RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HtbNDs/RM_3556.MonJun241450262024 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: 1719265824 Database = /dev/shm/rModeler.HtbNDs/GCF_022682495.1_HLdesRot8A - Sequences = 573 - Bases = 2113489943 - N50 = 167477801 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198107767-212258161 | [ 3 ] 183957374-198107767 | [ ] 169806981-183957374 | [ 1 ] 155656588-169806981 | [ 2 ] 141506195-155656588 | [ ] 127355801-141506194 | [ 2 ] 113205408-127355801 | [ 2 ] 99055015-113205408 | [ 3 ] 84904622-99055015 | [ 1 ] 70754229-84904622 | [ ] 56603835-70754228 | [ ] 42453442-56603835 | [ ] 28303049-42453442 | [ ] 14152656-28303049 | [ ] 2263-14152656 |************************************************** [ 559 ] Storage Throughput = excellent ( 1001.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018869 bp ( 40013169 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:21 (hh:mm:ss) Elapsed Time Round Time: 00:34:55 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7231 repeats masked totaling 2138028 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039317 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10038317 bp After Masking: 7811722 bp Masked: 22.18 % -- Input Database Coverage: 10039317 bp out of 2113489943 bp ( 0.48 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 11875 HSPs Collected Number of families returned by RECON: 955 Round Time: 00:07:07 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26082 repeats masked totaling 7412551 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019471 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30014771 bp After Masking: 22332161 bp Masked: 25.60 % -- Input Database Coverage: 40058788 bp out of 2113489943 bp ( 1.90 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:28:52 (hh:mm:ss) Elapsed Time, 42155 HSPs Collected Number of families returned by RECON: 2620 Round Time: 00:33:35 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89009 repeats masked totaling 25326803 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037637 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90026497 bp After Masking: 63538416 bp Masked: 29.42 % -- Input Database Coverage: 130096425 bp out of 2113489943 bp ( 6.16 % ) Sampling Time: 00:11:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:19:01 (hh:mm:ss) Elapsed Time, 150879 HSPs Collected Number of families returned by RECON: 8758 Round Time: 03:34:45 (hh:mm:ss) Elapsed Time : 154 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 308380 repeats masked totaling 83860337 bp(s). - TE Masking time 00:05:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270057103 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 270018251 bp After Masking: 183280831 bp Masked: 32.12 % -- Input Database Coverage: 400153528 bp out of 2113489943 bp ( 18.93 % ) Sampling Time: 00:35:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 26:05:14 (hh:mm:ss) Elapsed Time, 998028 HSPs Collected Number of families returned by RECON: 39638 Round Time: 27:18:13 (hh:mm:ss) Elapsed Time : 388 families discovered. RepeatScout/RECON discovery complete: 816 families found Classification Time: 00:33:48 (hh:mm:ss) Elapsed Time Program Time: 32:42:23 (hh:mm:ss) Elapsed Time