RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.R3dy5s/RM_4132373.ThuFeb61845212025 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: 1738896320 Database = /dev/shm/rModeler.R3dy5s/GCF_031021105.1_rEryReg1.hap1 - Sequences = 400 - Bases = 1964049041 - N50 = 355369171 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 398122580-426559836 | [ 1 ] 369685324-398122579 | [ ] 341248068-369685323 | [ 1 ] 312810813-341248068 | [ ] 284373557-312810812 | [ ] 255936301-284373556 | [ 1 ] 227499045-255936300 | [ ] 199061790-227499045 | [ ] 170624534-199061789 | [ ] 142187278-170624533 | [ 1 ] 113750022-142187277 | [ 2 ] 85312767-113750022 | [ 2 ] 56875511-85312766 | [ 2 ] 28438255-56875510 | [ 3 ] 1000-28438255 |************************************************** [ 387 ] Storage Throughput = excellent ( 1318.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031384 bp ( 40026452 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:00 (hh:mm:ss) Elapsed Time Round Time: 00:17:05 (hh:mm:ss) Elapsed Time : 673 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21245 repeats masked totaling 4883459 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007749 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10006549 bp After Masking: 4576369 bp Masked: 54.27 % -- Input Database Coverage: 10007749 bp out of 1964049041 bp ( 0.51 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:16 (hh:mm:ss) Elapsed Time, 9578 HSPs Collected Number of families returned by RECON: 953 Round Time: 00:05:03 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64017 repeats masked totaling 14300961 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023555 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30019823 bp After Masking: 14235681 bp Masked: 52.58 % -- Input Database Coverage: 40031304 bp out of 1964049041 bp ( 2.04 % ) Sampling Time: 00:03:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:15:41 (hh:mm:ss) Elapsed Time, 33356 HSPs Collected Number of families returned by RECON: 3013 Round Time: 00:19:59 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 202814 repeats masked totaling 44296246 bp(s). - TE Masking time 00:05:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028431 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90015170 bp After Masking: 41149534 bp Masked: 54.29 % -- Input Database Coverage: 130059735 bp out of 1964049041 bp ( 6.62 % ) Sampling Time: 00:15:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:07:19 (hh:mm:ss) Elapsed Time, 188182 HSPs Collected Number of families returned by RECON: 8708 Round Time: 01:34:20 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 660801 repeats masked totaling 142991509 bp(s). - TE Masking time 00:20:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270073056 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 270039902 bp After Masking: 113388742 bp Masked: 58.01 % -- Input Database Coverage: 400132791 bp out of 1964049041 bp ( 20.37 % ) Sampling Time: 00:53:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 08:29:12 (hh:mm:ss) Elapsed Time, 604338 HSPs Collected Number of families returned by RECON: 25986 Round Time: 09:35:51 (hh:mm:ss) Elapsed Time : 911 families discovered. RepeatScout/RECON discovery complete: 2064 families found Classification Time: 00:36:05 (hh:mm:ss) Elapsed Time Program Time: 12:28:23 (hh:mm:ss) Elapsed Time