RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tTUEaF/RM_31115.SatJun291608592024 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: 1719702538 Database = /dev/shm/rModeler.tTUEaF/GCA_022749685.1_fSemPul1.0.p - Sequences = 179 - Bases = 794122974 - N50 = 32417510 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35960595-38528027 |* [ 3 ] 33393163-35960594 |* [ 4 ] 30825731-33393162 |** [ 7 ] 28258299-30825730 |* [ 3 ] 25690867-28258298 | [ 1 ] 23123435-25690866 |* [ 3 ] 20556003-23123434 | [ 1 ] 17988571-20556002 | [ ] 15421139-17988570 | [ 2 ] 12853707-15421138 | [ ] 10286275-12853706 | [ 2 ] 7718843-10286274 | [ 2 ] 5151411-7718842 | [ ] 2583979-5151410 | [ 1 ] 16548-2583979 |************************************************** [ 150 ] Storage Throughput = excellent ( 1024.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036486 bp ( 40036486 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:23 (hh:mm:ss) Elapsed Time Round Time: 00:26:50 (hh:mm:ss) Elapsed Time : 585 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9491 repeats masked totaling 1699429 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002169 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10002169 bp After Masking: 7571585 bp Masked: 24.30 % -- Input Database Coverage: 10002169 bp out of 794122974 bp ( 1.26 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 5381 HSPs Collected Number of families returned by RECON: 1340 Round Time: 00:09:44 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29423 repeats masked totaling 5089132 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034237 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30034237 bp After Masking: 22735859 bp Masked: 24.30 % -- Input Database Coverage: 40036406 bp out of 794122974 bp ( 5.04 % ) Sampling Time: 00:11:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:28:48 (hh:mm:ss) Elapsed Time, 41569 HSPs Collected Number of families returned by RECON: 4631 Round Time: 00:42:13 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 96776 repeats masked totaling 16546152 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028857 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90028756 bp After Masking: 66516118 bp Masked: 26.12 % -- Input Database Coverage: 130065263 bp out of 794122974 bp ( 16.38 % ) Sampling Time: 00:43:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:27:47 (hh:mm:ss) Elapsed Time, 250380 HSPs Collected Number of families returned by RECON: 16766 Round Time: 04:33:29 (hh:mm:ss) Elapsed Time : 474 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:56:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 360155 repeats masked totaling 64505547 bp(s). - TE Masking time 00:11:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011461 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270011260 bp After Masking: 184388429 bp Masked: 31.71 % -- Input Database Coverage: 400076724 bp out of 794122974 bp ( 50.38 % ) Sampling Time: 02:11:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 26:00:52 (hh:mm:ss) Elapsed Time, 671314 HSPs Collected Number of families returned by RECON: 60418 Round Time: 30:22:18 (hh:mm:ss) Elapsed Time : 1019 families discovered. RepeatScout/RECON discovery complete: 2178 families found Classification Time: 01:49:28 (hh:mm:ss) Elapsed Time Program Time: 38:04:02 (hh:mm:ss) Elapsed Time