RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EkPYbn/RM_26484.WedNov291510452023 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: 1701299444 Database = /dev/shm/rModeler.EkPYbn/GCA_028858755.1_bAraAra1.hap1 - Sequences = 246 - Bases = 1224360198 - N50 = 126903807 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 158054868-169343748 | [ 2 ] 146765988-158054867 | [ ] 135477108-146765987 | [ ] 124188229-135477108 | [ 2 ] 112899349-124188228 | [ ] 101610469-112899348 | [ 1 ] 90321589-101610468 | [ 2 ] 79032710-90321589 | [ ] 67743830-79032709 | [ 1 ] 56454950-67743829 | [ ] 45166070-56454949 | [ ] 33877191-45166070 | [ 1 ] 22588311-33877190 | [ 2 ] 11299431-22588310 | [ 4 ] 10552-11299431 |************************************************** [ 231 ] Storage Throughput = excellent ( 1168.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40069365 bp ( 40029349 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:14 (hh:mm:ss) Elapsed Time Round Time: 00:49:45 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3788 repeats masked totaling 1259711 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027570 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10027570 bp After Masking: 8309691 bp Masked: 17.13 % -- Input Database Coverage: 10027570 bp out of 1224360198 bp ( 0.82 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 294 HSPs Collected Number of families returned by RECON: 138 Round Time: 00:07:47 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12052 repeats masked totaling 3725187 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041715 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30001699 bp After Masking: 24575666 bp Masked: 18.09 % -- Input Database Coverage: 40069285 bp out of 1224360198 bp ( 3.27 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:32:40 (hh:mm:ss) Elapsed Time, 21605 HSPs Collected Number of families returned by RECON: 1120 Round Time: 00:38:20 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37440 repeats masked totaling 10801817 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043031 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90036546 bp After Masking: 75036503 bp Masked: 16.66 % -- Input Database Coverage: 130112316 bp out of 1224360198 bp ( 10.63 % ) Sampling Time: 00:12:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 05:13:13 (hh:mm:ss) Elapsed Time, 93311 HSPs Collected Number of families returned by RECON: 7486 Round Time: 05:31:57 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115418 repeats masked totaling 34474863 bp(s). - TE Masking time 00:04:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270166891 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270025319 bp After Masking: 224871582 bp Masked: 16.72 % -- Input Database Coverage: 400279207 bp out of 1224360198 bp ( 32.69 % ) Sampling Time: 00:35:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 37:21:55 (hh:mm:ss) Elapsed Time, 225155 HSPs Collected Number of families returned by RECON: 52964 Round Time: 38:39:03 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatScout/RECON discovery complete: 363 families found Classification Time: 00:36:01 (hh:mm:ss) Elapsed Time Program Time: 46:22:53 (hh:mm:ss) Elapsed Time