RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.oubxmW/RM_149372.SatDec312318442022 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: 1672557524 Database = /dev/shm/rModeler.oubxmW/GCF_910596095.1_fThuMac1.1 - Sequences = 58 - Bases = 782423979 Storage Throughput = excellent ( 1110.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009899 bp ( 40009399 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:46 (hh:mm:ss) Elapsed Time Round Time: 00:19:26 (hh:mm:ss) Elapsed Time : 584 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (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... 10142 repeats masked totaling 1419261 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002020 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10002020 bp After Masking: 8362055 bp Masked: 16.40 % -- Input Database Coverage: 10002020 bp out of 782423979 bp ( 1.28 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:54 (hh:mm:ss) Elapsed Time, 8112 HSPs Collected Number of families returned by RECON: 1896 Round Time: 00:07:05 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31411 repeats masked totaling 4575811 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007868 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30007368 bp After Masking: 24796581 bp Masked: 17.37 % -- Input Database Coverage: 40009888 bp out of 782423979 bp ( 5.11 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:29:24 (hh:mm:ss) Elapsed Time, 58702 HSPs Collected Number of families returned by RECON: 6570 Round Time: 00:34:03 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107871 repeats masked totaling 15894273 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013839 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90009839 bp After Masking: 72143413 bp Masked: 19.85 % -- Input Database Coverage: 130023727 bp out of 782423979 bp ( 16.62 % ) Sampling Time: 00:08:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:23:32 (hh:mm:ss) Elapsed Time, 331502 HSPs Collected Number of families returned by RECON: 22389 Round Time: 03:51:20 (hh:mm:ss) Elapsed Time : 618 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 401638 repeats masked totaling 63284863 bp(s). - TE Masking time 00:10:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030245 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270019745 bp After Masking: 201129417 bp Masked: 25.51 % -- Input Database Coverage: 400053972 bp out of 782423979 bp ( 51.13 % ) Sampling Time: 00:33:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 27:03:56 (hh:mm:ss) Elapsed Time, 1081383 HSPs Collected Number of families returned by RECON: 78319 Round Time: 30:05:19 (hh:mm:ss) Elapsed Time : 1465 families discovered. RepeatScout/RECON discovery complete: 2832 families found Classification Time: 02:00:13 (hh:mm:ss) Elapsed Time Program Time: 36:57:26 (hh:mm:ss) Elapsed Time