RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lSrJax/RM_813792.SatJul201946232024 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: 1721529981 Database = /dev/shm/rModeler.lSrJax/GCF_023375685.1_Billie_1.0 - Sequences = 43 - Bases = 825475682 Storage Throughput = good ( 764.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40812500 bp ( 40010065 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:25 (hh:mm:ss) Elapsed Time Round Time: 00:22:21 (hh:mm:ss) Elapsed Time : 648 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14525 repeats masked totaling 2584804 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10203667 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10018701 bp After Masking: 6845461 bp Masked: 31.67 % -- Input Database Coverage: 10203667 bp out of 825475682 bp ( 1.24 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:13:02 (hh:mm:ss) Elapsed Time, 9459 HSPs Collected Number of families returned by RECON: 1650 Round Time: 00:15:49 (hh:mm:ss) Elapsed Time : 23 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 00:04:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43784 repeats masked totaling 7781787 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30648753 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30031284 bp After Masking: 20455128 bp Masked: 31.89 % -- Input Database Coverage: 40852420 bp out of 825475682 bp ( 4.95 % ) Sampling Time: 00:05:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:58:27 (hh:mm:ss) Elapsed Time, 70229 HSPs Collected Number of families returned by RECON: 5843 Round Time: 01:07:11 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148551 repeats masked totaling 26727992 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91759236 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90000109 bp After Masking: 58140840 bp Masked: 35.40 % -- Input Database Coverage: 132611656 bp out of 825475682 bp ( 16.06 % ) Sampling Time: 00:16:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2634660 Comparison Time: 04:14:18 (hh:mm:ss) Elapsed Time, 277472 HSPs Collected Number of families returned by RECON: 16707 Round Time: 04:46:11 (hh:mm:ss) Elapsed Time : 480 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 521544 repeats masked totaling 95387425 bp(s). - TE Masking time 00:10:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275500072 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270032229 bp After Masking: 159507688 bp Masked: 40.93 % -- Input Database Coverage: 408111728 bp out of 825475682 bp ( 49.44 % ) Sampling Time: 00:50:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23767065 Comparison Time: 25:20:50 (hh:mm:ss) Elapsed Time, 661065 HSPs Collected Number of families returned by RECON: 54953 Round Time: 27:43:57 (hh:mm:ss) Elapsed Time : 1137 families discovered. RepeatScout/RECON discovery complete: 2441 families found Classification Time: 01:37:07 (hh:mm:ss) Elapsed Time Program Time: 35:52:36 (hh:mm:ss) Elapsed Time