RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Zo0wHk/RM_3035228.SatJul61339262024 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: 1720298366 Database = /dev/shm/rModeler.Zo0wHk/GCF_033978785.1_RoL_Eaeq_v1.1 - Sequences = 424 - Bases = 1892198045 - N50 = 81372923 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 95612635-102441555 | [ 2 ] 88783715-95612634 | [ 2 ] 81954795-88783714 | [ 5 ] 75125875-81954794 | [ 2 ] 68296955-75125874 | [ 2 ] 61468035-68296954 | [ 1 ] 54639115-61468034 | [ 2 ] 47810195-54639114 | [ 5 ] 40981275-47810194 | [ 4 ] 34152355-40981274 | [ 3 ] 27323435-34152354 | [ ] 20494515-27323434 | [ ] 13665595-20494514 | [ ] 6836675-13665594 | [ ] 7756-6836675 |************************************************** [ 396 ] Storage Throughput = excellent ( 1336.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014214 bp ( 40013094 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:27 (hh:mm:ss) Elapsed Time Round Time: 00:46:19 (hh:mm:ss) Elapsed Time : 1183 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23685 repeats masked totaling 5355271 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031723 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10031443 bp After Masking: 3281755 bp Masked: 67.29 % -- Input Database Coverage: 10031723 bp out of 1892198045 bp ( 0.53 % ) Sampling Time: 00:03:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:33 (hh:mm:ss) Elapsed Time, 37098 HSPs Collected Number of families returned by RECON: 1078 Round Time: 00:09:31 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73263 repeats masked totaling 16409863 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022425 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30021585 bp After Masking: 8973212 bp Masked: 70.11 % -- Input Database Coverage: 40054148 bp out of 1892198045 bp ( 2.12 % ) Sampling Time: 00:12:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:18:36 (hh:mm:ss) Elapsed Time, 61056 HSPs Collected Number of families returned by RECON: 2996 Round Time: 00:32:06 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 230354 repeats masked totaling 50871702 bp(s). - TE Masking time 00:03:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022967 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90020507 bp After Masking: 25200500 bp Masked: 72.01 % -- Input Database Coverage: 130077115 bp out of 1892198045 bp ( 6.87 % ) Sampling Time: 00:35:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:29:07 (hh:mm:ss) Elapsed Time, 239139 HSPs Collected Number of families returned by RECON: 7556 Round Time: 02:10:03 (hh:mm:ss) Elapsed Time : 472 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:28:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 745808 repeats masked totaling 162776156 bp(s). - TE Masking time 00:13:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008363 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270001363 bp After Masking: 65673197 bp Masked: 75.68 % -- Input Database Coverage: 400085478 bp out of 1892198045 bp ( 21.14 % ) Sampling Time: 01:52:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 09:41:20 (hh:mm:ss) Elapsed Time, 576071 HSPs Collected Number of families returned by RECON: 19658 Round Time: 11:51:45 (hh:mm:ss) Elapsed Time : 912 families discovered. RepeatScout/RECON discovery complete: 2719 families found Classification Time: 01:24:40 (hh:mm:ss) Elapsed Time Program Time: 16:54:24 (hh:mm:ss) Elapsed Time