RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2Wvkp8/RM_2072.ThuDec71000272023 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: 1701972026 Database = /dev/shm/rModeler.2Wvkp8/GCA_949774975.1_mLagAlb1.1 - Sequences = 410 - Bases = 2544835795 - N50 = 115079701 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 179702704-192538540 | [ 2 ] 166866868-179702704 | [ 1 ] 154031032-166866868 | [ ] 141195196-154031032 | [ 2 ] 128359360-141195196 | [ 1 ] 115523524-128359360 | [ 1 ] 102687688-115523524 | [ 5 ] 89851852-102687688 | [ 1 ] 77016016-89851852 | [ 6 ] 64180180-77016016 | [ ] 51344344-64180180 | [ 2 ] 38508508-51344344 | [ ] 25672672-38508508 | [ 1 ] 12836836-25672672 | [ ] 1000-12836836 |************************************************** [ 388 ] Storage Throughput = excellent ( 1211.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028375 bp ( 40024775 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:21 (hh:mm:ss) Elapsed Time Round Time: 00:36:47 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (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... 9146 repeats masked totaling 2921022 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006162 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10005362 bp After Masking: 6940891 bp Masked: 30.63 % -- Input Database Coverage: 10006162 bp out of 2544835795 bp ( 0.39 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:43 (hh:mm:ss) Elapsed Time, 185891 HSPs Collected Number of families returned by RECON: 762 Round Time: 00:10:17 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32911 repeats masked totaling 9957510 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022210 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30019410 bp After Masking: 19565132 bp Masked: 34.83 % -- Input Database Coverage: 40028372 bp out of 2544835795 bp ( 1.57 % ) Sampling Time: 00:03:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:13 (hh:mm:ss) Elapsed Time, 30790 HSPs Collected Number of families returned by RECON: 2309 Round Time: 00:34:00 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109814 repeats masked totaling 33151846 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020091 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 90012837 bp After Masking: 55141462 bp Masked: 38.74 % -- Input Database Coverage: 130048463 bp out of 2544835795 bp ( 5.11 % ) Sampling Time: 00:11:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:22:32 (hh:mm:ss) Elapsed Time, 293071 HSPs Collected Number of families returned by RECON: 7496 Round Time: 03:37:18 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 361981 repeats masked totaling 104455482 bp(s). - TE Masking time 00:05:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270029163 bp Num Contigs Represented = 212 Non ambiguous bp: Initial: 270007411 bp After Masking: 161198106 bp Masked: 40.30 % -- Input Database Coverage: 400077626 bp out of 2544835795 bp ( 15.72 % ) Sampling Time: 00:33:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 23:54:21 (hh:mm:ss) Elapsed Time, 2536444 HSPs Collected Number of families returned by RECON: 33266 Round Time: 25:10:52 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatScout/RECON discovery complete: 800 families found Classification Time: 00:30:17 (hh:mm:ss) Elapsed Time Program Time: 30:39:31 (hh:mm:ss) Elapsed Time