RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.RPzK24/RM_450977.SunApr131200032025 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: 1744570803 Database = /data/tmp/rModeler.RPzK24/GCA_045781085.1_rPanTec1.hap2 - Sequences = 449 - Bases = 2174585695 - N50 = 145055026 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 330599136-354212379 | [ 1 ] 306985893-330599135 | [ ] 283372650-306985892 | [ 1 ] 259759407-283372649 | [ ] 236146164-259759406 | [ ] 212532921-236146163 | [ ] 188919678-212532920 | [ 1 ] 165306435-188919677 | [ ] 141693192-165306434 | [ 1 ] 118079949-141693191 | [ 3 ] 94466706-118079948 | [ 2 ] 70853463-94466705 | [ 2 ] 47240220-70853462 | [ ] 23626977-47240219 | [ 6 ] 13735-23626977 |************************************************** [ 432 ] Storage Throughput = good ( 902.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027794 bp ( 40026794 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:03:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:20 (hh:mm:ss) Elapsed Time Round Time: 00:24:04 (hh:mm:ss) Elapsed Time : 593 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14403 repeats masked totaling 3144766 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038796 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10038196 bp After Masking: 6810822 bp Masked: 32.15 % -- Input Database Coverage: 10038796 bp out of 2174585695 bp ( 0.46 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 8918 HSPs Collected Number of families returned by RECON: 1441 Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44695 repeats masked totaling 9786325 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028922 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30028522 bp After Masking: 19908044 bp Masked: 33.70 % -- Input Database Coverage: 40067718 bp out of 2174585695 bp ( 1.84 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:24:41 (hh:mm:ss) Elapsed Time, 54990 HSPs Collected Number of families returned by RECON: 4675 Round Time: 00:35:08 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151311 repeats masked totaling 32150124 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031019 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 90029219 bp After Masking: 56977118 bp Masked: 36.71 % -- Input Database Coverage: 130098737 bp out of 2174585695 bp ( 5.98 % ) Sampling Time: 00:13:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 02:32:31 (hh:mm:ss) Elapsed Time, 241183 HSPs Collected Number of families returned by RECON: 13841 Round Time: 03:15:12 (hh:mm:ss) Elapsed Time : 429 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 518183 repeats masked totaling 109853081 bp(s). - TE Masking time 00:09:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035517 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270028117 bp After Masking: 156756051 bp Masked: 41.95 % -- Input Database Coverage: 400134254 bp out of 2174585695 bp ( 18.40 % ) Sampling Time: 00:43:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 17:44:54 (hh:mm:ss) Elapsed Time, 581399 HSPs Collected Number of families returned by RECON: 44684 Round Time: 21:25:55 (hh:mm:ss) Elapsed Time : 1057 families discovered. RepeatScout/RECON discovery complete: 2233 families found Classification Time: 01:27:03 (hh:mm:ss) Elapsed Time Program Time: 27:16:32 (hh:mm:ss) Elapsed Time