RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jZKWoH/RM_1017263.TueApr151839132025 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: 1744767552 Database = /dev/shm/rModeler.jZKWoH/GCA_043748575.1_ASM4374857v1 - Sequences = 66 - Bases = 2185535924 Storage Throughput = excellent ( 1779.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003250 bp ( 40003010 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:14 (hh:mm:ss) Elapsed Time Round Time: 00:13:11 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8328 repeats masked totaling 2338302 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000901 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000661 bp After Masking: 7481235 bp Masked: 25.19 % -- Input Database Coverage: 10000901 bp out of 2185535924 bp ( 0.46 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 6135 HSPs Collected Number of families returned by RECON: 854 Round Time: 00:04:01 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28495 repeats masked totaling 7494774 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002345 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30002345 bp After Masking: 22155191 bp Masked: 26.16 % -- Input Database Coverage: 40003246 bp out of 2185535924 bp ( 1.83 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:57 (hh:mm:ss) Elapsed Time, 30430 HSPs Collected Number of families returned by RECON: 2746 Round Time: 00:15:22 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 98271 repeats masked totaling 25175224 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017309 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90015569 bp After Masking: 63617885 bp Masked: 29.33 % -- Input Database Coverage: 130020555 bp out of 2185535924 bp ( 5.95 % ) Sampling Time: 00:06:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 01:13:42 (hh:mm:ss) Elapsed Time, 100103 HSPs Collected Number of families returned by RECON: 9094 Round Time: 01:21:26 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 336475 repeats masked totaling 86075474 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270004647 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 270001467 bp After Masking: 180470436 bp Masked: 33.16 % -- Input Database Coverage: 400025202 bp out of 2185535924 bp ( 18.30 % ) Sampling Time: 00:18:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 08:27:46 (hh:mm:ss) Elapsed Time, 238752 HSPs Collected Number of families returned by RECON: 36327 Round Time: 08:56:45 (hh:mm:ss) Elapsed Time : 331 families discovered. RepeatScout/RECON discovery complete: 789 families found Classification Time: 00:19:22 (hh:mm:ss) Elapsed Time Program Time: 11:10:07 (hh:mm:ss) Elapsed Time