RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.AEPx3z/RM_4066350.FriNov150705452024 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: 1731683145 Database = /scratch/tmp/rModeler.AEPx3z/GCA_038048845.1_aMixFle1.hap1 - Sequences = 2806 - Bases = 2969628263 - N50 = 349193765 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 432740199-463649476 | [ 1 ] 401830923-432740199 | [ ] 370921646-401830922 | [ 1 ] 340012370-370921646 | [ 2 ] 309103093-340012369 | [ ] 278193817-309103093 | [ 1 ] 247284540-278193816 | [ ] 216375264-247284540 | [ 1 ] 185465987-216375263 | [ ] 154556711-185465987 | [ 1 ] 123647434-154556710 | [ 2 ] 92738158-123647434 | [ 2 ] 61828881-92738157 | [ 1 ] 30919605-61828881 | [ ] 10329-30919605 |************************************************** [ 2794 ] Storage Throughput = excellent ( 1197.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40075790 bp ( 40004539 non ambiguous ) - Num Contigs Represented = 103 - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:46 (hh:mm:ss) Elapsed Time Round Time: 00:21:15 (hh:mm:ss) Elapsed Time : 752 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14052 repeats masked totaling 3797860 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031570 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10026635 bp After Masking: 5129130 bp Masked: 48.84 % -- Input Database Coverage: 10031570 bp out of 2969628263 bp ( 0.34 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 9022 HSPs Collected Number of families returned by RECON: 1423 Round Time: 00:08:11 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43078 repeats masked totaling 12113543 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30084139 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 30017823 bp After Masking: 14635450 bp Masked: 51.24 % -- Input Database Coverage: 40115709 bp out of 2969628263 bp ( 1.35 % ) Sampling Time: 00:13:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:12:20 (hh:mm:ss) Elapsed Time, 54068 HSPs Collected Number of families returned by RECON: 5056 Round Time: 00:27:02 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142601 repeats masked totaling 37578358 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90068851 bp Num Contigs Represented = 194 Non ambiguous bp: Initial: 90026237 bp After Masking: 42669511 bp Masked: 52.60 % -- Input Database Coverage: 130184560 bp out of 2969628263 bp ( 4.38 % ) Sampling Time: 00:37:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2614041 Comparison Time: 01:03:04 (hh:mm:ss) Elapsed Time, 260442 HSPs Collected Number of families returned by RECON: 14284 Round Time: 01:46:19 (hh:mm:ss) Elapsed Time : 501 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:24:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 502132 repeats masked totaling 129030430 bp(s). - TE Masking time 00:04:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270423041 bp Num Contigs Represented = 471 Non ambiguous bp: Initial: 270012449 bp After Masking: 113056689 bp Masked: 58.13 % -- Input Database Coverage: 400607601 bp out of 2969628263 bp ( 13.49 % ) Sampling Time: 01:47:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23629375 Comparison Time: 06:16:38 (hh:mm:ss) Elapsed Time, 809362 HSPs Collected Number of families returned by RECON: 38607 Round Time: 08:33:20 (hh:mm:ss) Elapsed Time : 1358 families discovered. RepeatScout/RECON discovery complete: 2736 families found Classification Time: 00:55:30 (hh:mm:ss) Elapsed Time Program Time: 12:11:37 (hh:mm:ss) Elapsed Time