RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zHQayO/RM_640647.MonApr211259112025 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: 1745265550 Database = /dev/shm/rModeler.zHQayO/GCA_965178545.1_bColMon1.hap1.1 - Sequences = 729 - Bases = 1263996688 - N50 = 76532137 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 150333520-161071558 | [ 1 ] 139595483-150333520 | [ ] 128857446-139595483 | [ ] 118119409-128857446 | [ 2 ] 107381372-118119409 | [ ] 96643334-107381371 | [ ] 85905297-96643334 | [ ] 75167260-85905297 | [ 3 ] 64429223-75167260 | [ 1 ] 53691186-64429223 | [ ] 42953148-53691185 | [ ] 32215111-42953148 | [ 4 ] 21477074-32215111 | [ 2 ] 10739037-21477074 | [ 10 ] 1000-10739037 |************************************************** [ 706 ] Storage Throughput = excellent ( 1791.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025912 bp ( 40021431 non ambiguous ) - Num Contigs Represented = 128 - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:23 (hh:mm:ss) Elapsed Time Round Time: 00:18:54 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3566 repeats masked totaling 1297475 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032309 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10031228 bp After Masking: 8308473 bp Masked: 17.17 % -- Input Database Coverage: 10032309 bp out of 1263996688 bp ( 0.79 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 2102 HSPs Collected Number of families returned by RECON: 248 Round Time: 00:03:56 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11088 repeats masked totaling 5327581 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033529 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 30030129 bp After Masking: 23512758 bp Masked: 21.70 % -- Input Database Coverage: 40065838 bp out of 1263996688 bp ( 3.17 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:13:18 (hh:mm:ss) Elapsed Time, 11676 HSPs Collected Number of families returned by RECON: 1309 Round Time: 00:15:19 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33482 repeats masked totaling 14271922 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018303 bp Num Contigs Represented = 218 Non ambiguous bp: Initial: 90010903 bp After Masking: 71955850 bp Masked: 20.06 % -- Input Database Coverage: 130084141 bp out of 1263996688 bp ( 10.29 % ) Sampling Time: 00:05:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 01:27:24 (hh:mm:ss) Elapsed Time, 71341 HSPs Collected Number of families returned by RECON: 8069 Round Time: 01:34:13 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111792 repeats masked totaling 45926013 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051560 bp Num Contigs Represented = 393 Non ambiguous bp: Initial: 270025071 bp After Masking: 212338154 bp Masked: 21.36 % -- Input Database Coverage: 400135701 bp out of 1263996688 bp ( 31.66 % ) Sampling Time: 00:17:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 10:43:19 (hh:mm:ss) Elapsed Time, 244178 HSPs Collected Number of families returned by RECON: 54350 Round Time: 11:23:32 (hh:mm:ss) Elapsed Time : 270 families discovered. RepeatScout/RECON discovery complete: 528 families found Classification Time: 00:23:15 (hh:mm:ss) Elapsed Time Program Time: 13:59:09 (hh:mm:ss) Elapsed Time