RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.a7uiel/RM_18638.TueJul161614372024 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: 1721171671 Database = /dev/shm/rModeler.a7uiel/GCF_011397635.1_E.fuscoguttatus.final_Chr_v1 - Sequences = 26 - Bases = 1047012452 Storage Throughput = excellent ( 1005.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002829 bp ( 40002229 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:44 (hh:mm:ss) Elapsed Time Round Time: 00:40:33 (hh:mm:ss) Elapsed Time : 1021 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16838 repeats masked totaling 2741833 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037805 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10037705 bp After Masking: 6994279 bp Masked: 30.32 % -- Input Database Coverage: 10037805 bp out of 1047012452 bp ( 0.96 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:30:01 (hh:mm:ss) Elapsed Time, 11612 HSPs Collected Number of families returned by RECON: 1974 Round Time: 00:33:06 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51694 repeats masked totaling 8544012 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005103 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30004603 bp After Masking: 20852571 bp Masked: 30.50 % -- Input Database Coverage: 40042908 bp out of 1047012452 bp ( 3.82 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 01:54:09 (hh:mm:ss) Elapsed Time, 79832 HSPs Collected Number of families returned by RECON: 6432 Round Time: 02:05:11 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 175893 repeats masked totaling 28697584 bp(s). - TE Masking time 00:03:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040515 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90038815 bp After Masking: 59485106 bp Masked: 33.93 % -- Input Database Coverage: 130083423 bp out of 1047012452 bp ( 12.42 % ) Sampling Time: 00:09:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 07:27:59 (hh:mm:ss) Elapsed Time, 381868 HSPs Collected Number of families returned by RECON: 18146 Round Time: 08:13:50 (hh:mm:ss) Elapsed Time : 727 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 610407 repeats masked totaling 104256105 bp(s). - TE Masking time 00:16:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009722 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270004014 bp After Masking: 160115133 bp Masked: 40.70 % -- Input Database Coverage: 400093145 bp out of 1047012452 bp ( 38.21 % ) Sampling Time: 00:35:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 44:45:38 (hh:mm:ss) Elapsed Time, 940513 HSPs Collected Number of families returned by RECON: 55668 Round Time: 47:40:58 (hh:mm:ss) Elapsed Time : 1647 families discovered. RepeatScout/RECON discovery complete: 3633 families found Classification Time: 02:13:58 (hh:mm:ss) Elapsed Time Program Time: 61:27:36 (hh:mm:ss) Elapsed Time