RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wxfsQ0/RM_5736.MonNov271039412023 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: 1701110380 Database = /dev/shm/rModeler.wxfsQ0/GCA_027789725.1_aDenEbr1.mat - Sequences = 2570 - Bases = 2352821159 - N50 = 63877015 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 126944166-136011543 | [ 2 ] 117876790-126944166 | [ ] 108809414-117876790 | [ 1 ] 99742038-108809414 | [ ] 90674662-99742038 | [ 1 ] 81607285-90674661 | [ 3 ] 72539909-81607285 | [ 3 ] 63472533-72539909 | [ 3 ] 54405157-63472533 | [ 2 ] 45337781-54405157 | [ 5 ] 36270404-45337780 | [ 1 ] 27203028-36270404 | [ 7 ] 18135652-27203028 | [ 5 ] 9068276-18135652 | [ 6 ] 900-9068276 |************************************************** [ 2531 ] Storage Throughput = excellent ( 1179.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42133634 bp ( 40038278 non ambiguous ) - Num Contigs Represented = 186 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:18 (hh:mm:ss) Elapsed Time Round Time: 00:30:07 (hh:mm:ss) Elapsed Time : 976 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 00:02:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21984 repeats masked totaling 3883490 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10744756 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 10016678 bp After Masking: 4811927 bp Masked: 51.96 % -- Input Database Coverage: 10744756 bp out of 2352821159 bp ( 0.46 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37950 Comparison Time: 00:07:30 (hh:mm:ss) Elapsed Time, 25821 HSPs Collected Number of families returned by RECON: 1551 Round Time: 00:11:08 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65965 repeats masked totaling 12113627 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31388874 bp Num Contigs Represented = 159 Non ambiguous bp: Initial: 30021596 bp After Masking: 13784331 bp Masked: 54.09 % -- Input Database Coverage: 42133630 bp out of 2352821159 bp ( 1.79 % ) Sampling Time: 00:08:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 321201 Comparison Time: 00:26:18 (hh:mm:ss) Elapsed Time, 91415 HSPs Collected Number of families returned by RECON: 4863 Round Time: 00:36:47 (hh:mm:ss) Elapsed Time : 136 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 208685 repeats masked totaling 37912570 bp(s). - TE Masking time 00:04:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94843843 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 90023160 bp After Masking: 39814795 bp Masked: 55.77 % -- Input Database Coverage: 136977473 bp out of 2352821159 bp ( 5.82 % ) Sampling Time: 00:29:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2924571 Comparison Time: 04:20:50 (hh:mm:ss) Elapsed Time, 311577 HSPs Collected Number of families returned by RECON: 13121 Round Time: 05:02:38 (hh:mm:ss) Elapsed Time : 539 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:16:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 704543 repeats masked totaling 128046271 bp(s). - TE Masking time 00:14:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 283439722 bp Num Contigs Represented = 691 Non ambiguous bp: Initial: 270031391 bp After Masking: 104555681 bp Masked: 61.28 % -- Input Database Coverage: 420417195 bp out of 2352821159 bp ( 17.87 % ) Sampling Time: 01:40:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26371953 Comparison Time: 19:25:11 (hh:mm:ss) Elapsed Time, 801975 HSPs Collected Number of families returned by RECON: 35859 Round Time: 22:17:27 (hh:mm:ss) Elapsed Time : 1309 families discovered. RepeatScout/RECON discovery complete: 2987 families found Classification Time: 01:36:49 (hh:mm:ss) Elapsed Time Program Time: 30:14:56 (hh:mm:ss) Elapsed Time