RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GUiYhi/RM_1524183.SunMay140911302023 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: 1684080690 Database = /dev/shm/rModeler.GUiYhi/GCA_902713435.2_fAciRut3.2_paternal_haplotype - Sequences = 1517 - Bases = 1882648115 - N50 = 42500551 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 111584003-119553658 | [ 2 ] 103614349-111584003 | [ 2 ] 95644694-103614348 | [ ] 87675040-95644694 | [ 1 ] 79705385-87675039 | [ 1 ] 71735731-79705385 | [ ] 63766076-71735730 | [ 2 ] 55796422-63766076 | [ 1 ] 47826767-55796421 | [ 1 ] 39857113-47826767 | [ 2 ] 31887458-39857112 | [ 8 ] 23917804-31887458 | [ 8 ] 15948149-23917803 | [ 3 ] 7978495-15948149 | [ 23 ] 8841-7978495 |************************************************** [ 1463 ] Storage Throughput = good ( 992.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008522 bp ( 40006852 non ambiguous ) - Num Contigs Represented = 114 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:28 (hh:mm:ss) Elapsed Time Round Time: 00:35:12 (hh:mm:ss) Elapsed Time : 913 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11714 repeats masked totaling 2609665 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015386 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10015386 bp After Masking: 6685583 bp Masked: 33.25 % -- Input Database Coverage: 10015386 bp out of 1882648115 bp ( 0.53 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 8168 HSPs Collected Number of families returned by RECON: 1897 Round Time: 00:08:20 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35513 repeats masked totaling 7977382 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033136 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 30031466 bp After Masking: 19360811 bp Masked: 35.53 % -- Input Database Coverage: 40048522 bp out of 1882648115 bp ( 2.13 % ) Sampling Time: 00:07:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:29:59 (hh:mm:ss) Elapsed Time, 60331 HSPs Collected Number of families returned by RECON: 5842 Round Time: 00:39:44 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120107 repeats masked totaling 26139838 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018913 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 90013912 bp After Masking: 56329959 bp Masked: 37.42 % -- Input Database Coverage: 130067435 bp out of 1882648115 bp ( 6.91 % ) Sampling Time: 00:34:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 03:15:18 (hh:mm:ss) Elapsed Time, 396583 HSPs Collected Number of families returned by RECON: 16616 Round Time: 04:10:09 (hh:mm:ss) Elapsed Time : 698 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 456133 repeats masked totaling 96015331 bp(s). - TE Masking time 00:17:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041148 bp Num Contigs Represented = 351 Non ambiguous bp: Initial: 270029059 bp After Masking: 152457137 bp Masked: 43.54 % -- Input Database Coverage: 400108583 bp out of 1882648115 bp ( 21.25 % ) Sampling Time: 01:18:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23382541 Comparison Time: 21:07:16 (hh:mm:ss) Elapsed Time, 1013507 HSPs Collected Number of families returned by RECON: 50430 Round Time: 23:58:48 (hh:mm:ss) Elapsed Time : 1489 families discovered. RepeatScout/RECON discovery complete: 3256 families found Classification Time: 02:53:58 (hh:mm:ss) Elapsed Time Program Time: 32:26:11 (hh:mm:ss) Elapsed Time