RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.D5Qjua/RM_1722790.SunJul71321532024 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: 1720383713 Database = /dev/shm/rModeler.D5Qjua/GCF_033458585.1_RoL_Styp_1.0 - Sequences = 495 - Bases = 435284570 - N50 = 15443615 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27870480-29860936 | [ 2 ] 25880024-27870479 | [ ] 23889569-25880024 | [ 2 ] 21899113-23889568 | [ ] 19908658-21899113 | [ 2 ] 17918202-19908657 | [ 1 ] 15927747-17918202 | [ 1 ] 13937291-15927746 | [ 3 ] 11946836-13937291 | [ 4 ] 9956380-11946835 | [ 3 ] 7965925-9956380 | [ 4 ] 5975469-7965924 | [ ] 3985014-5975469 | [ ] 1994558-3985013 | [ 1 ] 4103-1994558 |************************************************** [ 472 ] Storage Throughput = excellent ( 1138.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031978 bp ( 40031898 non ambiguous ) - Num Contigs Represented = 161 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:29 (hh:mm:ss) Elapsed Time Round Time: 00:41:46 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4412 repeats masked totaling 1456202 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019297 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 10019297 bp After Masking: 6586799 bp Masked: 34.26 % -- Input Database Coverage: 10019297 bp out of 435284570 bp ( 2.30 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:05:06 (hh:mm:ss) Elapsed Time, 17446 HSPs Collected Number of families returned by RECON: 783 Round Time: 00:07:01 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19115 repeats masked totaling 6248309 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012601 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 30012521 bp After Masking: 18300740 bp Masked: 39.02 % -- Input Database Coverage: 40031898 bp out of 435284570 bp ( 9.20 % ) Sampling Time: 00:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:22:17 (hh:mm:ss) Elapsed Time, 32020 HSPs Collected Number of families returned by RECON: 3079 Round Time: 00:29:32 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58069 repeats masked totaling 17820840 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038705 bp Num Contigs Represented = 251 Non ambiguous bp: Initial: 90038545 bp After Masking: 55180775 bp Masked: 38.71 % -- Input Database Coverage: 130070603 bp out of 435284570 bp ( 29.88 % ) Sampling Time: 00:16:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2636956 Comparison Time: 02:18:35 (hh:mm:ss) Elapsed Time, 189759 HSPs Collected Number of families returned by RECON: 12167 Round Time: 02:41:24 (hh:mm:ss) Elapsed Time : 259 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 217655 repeats masked totaling 63230197 bp(s). - TE Masking time 00:07:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031168 bp Num Contigs Represented = 418 Non ambiguous bp: Initial: 270030688 bp After Masking: 159306454 bp Masked: 41.00 % -- Input Database Coverage: 400101771 bp out of 435284570 bp ( 91.92 % ) Sampling Time: 00:49:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23801550 Comparison Time: 16:05:44 (hh:mm:ss) Elapsed Time, 845238 HSPs Collected Number of families returned by RECON: 49175 Round Time: 17:42:07 (hh:mm:ss) Elapsed Time : 721 families discovered. RepeatScout/RECON discovery complete: 1337 families found Classification Time: 01:18:32 (hh:mm:ss) Elapsed Time Program Time: 23:00:22 (hh:mm:ss) Elapsed Time