RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.qu3Uhv/RM_3357212.WedFeb260445052025 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: 1740573904 Database = /data/tmp/rModeler.qu3Uhv/GCA_043880545.1_ASM4388054v1 - Sequences = 106 - Bases = 2564586454 - N50 = 152795254 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 230778493-247261581 | [ 1 ] 214295405-230778492 | [ 1 ] 197812318-214295405 | [ ] 181329230-197812317 | [ 1 ] 164846143-181329230 |* [ 2 ] 148363055-164846142 | [ 1 ] 131879968-148363055 |* [ 2 ] 115396880-131879967 |* [ 2 ] 98913793-115396880 |* [ 2 ] 82430705-98913792 |* [ 2 ] 65947618-82430705 |* [ 2 ] 49464530-65947617 |* [ 3 ] 32981443-49464530 | [ ] 16498355-32981442 |* [ 2 ] 15268-16498355 |************************************************** [ 85 ] Storage Throughput = excellent ( 1612.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005888 bp ( 40004148 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:00 (hh:mm:ss) Elapsed Time Round Time: 00:15:07 (hh:mm:ss) Elapsed Time : 273 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11104 repeats masked totaling 2864409 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000868 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10000868 bp After Masking: 6944956 bp Masked: 30.56 % -- Input Database Coverage: 10000868 bp out of 2564586454 bp ( 0.39 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:16 (hh:mm:ss) Elapsed Time, 13692 HSPs Collected Number of families returned by RECON: 876 Round Time: 00:05:04 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36489 repeats masked totaling 9878152 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005019 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30003279 bp After Masking: 19690783 bp Masked: 34.37 % -- Input Database Coverage: 40005887 bp out of 2564586454 bp ( 1.56 % ) Sampling Time: 00:03:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:19:15 (hh:mm:ss) Elapsed Time, 46192 HSPs Collected Number of families returned by RECON: 2602 Round Time: 00:22:47 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116606 repeats masked totaling 30777353 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041620 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90039120 bp After Masking: 57979947 bp Masked: 35.61 % -- Input Database Coverage: 130047507 bp out of 2564586454 bp ( 5.07 % ) Sampling Time: 00:08:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:46:39 (hh:mm:ss) Elapsed Time, 441185 HSPs Collected Number of families returned by RECON: 8748 Round Time: 01:57:16 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 408113 repeats masked totaling 104917231 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036761 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 270029061 bp After Masking: 161273116 bp Masked: 40.28 % -- Input Database Coverage: 400084268 bp out of 2564586454 bp ( 15.60 % ) Sampling Time: 00:22:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 12:12:11 (hh:mm:ss) Elapsed Time, 2644244 HSPs Collected Number of families returned by RECON: 31017 Round Time: 12:45:48 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatScout/RECON discovery complete: 958 families found Classification Time: 00:25:40 (hh:mm:ss) Elapsed Time Program Time: 15:51:42 (hh:mm:ss) Elapsed Time