RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SlkSRI/RM_21760.SatDec311117492022 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: 1672514268 Database = /dev/shm/rModeler.SlkSRI/GCF_902362185.1_fChaCha1.1 - Sequences = 31 - Bases = 656929047 Storage Throughput = good ( 994.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40264631 bp ( 40024301 non ambiguous ) - Num Contigs Represented = 16 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:13 (hh:mm:ss) Elapsed Time Round Time: 00:29:45 (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 : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2744 repeats masked totaling 573884 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041181 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10000976 bp After Masking: 8753254 bp Masked: 12.48 % -- Input Database Coverage: 10041181 bp out of 656929047 bp ( 1.53 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:55 (hh:mm:ss) Elapsed Time, 3755 HSPs Collected Number of families returned by RECON: 1049 Round Time: 00:09:35 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8719 repeats masked totaling 1728075 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30223449 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 30023324 bp After Masking: 25937457 bp Masked: 13.61 % -- Input Database Coverage: 40264630 bp out of 656929047 bp ( 6.13 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:45:52 (hh:mm:ss) Elapsed Time, 25232 HSPs Collected Number of families returned by RECON: 4450 Round Time: 00:51:18 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29556 repeats masked totaling 5733313 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90711316 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90027811 bp After Masking: 77215527 bp Masked: 14.23 % -- Input Database Coverage: 130975946 bp out of 656929047 bp ( 19.94 % ) Sampling Time: 00:13:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 05:40:55 (hh:mm:ss) Elapsed Time, 186425 HSPs Collected Number of families returned by RECON: 19254 Round Time: 06:07:04 (hh:mm:ss) Elapsed Time : 268 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123404 repeats masked totaling 25763465 bp(s). - TE Masking time 00:09:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271901856 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270000423 bp After Masking: 223371568 bp Masked: 17.27 % -- Input Database Coverage: 402877802 bp out of 656929047 bp ( 61.33 % ) Sampling Time: 00:47:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 45:26:24 (hh:mm:ss) Elapsed Time, 834002 HSPs Collected Number of families returned by RECON: 82878 Round Time: 48:52:33 (hh:mm:ss) Elapsed Time : 834 families discovered. RepeatScout/RECON discovery complete: 1394 families found Classification Time: 01:34:00 (hh:mm:ss) Elapsed Time Program Time: 58:04:15 (hh:mm:ss) Elapsed Time