RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.T0g3Oq/RM_20581.ThuJul110502212024 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: 1720699340 Database = /dev/shm/rModeler.T0g3Oq/GCF_002021735.2_Okis_V2 - Sequences = 4087 - Bases = 2375911593 - N50 = 68916532 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 89513036-95906753 | [ 3 ] 83119319-89513035 | [ 4 ] 76725603-83119319 | [ 5 ] 70331886-76725602 | [ 1 ] 63938169-70331885 | [ 2 ] 57544453-63938169 | [ 2 ] 51150736-57544452 | [ 5 ] 44757019-51150735 | [ 7 ] 38363303-44757019 | [ 1 ] 31969586-38363302 | [ ] 25575869-31969585 | [ ] 19182153-25575869 | [ 2 ] 12788436-19182152 | [ 5 ] 6394719-12788435 | [ 1 ] 1003-6394719 |************************************************** [ 4049 ] Storage Throughput = excellent ( 1027.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013473 bp ( 40005855 non ambiguous ) - Num Contigs Represented = 178 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:35 (hh:mm:ss) Elapsed Time Round Time: 00:28:50 (hh:mm:ss) Elapsed Time : 839 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13495 repeats masked totaling 3523853 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039521 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 10037216 bp After Masking: 4066075 bp Masked: 59.49 % -- Input Database Coverage: 10039521 bp out of 2375911593 bp ( 0.42 % ) Sampling Time: 00:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 6089 HSPs Collected Number of families returned by RECON: 1059 Round Time: 00:12:32 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40842 repeats masked totaling 10621082 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014990 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 30009677 bp After Masking: 12208407 bp Masked: 59.32 % -- Input Database Coverage: 40054511 bp out of 2375911593 bp ( 1.69 % ) Sampling Time: 00:17:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:22:13 (hh:mm:ss) Elapsed Time, 39139 HSPs Collected Number of families returned by RECON: 3505 Round Time: 00:40:52 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128514 repeats masked totaling 32848484 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032308 bp Num Contigs Represented = 357 Non ambiguous bp: Initial: 90015248 bp After Masking: 35950359 bp Masked: 60.06 % -- Input Database Coverage: 130086819 bp out of 2375911593 bp ( 5.48 % ) Sampling Time: 00:53:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2734291 Comparison Time: 02:07:02 (hh:mm:ss) Elapsed Time, 294651 HSPs Collected Number of families returned by RECON: 10600 Round Time: 03:17:50 (hh:mm:ss) Elapsed Time : 483 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:26:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 438388 repeats masked totaling 111690065 bp(s). - TE Masking time 00:10:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270065579 bp Num Contigs Represented = 816 Non ambiguous bp: Initial: 270013377 bp After Masking: 96568134 bp Masked: 64.24 % -- Input Database Coverage: 400152398 bp out of 2375911593 bp ( 16.84 % ) Sampling Time: 02:45:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24335776 Comparison Time: 13:53:06 (hh:mm:ss) Elapsed Time, 759306 HSPs Collected Number of families returned by RECON: 34686 Round Time: 17:32:02 (hh:mm:ss) Elapsed Time : 987 families discovered. RepeatScout/RECON discovery complete: 2433 families found Classification Time: 01:35:48 (hh:mm:ss) Elapsed Time Program Time: 23:47:54 (hh:mm:ss) Elapsed Time