RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Y8nHji/RM_28494.FriDec11545292023 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: 1701474327 Database = /dev/shm/rModeler.Y8nHji/GCA_030020945.1_mManPen7.hap2 - Sequences = 700 - Bases = 2869287698 - N50 = 146724930 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 219706455-235399238 | [ 2 ] 204013672-219706454 | [ 1 ] 188320889-204013671 | [ ] 172628106-188320888 | [ 2 ] 156935323-172628105 | [ ] 141242540-156935322 | [ 2 ] 125549757-141242539 | [ 2 ] 109856974-125549756 | [ 1 ] 94164191-109856973 | [ 3 ] 78471408-94164190 | [ 1 ] 62778625-78471407 | [ 4 ] 47085842-62778624 | [ 1 ] 31393059-47085841 | [ 1 ] 15700276-31393058 | [ 2 ] 7494-15700276 |************************************************** [ 678 ] Storage Throughput = excellent ( 1158.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40213010 bp ( 40001518 non ambiguous ) - Num Contigs Represented = 125 - Sequence extraction : 00:02:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:53 (hh:mm:ss) Elapsed Time Round Time: 00:43:04 (hh:mm:ss) Elapsed Time : 194 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6459 repeats masked totaling 3047132 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10148839 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10028791 bp After Masking: 6894389 bp Masked: 31.25 % -- Input Database Coverage: 10148839 bp out of 2869287698 bp ( 0.35 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:13:10 (hh:mm:ss) Elapsed Time, 88084 HSPs Collected Number of families returned by RECON: 757 Round Time: 00:16:03 (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 : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25378 repeats masked totaling 10855813 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30104091 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 30012647 bp After Masking: 18907267 bp Masked: 37.00 % -- Input Database Coverage: 40252930 bp out of 2869287698 bp ( 1.40 % ) Sampling Time: 00:06:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 01:37:54 (hh:mm:ss) Elapsed Time, 457279 HSPs Collected Number of families returned by RECON: 1902 Round Time: 20:37:45 (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 : 00:06:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77381 repeats masked totaling 32936660 bp(s). - TE Masking time 00:20:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90443043 bp Num Contigs Represented = 168 Non ambiguous bp: Initial: 90012095 bp After Masking: 56577309 bp Masked: 37.14 % -- Input Database Coverage: 130695973 bp out of 2869287698 bp ( 4.55 % ) Sampling Time: 00:33:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 04:11:35 (hh:mm:ss) Elapsed Time, 775414 HSPs Collected Number of families returned by RECON: 7831 Round Time: 05:42:37 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 272225 repeats masked totaling 105817121 bp(s). - TE Masking time 00:30:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271432021 bp Num Contigs Represented = 304 Non ambiguous bp: Initial: 270010619 bp After Masking: 162186642 bp Masked: 39.93 % -- Input Database Coverage: 402127994 bp out of 2869287698 bp ( 14.01 % ) Sampling Time: 01:11:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 32:09:38 (hh:mm:ss) Elapsed Time, 11802900 HSPs Collected Number of families returned by RECON: 31487 Round Time: 33:56:37 (hh:mm:ss) Elapsed Time : 312 families discovered. RepeatScout/RECON discovery complete: 725 families found Classification Time: 00:46:29 (hh:mm:ss) Elapsed Time Program Time: 62:02:35 (hh:mm:ss) Elapsed Time