RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.pzVVyP/RM_3467385.WedNov132156312024 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: 1731563791 Database = /scratch/tmp/rModeler.pzVVyP/GCA_039877785.1_fChaTrf1.hap1 - Sequences = 37 - Bases = 662505520 Storage Throughput = excellent ( 1546.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027111 bp ( 40026511 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:09 (hh:mm:ss) Elapsed Time Round Time: 00:09:25 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5374 repeats masked totaling 866510 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018858 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10018658 bp After Masking: 8922722 bp Masked: 10.94 % -- Input Database Coverage: 10018858 bp out of 662505520 bp ( 1.51 % ) Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 7412 HSPs Collected Number of families returned by RECON: 1535 Round Time: 00:03:30 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17464 repeats masked totaling 3114113 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008234 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30007834 bp After Masking: 26130854 bp Masked: 12.92 % -- Input Database Coverage: 40027092 bp out of 662505520 bp ( 6.04 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:14:36 (hh:mm:ss) Elapsed Time, 51886 HSPs Collected Number of families returned by RECON: 6088 Round Time: 00:16:33 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65839 repeats masked totaling 11666180 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009053 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90008153 bp After Masking: 75616465 bp Masked: 15.99 % -- Input Database Coverage: 130036145 bp out of 662505520 bp ( 19.63 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:30:38 (hh:mm:ss) Elapsed Time, 277638 HSPs Collected Number of families returned by RECON: 21589 Round Time: 01:40:48 (hh:mm:ss) Elapsed Time : 436 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 265121 repeats masked totaling 47622045 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022004 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 270017504 bp After Masking: 214578454 bp Masked: 20.53 % -- Input Database Coverage: 400058149 bp out of 662505520 bp ( 60.39 % ) Sampling Time: 00:11:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 11:26:37 (hh:mm:ss) Elapsed Time, 787497 HSPs Collected Number of families returned by RECON: 82497 Round Time: 12:35:58 (hh:mm:ss) Elapsed Time : 1130 families discovered. RepeatScout/RECON discovery complete: 2055 families found Classification Time: 00:48:14 (hh:mm:ss) Elapsed Time Program Time: 15:34:28 (hh:mm:ss) Elapsed Time