RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.C7Lqrn/RM_21228.SunNov172347212024 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: 1731916040 Database = /scratch/tmp/rModeler.C7Lqrn/GCA_964035555.1_bNetRuf1.1 - Sequences = 141 - Bases = 1166978622 - N50 = 121819845 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193007901-206794109 | [ 1 ] 179221694-193007901 | [ ] 165435487-179221694 | [ ] 151649279-165435486 | [ 1 ] 137863072-151649279 | [ ] 124076865-137863072 | [ ] 110290658-124076865 | [ 1 ] 96504450-110290657 | [ ] 82718243-96504450 | [ ] 68932036-82718243 | [ 2 ] 55145829-68932036 | [ 1 ] 41359621-55145828 | [ ] 27573414-41359621 |* [ 3 ] 13787207-27573414 |**** [ 11 ] 1000-13787207 |************************************************** [ 121 ] Storage Throughput = excellent ( 1446.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018690 bp ( 40012840 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:14 (hh:mm:ss) Elapsed Time Round Time: 00:11:18 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2084 repeats masked totaling 828934 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022819 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10021375 bp After Masking: 8902935 bp Masked: 11.16 % -- Input Database Coverage: 10022819 bp out of 1166978622 bp ( 0.86 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:50 (hh:mm:ss) Elapsed Time, 598 HSPs Collected Number of families returned by RECON: 309 Round Time: 00:04:42 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7083 repeats masked totaling 2965271 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035922 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30031516 bp After Masking: 26244479 bp Masked: 12.61 % -- Input Database Coverage: 40058741 bp out of 1166978622 bp ( 3.43 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:19:39 (hh:mm:ss) Elapsed Time, 6754 HSPs Collected Number of families returned by RECON: 1724 Round Time: 00:21:40 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18680 repeats masked totaling 7270593 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028840 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 90015640 bp After Masking: 79324530 bp Masked: 11.88 % -- Input Database Coverage: 130087581 bp out of 1166978622 bp ( 11.15 % ) Sampling Time: 00:08:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 02:10:11 (hh:mm:ss) Elapsed Time, 44766 HSPs Collected Number of families returned by RECON: 10595 Round Time: 02:20:30 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68180 repeats masked totaling 25579884 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032414 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 270000913 bp After Masking: 236548530 bp Masked: 12.39 % -- Input Database Coverage: 400119995 bp out of 1166978622 bp ( 34.29 % ) Sampling Time: 00:21:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 16:44:52 (hh:mm:ss) Elapsed Time, 263778 HSPs Collected Number of families returned by RECON: 65251 Round Time: 17:32:25 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatScout/RECON discovery complete: 344 families found Classification Time: 00:12:12 (hh:mm:ss) Elapsed Time Program Time: 20:42:47 (hh:mm:ss) Elapsed Time