RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.09PyUo/RM_22849.ThuMay110930002023 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: 1683822599 Database = /dev/shm/rModeler.09PyUo/GCA_028018845.1_bMelGeo1.pri - Sequences = 40 - Bases = 1162015399 Storage Throughput = excellent ( 1183.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40088684 bp ( 40007169 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:41 (hh:mm:ss) Elapsed Time Round Time: 00:31:06 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3082 repeats masked totaling 917335 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10081817 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10016043 bp After Masking: 8323780 bp Masked: 16.90 % -- Input Database Coverage: 10081817 bp out of 1162015399 bp ( 0.87 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:05 (hh:mm:ss) Elapsed Time, 1250 HSPs Collected Number of families returned by RECON: 352 Round Time: 00:08:29 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8114 repeats masked totaling 2286804 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046867 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30031126 bp After Masking: 25865866 bp Masked: 13.87 % -- Input Database Coverage: 40128684 bp out of 1162015399 bp ( 3.45 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:38:45 (hh:mm:ss) Elapsed Time, 9328 HSPs Collected Number of families returned by RECON: 1884 Round Time: 00:42:32 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29144 repeats masked totaling 8612322 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90133355 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90026349 bp After Masking: 75678997 bp Masked: 15.94 % -- Input Database Coverage: 130262039 bp out of 1162015399 bp ( 11.21 % ) Sampling Time: 00:10:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 04:32:58 (hh:mm:ss) Elapsed Time, 117336 HSPs Collected Number of families returned by RECON: 10849 Round Time: 04:53:10 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99781 repeats masked totaling 31634288 bp(s). - TE Masking time 00:07:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270347433 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 270026823 bp After Masking: 221232448 bp Masked: 18.07 % -- Input Database Coverage: 400609472 bp out of 1162015399 bp ( 34.48 % ) Sampling Time: 00:37:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 36:08:17 (hh:mm:ss) Elapsed Time, 255828 HSPs Collected Number of families returned by RECON: 71383 Round Time: 38:04:29 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatScout/RECON discovery complete: 586 families found Classification Time: 00:52:43 (hh:mm:ss) Elapsed Time Program Time: 45:12:29 (hh:mm:ss) Elapsed Time