RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pexvzD/RM_1886010.SunJan212005112024 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: 1705896310 Database = /dev/shm/rModeler.pexvzD/GCA_028858805.2_NHGRI_mPanTro3-v2.0_alt - Sequences = 23 - Bases = 2998472174 Storage Throughput = good ( 969.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040125 bp ( 40000125 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:38 (hh:mm:ss) Elapsed Time Round Time: 00:25:12 (hh:mm:ss) Elapsed Time : 247 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13388 repeats masked totaling 2726173 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039977 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 9999977 bp After Masking: 6210437 bp Masked: 37.90 % -- Input Database Coverage: 10039977 bp out of 2998472174 bp ( 0.33 % ) Sampling Time: 00:03:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 5231 HSPs Collected Number of families returned by RECON: 832 Round Time: 00:08:59 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42806 repeats masked totaling 8922161 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000068 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30000068 bp After Masking: 18141455 bp Masked: 39.53 % -- Input Database Coverage: 40040045 bp out of 2998472174 bp ( 1.34 % ) Sampling Time: 00:07:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:26:11 (hh:mm:ss) Elapsed Time, 31176 HSPs Collected Number of families returned by RECON: 2376 Round Time: 00:35:00 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137101 repeats masked totaling 29474794 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90120455 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90000455 bp After Masking: 50903638 bp Masked: 43.44 % -- Input Database Coverage: 130160500 bp out of 2998472174 bp ( 4.34 % ) Sampling Time: 00:21:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:35:56 (hh:mm:ss) Elapsed Time, 105530 HSPs Collected Number of families returned by RECON: 7417 Round Time: 03:01:05 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 461389 repeats masked totaling 97649897 bp(s). - TE Masking time 00:05:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270490916 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270014782 bp After Masking: 146282493 bp Masked: 45.82 % -- Input Database Coverage: 400651416 bp out of 2998472174 bp ( 13.36 % ) Sampling Time: 00:59:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 22:32:10 (hh:mm:ss) Elapsed Time, 269026 HSPs Collected Number of families returned by RECON: 29423 Round Time: 23:55:12 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatScout/RECON discovery complete: 896 families found Classification Time: 00:39:57 (hh:mm:ss) Elapsed Time Program Time: 28:45:25 (hh:mm:ss) Elapsed Time