RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GVVxRh/RM_1242989.SatJan130844382024 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: 1705164278 Database = /dev/shm/rModeler.GVVxRh/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri - Sequences = 1471 - Bases = 3225356997 - N50 = 153892427 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215902054-231323237 | [ 1 ] 200480871-215902053 | [ 1 ] 185059689-200480871 | [ 1 ] 169638506-185059688 | [ 2 ] 154217324-169638506 | [ 2 ] 138796141-154217323 | [ 2 ] 123374958-138796140 | [ 3 ] 107953776-123374958 | [ 3 ] 92532593-107953775 | [ 4 ] 77111411-92532593 | [ 2 ] 61690228-77111410 | [ 1 ] 46269045-61690227 | [ 2 ] 30847863-46269045 | [ 1 ] 15426680-30847862 | [ ] 5498-15426680 |************************************************** [ 1446 ] Storage Throughput = good ( 968.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006298 bp ( 40006298 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:02:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:42 (hh:mm:ss) Elapsed Time Round Time: 00:39:20 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11513 repeats masked totaling 2819738 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016458 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10016458 bp After Masking: 6079797 bp Masked: 39.30 % -- Input Database Coverage: 10016458 bp out of 3225356997 bp ( 0.31 % ) Sampling Time: 00:04:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:09:31 (hh:mm:ss) Elapsed Time, 5453 HSPs Collected Number of families returned by RECON: 731 Round Time: 00:14:04 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37530 repeats masked totaling 9520560 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029760 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30029760 bp After Masking: 17856031 bp Masked: 40.54 % -- Input Database Coverage: 40046218 bp out of 3225356997 bp ( 1.24 % ) Sampling Time: 00:10:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:27:21 (hh:mm:ss) Elapsed Time, 33878 HSPs Collected Number of families returned by RECON: 2551 Round Time: 00:39:27 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 126572 repeats masked totaling 31211440 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90135689 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90004299 bp After Masking: 50877945 bp Masked: 43.47 % -- Input Database Coverage: 130181907 bp out of 3225356997 bp ( 4.04 % ) Sampling Time: 00:26:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 03:33:44 (hh:mm:ss) Elapsed Time, 151836 HSPs Collected Number of families returned by RECON: 7550 Round Time: 04:04:48 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:53:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 423251 repeats masked totaling 102345106 bp(s). - TE Masking time 00:05:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270192186 bp Num Contigs Represented = 234 Non ambiguous bp: Initial: 270007677 bp After Masking: 142636303 bp Masked: 47.17 % -- Input Database Coverage: 400374093 bp out of 3225356997 bp ( 12.41 % ) Sampling Time: 01:14:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 18:37:20 (hh:mm:ss) Elapsed Time, 327818 HSPs Collected Number of families returned by RECON: 28861 Round Time: 20:10:12 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatScout/RECON discovery complete: 944 families found Classification Time: 00:40:07 (hh:mm:ss) Elapsed Time Program Time: 26:27:58 (hh:mm:ss) Elapsed Time