RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.vImkY8/RM_1997337.SatDec70832092024 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: 1733589129 Database = /scratch/tmp/rModeler.vImkY8/GCA_964188365.1_rPodMur119.hap2.1 - Sequences = 91 - Bases = 1433931530 Storage Throughput = excellent ( 1635.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034153 bp ( 40030953 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:54 (hh:mm:ss) Elapsed Time Round Time: 00:11:06 (hh:mm:ss) Elapsed Time : 537 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17233 repeats masked totaling 3084622 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040422 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10039422 bp After Masking: 6545985 bp Masked: 34.80 % -- Input Database Coverage: 10040422 bp out of 1433931530 bp ( 0.70 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 9252 HSPs Collected Number of families returned by RECON: 1298 Round Time: 00:03:34 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56939 repeats masked totaling 9728746 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033655 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30031455 bp After Masking: 19355985 bp Masked: 35.55 % -- Input Database Coverage: 40074077 bp out of 1433931530 bp ( 2.79 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:18 (hh:mm:ss) Elapsed Time, 53604 HSPs Collected Number of families returned by RECON: 4386 Round Time: 00:14:41 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181611 repeats masked totaling 31525658 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034027 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90022390 bp After Masking: 55243889 bp Masked: 38.63 % -- Input Database Coverage: 130108104 bp out of 1433931530 bp ( 9.07 % ) Sampling Time: 00:04:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:07:26 (hh:mm:ss) Elapsed Time, 199461 HSPs Collected Number of families returned by RECON: 13631 Round Time: 01:16:23 (hh:mm:ss) Elapsed Time : 465 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 612798 repeats masked totaling 104441420 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270058589 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270032789 bp After Masking: 156617037 bp Masked: 42.00 % -- Input Database Coverage: 400166693 bp out of 1433931530 bp ( 27.91 % ) Sampling Time: 00:13:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 07:44:51 (hh:mm:ss) Elapsed Time, 473410 HSPs Collected Number of families returned by RECON: 48700 Round Time: 08:29:24 (hh:mm:ss) Elapsed Time : 1069 families discovered. RepeatScout/RECON discovery complete: 2222 families found Classification Time: 00:32:38 (hh:mm:ss) Elapsed Time Program Time: 10:47:46 (hh:mm:ss) Elapsed Time