RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lJztw3/RM_28203.SunJan210032512024 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: 1705825969 Database = /dev/shm/rModeler.lJztw3/GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri - Sequences = 30 - Bases = 3244888708 Storage Throughput = excellent ( 1402.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40120849 bp ( 40000837 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:58 (hh:mm:ss) Elapsed Time Round Time: 00:20:47 (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 : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12809 repeats masked totaling 2973727 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000155 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000155 bp After Masking: 5924384 bp Masked: 40.76 % -- Input Database Coverage: 10000155 bp out of 3244888708 bp ( 0.31 % ) Sampling Time: 00:03:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 4365 HSPs Collected Number of families returned by RECON: 688 Round Time: 00:09:35 (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 : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41167 repeats masked totaling 9311336 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30120614 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30000602 bp After Masking: 17549368 bp Masked: 41.50 % -- Input Database Coverage: 40120769 bp out of 3244888708 bp ( 1.24 % ) Sampling Time: 00:08:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:22:32 (hh:mm:ss) Elapsed Time, 23299 HSPs Collected Number of families returned by RECON: 2298 Round Time: 00:31:45 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133847 repeats masked totaling 29978131 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90202108 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90002080 bp After Masking: 50116488 bp Masked: 44.32 % -- Input Database Coverage: 130322877 bp out of 3244888708 bp ( 4.02 % ) Sampling Time: 00:25:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:53:50 (hh:mm:ss) Elapsed Time, 117121 HSPs Collected Number of families returned by RECON: 7649 Round Time: 02:21:36 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:11:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 439716 repeats masked totaling 97740185 bp(s). - TE Masking time 00:03:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270206149 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270027807 bp After Masking: 143231061 bp Masked: 46.96 % -- Input Database Coverage: 400529026 bp out of 3244888708 bp ( 12.34 % ) Sampling Time: 01:22:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 11:51:08 (hh:mm:ss) Elapsed Time, 337555 HSPs Collected Number of families returned by RECON: 30102 Round Time: 13:31:11 (hh:mm:ss) Elapsed Time : 403 families discovered. RepeatScout/RECON discovery complete: 906 families found Classification Time: 00:29:29 (hh:mm:ss) Elapsed Time Program Time: 17:24:23 (hh:mm:ss) Elapsed Time