RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uwt6rH/RM_75219.ThuJan51724152023 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: 1672968254 Database = /dev/shm/rModeler.uwt6rH/GCF_015227805.1_bHirRus1.pri.v2 - Sequences = 617 - Bases = 1105955550 - N50 = 90132487 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 145633387-156035725 | [ 1 ] 135231050-145633387 | [ ] 124828713-135231050 | [ ] 114426376-124828713 | [ 2 ] 104024039-114426376 | [ ] 93621702-104024039 | [ ] 83219365-93621702 | [ 1 ] 72817027-83219364 | [ 2 ] 62414690-72817027 | [ 1 ] 52012353-62414690 | [ ] 41610016-52012353 | [ ] 31207679-41610016 | [ 4 ] 20805342-31207679 | [ 3 ] 10403005-20805342 | [ 8 ] 668-10403005 |************************************************** [ 595 ] Storage Throughput = excellent ( 1210.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40938716 bp ( 40002485 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:07 (hh:mm:ss) Elapsed Time Round Time: 00:25:07 (hh:mm:ss) Elapsed Time : 164 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 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2843 repeats masked totaling 976404 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10342609 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10013705 bp After Masking: 8874985 bp Masked: 11.37 % -- Input Database Coverage: 10342609 bp out of 1105955550 bp ( 0.94 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:07:50 (hh:mm:ss) Elapsed Time, 737 HSPs Collected Number of families returned by RECON: 333 Round Time: 00:09:07 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8943 repeats masked totaling 2953540 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30636027 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30028700 bp After Masking: 26646336 bp Masked: 11.26 % -- Input Database Coverage: 40978636 bp out of 1105955550 bp ( 3.71 % ) Sampling Time: 00:03:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 301476 Comparison Time: 00:40:11 (hh:mm:ss) Elapsed Time, 7261 HSPs Collected Number of families returned by RECON: 1781 Round Time: 00:43:47 (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 : 00:04:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26578 repeats masked totaling 8781231 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92268722 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 90023643 bp After Masking: 79798589 bp Masked: 11.36 % -- Input Database Coverage: 133247358 bp out of 1105955550 bp ( 12.05 % ) Sampling Time: 00:10:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2715615 Comparison Time: 04:43:03 (hh:mm:ss) Elapsed Time, 75534 HSPs Collected Number of families returned by RECON: 10795 Round Time: 04:59:42 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89579 repeats masked totaling 29163262 bp(s). - TE Masking time 00:03:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276271493 bp Num Contigs Represented = 223 Non ambiguous bp: Initial: 270007675 bp After Masking: 236737591 bp Masked: 12.32 % -- Input Database Coverage: 409518851 bp out of 1105955550 bp ( 37.03 % ) Sampling Time: 00:29:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24328800 Comparison Time: 37:25:42 (hh:mm:ss) Elapsed Time, 319700 HSPs Collected Number of families returned by RECON: 70249 Round Time: 38:54:27 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 479 families found Classification Time: 00:33:31 (hh:mm:ss) Elapsed Time Program Time: 45:45:41 (hh:mm:ss) Elapsed Time