RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6X9XcJ/RM_89581.MonJan91029472023 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: 1673288987 Database = /dev/shm/rModeler.6X9XcJ/GCF_015227675.2_mRatBN7.2 - Sequences = 176 - Bases = 2647915728 - N50 = 152453651 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 243153931-260522016 | [ 2 ] 225785846-243153930 | [ ] 208417762-225785846 | [ ] 191049677-208417761 | [ ] 173681592-191049676 | [ 1 ] 156313508-173681592 | [ 2 ] 138945423-156313507 | [ 2 ] 121577338-138945422 | [ 2 ] 104209254-121577338 |* [ 4 ] 86841169-104209253 | [ 1 ] 69473084-86841168 |* [ 4 ] 52105000-69473084 | [ 2 ] 34736915-52104999 | [ 1 ] 17368830-34736914 | [ 1 ] 746-17368830 |************************************************** [ 154 ] Storage Throughput = excellent ( 1000.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40245122 bp ( 40008768 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:56 (hh:mm:ss) Elapsed Time Round Time: 00:33:16 (hh:mm:ss) Elapsed Time : 260 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11801 repeats masked totaling 2873366 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040481 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10004275 bp After Masking: 6866858 bp Masked: 31.36 % -- Input Database Coverage: 10040481 bp out of 2647915728 bp ( 0.38 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 9228 HSPs Collected Number of families returned by RECON: 832 Round Time: 00:09:00 (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 : 00:03:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37987 repeats masked totaling 9982157 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30204638 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30004490 bp After Masking: 19225045 bp Masked: 35.93 % -- Input Database Coverage: 40245119 bp out of 2647915728 bp ( 1.52 % ) Sampling Time: 00:05:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:26:28 (hh:mm:ss) Elapsed Time, 21344 HSPs Collected Number of families returned by RECON: 2355 Round Time: 00:32:52 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124571 repeats masked totaling 30166048 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90724174 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90035196 bp After Masking: 57418029 bp Masked: 36.23 % -- Input Database Coverage: 130969293 bp out of 2647915728 bp ( 4.95 % ) Sampling Time: 00:17:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 02:52:01 (hh:mm:ss) Elapsed Time, 81310 HSPs Collected Number of families returned by RECON: 7985 Round Time: 03:12:56 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415852 repeats masked totaling 98215841 bp(s). - TE Masking time 00:04:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272813040 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 270026060 bp After Masking: 164470195 bp Masked: 39.09 % -- Input Database Coverage: 403782333 bp out of 2647915728 bp ( 15.25 % ) Sampling Time: 00:46:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 21:40:01 (hh:mm:ss) Elapsed Time, 245201 HSPs Collected Number of families returned by RECON: 31884 Round Time: 22:47:05 (hh:mm:ss) Elapsed Time : 381 families discovered. RepeatScout/RECON discovery complete: 881 families found Classification Time: 00:41:09 (hh:mm:ss) Elapsed Time Program Time: 27:56:18 (hh:mm:ss) Elapsed Time