RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bqejEx/RM_11006.WedJul240718582024 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: 1721830727 Database = /dev/shm/rModeler.bqejEx/GCF_019097595.1_SWU_Hwy_1.0 - Sequences = 73 - Bases = 789816092 Storage Throughput = excellent ( 1080.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002471 bp ( 40002095 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:17 (hh:mm:ss) Elapsed Time Round Time: 00:38:34 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8416 repeats masked totaling 1561414 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031216 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10031216 bp After Masking: 7229638 bp Masked: 27.93 % -- Input Database Coverage: 10031216 bp out of 789816092 bp ( 1.27 % ) Sampling Time: 00:06:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:45:17 (hh:mm:ss) Elapsed Time, 7203 HSPs Collected Number of families returned by RECON: 1421 Round Time: 00:54:48 (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 : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26917 repeats masked totaling 5117817 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011175 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30010799 bp After Masking: 21306854 bp Masked: 29.00 % -- Input Database Coverage: 40042391 bp out of 789816092 bp ( 5.07 % ) Sampling Time: 00:19:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 02:45:27 (hh:mm:ss) Elapsed Time, 55875 HSPs Collected Number of families returned by RECON: 5474 Round Time: 03:12:08 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93150 repeats masked totaling 17770637 bp(s). - TE Masking time 00:02:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017080 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90015780 bp After Masking: 60893548 bp Masked: 32.35 % -- Input Database Coverage: 130059471 bp out of 789816092 bp ( 16.47 % ) Sampling Time: 01:05:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 10:07:19 (hh:mm:ss) Elapsed Time, 239973 HSPs Collected Number of families returned by RECON: 17834 Round Time: 11:46:22 (hh:mm:ss) Elapsed Time : 388 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:19:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 337911 repeats masked totaling 64762085 bp(s). - TE Masking time 00:12:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014094 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270010394 bp After Masking: 169638000 bp Masked: 37.17 % -- Input Database Coverage: 400073565 bp out of 789816092 bp ( 50.65 % ) Sampling Time: 03:36:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 50:59:18 (hh:mm:ss) Elapsed Time, 792280 HSPs Collected Number of families returned by RECON: 61397 Round Time: 56:20:11 (hh:mm:ss) Elapsed Time : 883 families discovered. RepeatScout/RECON discovery complete: 1799 families found Classification Time: 01:36:57 (hh:mm:ss) Elapsed Time Program Time: 74:29:00 (hh:mm:ss) Elapsed Time