RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Y7L6hV/RM_1699886.SatJul192240552025 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: 1752990053 Database = /dev/shm/rModeler.Y7L6hV/GCA_048771865.1_mCteGun2.hap2 - Sequences = 1031 - Bases = 2329663899 - N50 = 108649992 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197620714-211735621 | [ 1 ] 183505807-197620714 | [ ] 169390900-183505807 | [ ] 155275993-169390900 | [ ] 141161086-155275993 | [ 2 ] 127046179-141161086 | [ 1 ] 112931272-127046179 | [ 3 ] 98816365-112931272 | [ 4 ] 84701458-98816365 | [ 3 ] 70586551-84701458 | [ 4 ] 56471644-70586551 | [ 1 ] 42356737-56471644 | [ 1 ] 28241830-42356737 | [ ] 14126923-28241830 | [ ] 12016-14126923 |************************************************** [ 1011 ] Storage Throughput = excellent ( 1690.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038388 bp ( 40037888 non ambiguous ) - Num Contigs Represented = 106 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:36 (hh:mm:ss) Elapsed Time Round Time: 00:12:51 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15727 repeats masked totaling 3107003 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036658 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10036358 bp After Masking: 6798014 bp Masked: 32.27 % -- Input Database Coverage: 10036658 bp out of 2329663899 bp ( 0.43 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:45 (hh:mm:ss) Elapsed Time, 2086 HSPs Collected Number of families returned by RECON: 432 Round Time: 00:03:29 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45633 repeats masked totaling 9634436 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001650 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 30001450 bp After Masking: 19992418 bp Masked: 33.36 % -- Input Database Coverage: 40038308 bp out of 2329663899 bp ( 1.72 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:11:47 (hh:mm:ss) Elapsed Time, 17065 HSPs Collected Number of families returned by RECON: 1882 Round Time: 00:13:44 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138054 repeats masked totaling 29239010 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015849 bp Num Contigs Represented = 204 Non ambiguous bp: Initial: 90015449 bp After Masking: 59723949 bp Masked: 33.65 % -- Input Database Coverage: 130054157 bp out of 2329663899 bp ( 5.58 % ) Sampling Time: 00:04:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:05:36 (hh:mm:ss) Elapsed Time, 62539 HSPs Collected Number of families returned by RECON: 6229 Round Time: 01:11:33 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 440769 repeats masked totaling 92462816 bp(s). - TE Masking time 00:03:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027316 bp Num Contigs Represented = 426 Non ambiguous bp: Initial: 270025716 bp After Masking: 174297594 bp Masked: 35.45 % -- Input Database Coverage: 400081473 bp out of 2329663899 bp ( 17.17 % ) Sampling Time: 00:15:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 07:59:55 (hh:mm:ss) Elapsed Time, 209478 HSPs Collected Number of families returned by RECON: 28926 Round Time: 08:22:46 (hh:mm:ss) Elapsed Time : 361 families discovered. RepeatScout/RECON discovery complete: 737 families found Classification Time: 00:24:08 (hh:mm:ss) Elapsed Time Program Time: 10:28:31 (hh:mm:ss) Elapsed Time