RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2hBsIs/RM_3664.SatJan131047572024 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: 1705171675 Database = /dev/shm/rModeler.2hBsIs/GCA_028885525.1_NHGRI_mPonPyg2-v1.1-hic.freeze_alt - Sequences = 215 - Bases = 3038229980 - N50 = 137870513 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 211105090-226183312 | [ 1 ] 196026868-211105089 | [ 1 ] 180948647-196026868 | [ 1 ] 165870425-180948646 | [ 2 ] 150792204-165870425 | [ 2 ] 135713982-150792203 | [ 3 ] 120635760-135713981 | [ 3 ] 105557539-120635760 | [ 1 ] 90479317-105557538 | [ 3 ] 75401096-90479317 | [ 2 ] 60322874-75401095 | [ 2 ] 45244652-60322873 | [ 1 ] 30166431-45244652 | [ 1 ] 15088209-30166430 | [ 3 ] 9988-15088209 |************************************************** [ 189 ] Storage Throughput = excellent ( 1111.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40092266 bp ( 40011925 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:02:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:47 (hh:mm:ss) Elapsed Time Round Time: 00:36:54 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12396 repeats masked totaling 2839864 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026920 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10026920 bp After Masking: 6145973 bp Masked: 38.71 % -- Input Database Coverage: 10026920 bp out of 3038229980 bp ( 0.33 % ) Sampling Time: 00:05:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:11:52 (hh:mm:ss) Elapsed Time, 5721 HSPs Collected Number of families returned by RECON: 878 Round Time: 00:17:42 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42445 repeats masked totaling 9427554 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30105192 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30024851 bp After Masking: 17561397 bp Masked: 41.51 % -- Input Database Coverage: 40132112 bp out of 3038229980 bp ( 1.32 % ) Sampling Time: 00:14:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:44:28 (hh:mm:ss) Elapsed Time, 25994 HSPs Collected Number of families returned by RECON: 2213 Round Time: 01:00:16 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134928 repeats masked totaling 30456103 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90113691 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90033104 bp After Masking: 51049966 bp Masked: 43.30 % -- Input Database Coverage: 130245803 bp out of 3038229980 bp ( 4.29 % ) Sampling Time: 00:45:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:51:32 (hh:mm:ss) Elapsed Time, 104440 HSPs Collected Number of families returned by RECON: 7318 Round Time: 04:41:12 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:49:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 435453 repeats masked totaling 99621976 bp(s). - TE Masking time 00:07:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270314903 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 270019029 bp After Masking: 145398740 bp Masked: 46.15 % -- Input Database Coverage: 400560706 bp out of 3038229980 bp ( 13.18 % ) Sampling Time: 02:15:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 23:31:10 (hh:mm:ss) Elapsed Time, 253664 HSPs Collected Number of families returned by RECON: 29465 Round Time: 26:40:55 (hh:mm:ss) Elapsed Time : 398 families discovered. RepeatScout/RECON discovery complete: 918 families found Classification Time: 00:46:12 (hh:mm:ss) Elapsed Time Program Time: 34:03:11 (hh:mm:ss) Elapsed Time