RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1MlX6g/RM_1586516.SatJan200014392024 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: 1705738477 Database = /dev/shm/rModeler.1MlX6g/GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri - Sequences = 25 - Bases = 3177739762 Storage Throughput = excellent ( 1063.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40087174 bp ( 40007174 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:09 (hh:mm:ss) Elapsed Time Round Time: 00:29:23 (hh:mm:ss) Elapsed Time : 254 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12690 repeats masked totaling 3065948 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000374 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000374 bp After Masking: 5711247 bp Masked: 42.89 % -- Input Database Coverage: 10000374 bp out of 3177739762 bp ( 0.31 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:36 (hh:mm:ss) Elapsed Time, 4830 HSPs Collected Number of families returned by RECON: 789 Round Time: 00:08:12 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41910 repeats masked totaling 9577366 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30086796 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30006796 bp After Masking: 17519690 bp Masked: 41.61 % -- Input Database Coverage: 40087170 bp out of 3177739762 bp ( 1.26 % ) Sampling Time: 00:07:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:23:23 (hh:mm:ss) Elapsed Time, 27798 HSPs Collected Number of families returned by RECON: 2400 Round Time: 00:31:39 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135763 repeats masked totaling 30672208 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90194787 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90034769 bp After Masking: 50999657 bp Masked: 43.36 % -- Input Database Coverage: 130281957 bp out of 3177739762 bp ( 4.10 % ) Sampling Time: 00:24:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:32:40 (hh:mm:ss) Elapsed Time, 85223 HSPs Collected Number of families returned by RECON: 7508 Round Time: 03:02:08 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:55:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 438736 repeats masked totaling 98495531 bp(s). - TE Masking time 00:06:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270561319 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270010319 bp After Masking: 146514137 bp Masked: 45.74 % -- Input Database Coverage: 400843276 bp out of 3177739762 bp ( 12.61 % ) Sampling Time: 01:13:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 18:07:54 (hh:mm:ss) Elapsed Time, 271450 HSPs Collected Number of families returned by RECON: 30799 Round Time: 19:40:37 (hh:mm:ss) Elapsed Time : 390 families discovered. RepeatScout/RECON discovery complete: 915 families found Classification Time: 00:34:17 (hh:mm:ss) Elapsed Time Program Time: 24:26:16 (hh:mm:ss) Elapsed Time