RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.StHa9H/RM_4034438.WedMar271328102024 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: 1711571290 Database = /dev/shm/rModeler.StHa9H/GCA_963921795.1_fNanAch1.1 - Sequences = 673 - Bases = 1658848640 - N50 = 66577881 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 84162722-90174274 | [ 1 ] 78151170-84162721 | [ 1 ] 72139619-78151170 | [ 4 ] 66128067-72139618 | [ 6 ] 60116516-66128067 | [ 8 ] 54104964-60116515 | [ 2 ] 48093412-54104963 | [ 2 ] 42081861-48093412 | [ ] 36070309-42081860 | [ ] 30058758-36070309 | [ ] 24047206-30058757 | [ ] 18035654-24047205 | [ ] 12024103-18035654 | [ ] 6012551-12024102 | [ ] 1000-6012551 |************************************************** [ 649 ] Storage Throughput = excellent ( 1403.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047316 bp ( 40037427 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:44 (hh:mm:ss) Elapsed Time Round Time: 00:33:42 (hh:mm:ss) Elapsed Time : 1388 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28281 repeats masked totaling 4314695 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036505 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10034305 bp After Masking: 5105563 bp Masked: 49.12 % -- Input Database Coverage: 10036505 bp out of 1658848640 bp ( 0.61 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 10766 HSPs Collected Number of families returned by RECON: 1569 Round Time: 00:07:17 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87925 repeats masked totaling 13390312 bp(s). - TE Masking time 00:01:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010807 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30003118 bp After Masking: 14752810 bp Masked: 50.83 % -- Input Database Coverage: 40047312 bp out of 1658848640 bp ( 2.41 % ) Sampling Time: 00:05:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:23:39 (hh:mm:ss) Elapsed Time, 59158 HSPs Collected Number of families returned by RECON: 5591 Round Time: 00:30:17 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 271615 repeats masked totaling 40048641 bp(s). - TE Masking time 00:05:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045479 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 90017872 bp After Masking: 44139282 bp Masked: 50.97 % -- Input Database Coverage: 130092791 bp out of 1658848640 bp ( 7.84 % ) Sampling Time: 00:15:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:19:49 (hh:mm:ss) Elapsed Time, 459462 HSPs Collected Number of families returned by RECON: 16955 Round Time: 02:54:00 (hh:mm:ss) Elapsed Time : 700 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 896218 repeats masked totaling 135166760 bp(s). - TE Masking time 00:21:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270099048 bp Num Contigs Represented = 210 Non ambiguous bp: Initial: 270017154 bp After Masking: 117612814 bp Masked: 56.44 % -- Input Database Coverage: 400191839 bp out of 1658848640 bp ( 24.12 % ) Sampling Time: 00:52:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23273253 Comparison Time: 16:10:20 (hh:mm:ss) Elapsed Time, 2036571 HSPs Collected Number of families returned by RECON: 49153 Round Time: 18:33:37 (hh:mm:ss) Elapsed Time : 1958 families discovered. RepeatScout/RECON discovery complete: 4144 families found Classification Time: 02:24:01 (hh:mm:ss) Elapsed Time Program Time: 25:02:54 (hh:mm:ss) Elapsed Time