RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rqZJk4/RM_1128612.ThuApr171028342025 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: 1744910913 Database = /dev/shm/rModeler.rqZJk4/GCA_964656075.1_mPipNat1.hap2.1 - Sequences = 653 - Bases = 1961094329 - N50 = 96958210 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193318319-207126699 | [ 2 ] 179509939-193318318 | [ 1 ] 165701559-179509938 | [ ] 151893179-165701558 | [ ] 138084799-151893178 | [ ] 124276419-138084798 | [ ] 110468039-124276418 | [ ] 96659659-110468038 | [ 3 ] 82851279-96659658 | [ 3 ] 69042899-82851278 | [ 3 ] 55234519-69042898 | [ 1 ] 41426139-55234518 | [ 6 ] 27617759-41426138 | [ ] 13809379-27617758 | [ 2 ] 1000-13809379 |************************************************** [ 632 ] Storage Throughput = excellent ( 1650.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015026 bp ( 40007226 non ambiguous ) - Num Contigs Represented = 97 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:37 (hh:mm:ss) Elapsed Time Round Time: 00:11:34 (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 : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14376 repeats masked totaling 2204409 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007290 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10005290 bp After Masking: 6733285 bp Masked: 32.70 % -- Input Database Coverage: 10007290 bp out of 1961094329 bp ( 0.51 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 4822 HSPs Collected Number of families returned by RECON: 739 Round Time: 00:04:12 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46261 repeats masked totaling 7211585 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007656 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30001856 bp After Masking: 19553205 bp Masked: 34.83 % -- Input Database Coverage: 40014946 bp out of 1961094329 bp ( 2.04 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:13:36 (hh:mm:ss) Elapsed Time, 22311 HSPs Collected Number of families returned by RECON: 2153 Round Time: 00:15:57 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 147743 repeats masked totaling 23405535 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018325 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 90002172 bp After Masking: 58033847 bp Masked: 35.52 % -- Input Database Coverage: 130033271 bp out of 1961094329 bp ( 6.63 % ) Sampling Time: 00:06:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 01:12:29 (hh:mm:ss) Elapsed Time, 109818 HSPs Collected Number of families returned by RECON: 8174 Round Time: 01:20:14 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482939 repeats masked totaling 77361598 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270061182 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 270011182 bp After Masking: 165791409 bp Masked: 38.60 % -- Input Database Coverage: 400094453 bp out of 1961094329 bp ( 20.40 % ) Sampling Time: 00:19:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 08:12:31 (hh:mm:ss) Elapsed Time, 264266 HSPs Collected Number of families returned by RECON: 32639 Round Time: 08:40:48 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatScout/RECON discovery complete: 967 families found Classification Time: 00:16:49 (hh:mm:ss) Elapsed Time Program Time: 10:49:34 (hh:mm:ss) Elapsed Time