RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LOF3Re/RM_32085.WedMay170648312023 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: 1684331309 Database = /dev/shm/rModeler.LOF3Re/GCF_947347685.1_fPlePla1.1 - Sequences = 355 - Bases = 687388084 - N50 = 26962148 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31514232-33765178 | [ 3 ] 29263287-31514232 | [ 5 ] 27012342-29263287 | [ 2 ] 24761397-27012342 | [ 6 ] 22510452-24761397 | [ 2 ] 20259506-22510451 | [ 3 ] 18008561-20259506 | [ 1 ] 15757616-18008561 | [ 2 ] 13506671-15757616 | [ ] 11255726-13506671 | [ ] 9004780-11255725 | [ ] 6753835-9004780 | [ ] 4502890-6753835 | [ ] 2251945-4502890 | [ 2 ] 1000-2251945 |************************************************** [ 329 ] Storage Throughput = fair ( 514.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022192 bp ( 40009820 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:56:48 (hh:mm:ss) Elapsed Time Round Time: 01:23:18 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6565 repeats masked totaling 1295023 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036960 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10033760 bp After Masking: 7619428 bp Masked: 24.06 % -- Input Database Coverage: 10036960 bp out of 687388084 bp ( 1.46 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:10:05 (hh:mm:ss) Elapsed Time, 193602 HSPs Collected Number of families returned by RECON: 1005 Round Time: 00:13:08 (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 : 00:00:51 (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... 22991 repeats masked totaling 4451839 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025232 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30016060 bp After Masking: 22813813 bp Masked: 23.99 % -- Input Database Coverage: 40062192 bp out of 687388084 bp ( 5.83 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:42:53 (hh:mm:ss) Elapsed Time, 42613 HSPs Collected Number of families returned by RECON: 4126 Round Time: 00:55:45 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77946 repeats masked totaling 14317114 bp(s). - TE Masking time 00:02:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90065524 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 90039724 bp After Masking: 67059408 bp Masked: 25.52 % -- Input Database Coverage: 130127716 bp out of 687388084 bp ( 18.93 % ) Sampling Time: 00:33:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 04:53:43 (hh:mm:ss) Elapsed Time, 232215 HSPs Collected Number of families returned by RECON: 15789 Round Time: 05:54:45 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 287957 repeats masked totaling 55970572 bp(s). - TE Masking time 00:13:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270100285 bp Num Contigs Represented = 214 Non ambiguous bp: Initial: 270020293 bp After Masking: 189020306 bp Masked: 30.00 % -- Input Database Coverage: 400228001 bp out of 687388084 bp ( 58.22 % ) Sampling Time: 00:54:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23245971 Comparison Time: 36:35:13 (hh:mm:ss) Elapsed Time, 678634 HSPs Collected Number of families returned by RECON: 61103 Round Time: 39:12:39 (hh:mm:ss) Elapsed Time : 849 families discovered. RepeatScout/RECON discovery complete: 1585 families found Classification Time: 01:40:07 (hh:mm:ss) Elapsed Time Program Time: 49:19:42 (hh:mm:ss) Elapsed Time