RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QBfhQ5/RM_382807.TueJan101322372023 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: 1673385756 Database = /dev/shm/rModeler.QBfhQ5/GCA_003369685.2_UOA_Angus_1 - Sequences = 1435 - Bases = 2580764822 - N50 = 106503169 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146538201-157005132 | [ 1 ] 136071270-146538200 | [ ] 125604339-136071269 | [ 1 ] 115137409-125604339 | [ 4 ] 104670478-115137408 | [ 4 ] 94203547-104670477 | [ 1 ] 83736616-94203546 | [ 2 ] 73269686-83736616 | [ 3 ] 62802755-73269685 | [ 5 ] 52335824-62802754 | [ 2 ] 41868893-52335823 | [ 5 ] 31401963-41868893 | [ 1 ] 20935032-31401962 | [ ] 10468101-20935031 | [ 1 ] 1171-10468101 |************************************************** [ 1405 ] Storage Throughput = excellent ( 1329.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40240478 bp ( 40026091 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:22 (hh:mm:ss) Elapsed Time Round Time: 00:21:30 (hh:mm:ss) Elapsed Time : 226 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14329 repeats masked totaling 3359851 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043863 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10003863 bp After Masking: 6521745 bp Masked: 34.81 % -- Input Database Coverage: 10043863 bp out of 2580764822 bp ( 0.39 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 5318 HSPs Collected Number of families returned by RECON: 753 Round Time: 00:07:08 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46794 repeats masked totaling 11035466 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30196535 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30022148 bp After Masking: 18713190 bp Masked: 37.67 % -- Input Database Coverage: 40240398 bp out of 2580764822 bp ( 1.56 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:24:06 (hh:mm:ss) Elapsed Time, 36434 HSPs Collected Number of families returned by RECON: 1973 Round Time: 00:27:32 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145023 repeats masked totaling 33568013 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90354336 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 90028267 bp After Masking: 55698261 bp Masked: 38.13 % -- Input Database Coverage: 130594734 bp out of 2580764822 bp ( 5.06 % ) Sampling Time: 00:06:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 02:01:25 (hh:mm:ss) Elapsed Time, 74600 HSPs Collected Number of families returned by RECON: 7805 Round Time: 02:10:15 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 472242 repeats masked totaling 109340369 bp(s). - TE Masking time 00:03:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270903129 bp Num Contigs Represented = 277 Non ambiguous bp: Initial: 270000665 bp After Masking: 158248674 bp Masked: 41.39 % -- Input Database Coverage: 401497863 bp out of 2580764822 bp ( 15.56 % ) Sampling Time: 00:21:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 12:26:07 (hh:mm:ss) Elapsed Time, 192771 HSPs Collected Number of families returned by RECON: 31360 Round Time: 13:00:07 (hh:mm:ss) Elapsed Time : 296 families discovered. RepeatScout/RECON discovery complete: 778 families found Classification Time: 00:20:16 (hh:mm:ss) Elapsed Time Program Time: 16:26:48 (hh:mm:ss) Elapsed Time