RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Swsi7X/RM_16980.FriMay121000162023 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: 1683910815 Database = /dev/shm/rModeler.Swsi7X/GCA_900324465.3_fAnaTes1.3 - Sequences = 51 - Bases = 555658509 Storage Throughput = fair ( 548.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40184549 bp ( 40015979 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:50:13 (hh:mm:ss) Elapsed Time Round Time: 00:55:44 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3258 repeats masked totaling 652719 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10067408 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10026826 bp After Masking: 9224043 bp Masked: 8.01 % -- Input Database Coverage: 10067408 bp out of 555658509 bp ( 1.81 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:57 (hh:mm:ss) Elapsed Time, 3733 HSPs Collected Number of families returned by RECON: 972 Round Time: 00:11:29 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10836 repeats masked totaling 2036059 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30157126 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30029138 bp After Masking: 27578455 bp Masked: 8.16 % -- Input Database Coverage: 40224534 bp out of 555658509 bp ( 7.24 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:51:01 (hh:mm:ss) Elapsed Time, 31176 HSPs Collected Number of families returned by RECON: 4674 Round Time: 00:55:13 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40026 repeats masked totaling 7227795 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90799205 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90003327 bp After Masking: 81449515 bp Masked: 9.50 % -- Input Database Coverage: 131023739 bp out of 555658509 bp ( 23.58 % ) Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 06:12:18 (hh:mm:ss) Elapsed Time, 172444 HSPs Collected Number of families returned by RECON: 19193 Round Time: 06:32:17 (hh:mm:ss) Elapsed Time : 263 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 161474 repeats masked totaling 29515441 bp(s). - TE Masking time 00:09:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271840804 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270035092 bp After Masking: 236779640 bp Masked: 12.32 % -- Input Database Coverage: 402864543 bp out of 555658509 bp ( 72.50 % ) Sampling Time: 00:28:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 49:34:37 (hh:mm:ss) Elapsed Time, 650802 HSPs Collected Number of families returned by RECON: 84972 Round Time: 52:49:10 (hh:mm:ss) Elapsed Time : 823 families discovered. RepeatScout/RECON discovery complete: 1363 families found Classification Time: 01:19:23 (hh:mm:ss) Elapsed Time Program Time: 62:43:16 (hh:mm:ss) Elapsed Time