RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.vA0Qi9/RM_30055.MonDec21728212024 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: 1733189300 Database = /scratch/tmp/rModeler.vA0Qi9/GCA_028878085.3_NHGRI_mSymSyn1-v2.0_alt - Sequences = 40 - Bases = 3097367794 Storage Throughput = fair ( 619.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041886 bp ( 40001884 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:31:02 (hh:mm:ss) Elapsed Time Round Time: 01:01:19 (hh:mm:ss) Elapsed Time : 220 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10644 repeats masked totaling 2736634 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000636 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000636 bp After Masking: 5601190 bp Masked: 43.99 % -- Input Database Coverage: 10000636 bp out of 3097367794 bp ( 0.32 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:52 (hh:mm:ss) Elapsed Time, 6318 HSPs Collected Number of families returned by RECON: 855 Round Time: 00:06:57 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37691 repeats masked totaling 9319830 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041170 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001168 bp After Masking: 16653311 bp Masked: 44.49 % -- Input Database Coverage: 40041806 bp out of 3097367794 bp ( 1.29 % ) Sampling Time: 00:04:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:05 (hh:mm:ss) Elapsed Time, 23171 HSPs Collected Number of families returned by RECON: 2012 Round Time: 00:29:53 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123070 repeats masked totaling 30225575 bp(s). - TE Masking time 00:02:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004865 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90001275 bp After Masking: 47409263 bp Masked: 47.32 % -- Input Database Coverage: 130046671 bp out of 3097367794 bp ( 4.20 % ) Sampling Time: 00:14:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:36:11 (hh:mm:ss) Elapsed Time, 103267 HSPs Collected Number of families returned by RECON: 6648 Round Time: 02:55:39 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 406268 repeats masked totaling 99053860 bp(s). - TE Masking time 00:10:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270195329 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 270013807 bp After Masking: 135294943 bp Masked: 49.89 % -- Input Database Coverage: 400242000 bp out of 3097367794 bp ( 12.92 % ) Sampling Time: 00:44:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 19:45:58 (hh:mm:ss) Elapsed Time, 204840 HSPs Collected Number of families returned by RECON: 24722 Round Time: 20:54:24 (hh:mm:ss) Elapsed Time : 354 families discovered. RepeatScout/RECON discovery complete: 836 families found Classification Time: 00:52:09 (hh:mm:ss) Elapsed Time Program Time: 26:20:21 (hh:mm:ss) Elapsed Time