RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gP87em/RM_3241585.ThuApr170615492025 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: 1744895749 Database = /dev/shm/rModeler.gP87em/GCA_965113305.1_rPodVau1.hap2.1 - Sequences = 151 - Bases = 1510738089 - N50 = 106683503 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 135305484-144970091 | [ 1 ] 125640878-135305484 | [ 2 ] 115976272-125640878 | [ ] 106311666-115976272 |* [ 3 ] 96647060-106311666 | [ 1 ] 86982454-96647060 | [ 1 ] 77317848-86982454 | [ 1 ] 67653242-77317848 | [ 1 ] 57988636-67653242 |* [ 3 ] 48324030-57988636 | [ 1 ] 38659424-48324030 |* [ 3 ] 28994818-38659424 | [ ] 19330212-28994818 | [ ] 9665606-19330212 | [ 1 ] 1000-9665606 |************************************************** [ 133 ] Storage Throughput = excellent ( 1702.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010603 bp ( 40006003 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:58 (hh:mm:ss) Elapsed Time Round Time: 00:11:47 (hh:mm:ss) Elapsed Time : 572 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17094 repeats masked totaling 3155665 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003296 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001496 bp After Masking: 6251071 bp Masked: 37.50 % -- Input Database Coverage: 10003296 bp out of 1510738089 bp ( 0.66 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 9421 HSPs Collected Number of families returned by RECON: 1244 Round Time: 00:04:36 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54348 repeats masked totaling 10410408 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007303 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30004503 bp After Masking: 18314446 bp Masked: 38.96 % -- Input Database Coverage: 40010599 bp out of 1510738089 bp ( 2.65 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:11:45 (hh:mm:ss) Elapsed Time, 40119 HSPs Collected Number of families returned by RECON: 4232 Round Time: 00:15:53 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 174027 repeats masked totaling 32562247 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90050012 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90039412 bp After Masking: 53464618 bp Masked: 40.62 % -- Input Database Coverage: 130060611 bp out of 1510738089 bp ( 8.61 % ) Sampling Time: 00:11:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:03:08 (hh:mm:ss) Elapsed Time, 183542 HSPs Collected Number of families returned by RECON: 13095 Round Time: 01:17:37 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 590591 repeats masked totaling 108201785 bp(s). - TE Masking time 00:02:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037941 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 270010741 bp After Masking: 149164401 bp Masked: 44.76 % -- Input Database Coverage: 400098552 bp out of 1510738089 bp ( 26.48 % ) Sampling Time: 00:31:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 07:02:54 (hh:mm:ss) Elapsed Time, 472996 HSPs Collected Number of families returned by RECON: 45397 Round Time: 07:56:18 (hh:mm:ss) Elapsed Time : 969 families discovered. RepeatScout/RECON discovery complete: 2098 families found Classification Time: 00:30:08 (hh:mm:ss) Elapsed Time Program Time: 10:16:19 (hh:mm:ss) Elapsed Time