678536 Comparison Time: 31:11:47 (hh:mm:ss) Elapsed Time, 606384 HSPs Collected Number of families returned by RECON: 56849 Round Time: 33:06:31 (hh:mm:ss) Elapsed Time : 1051 families discovered. RepeatScout/RECON discovery complete: 2353 families found Classification Time: 01:19:26 (hh:mm:ss) Elapsed Time Program Time: 39:59:06 (hh:mm:ss) Elapsed Time