RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.WgtkEK/RM_16513.MonDec21728002024 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: 1733189279 Database = /scratch/tmp/rModeler.WgtkEK/GCA_028858625.2_bColStr4.1.hap2 - Sequences = 242 - Bases = 1153503718 - N50 = 98266943 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195839760-209827101 | [ 1 ] 181852419-195839759 | [ ] 167865078-181852418 | [ ] 153877738-167865078 | [ ] 139890397-153877737 | [ ] 125903056-139890396 | [ ] 111915715-125903055 | [ 1 ] 97928375-111915715 | [ 2 ] 83941034-97928374 | [ ] 69953693-83941033 | [ ] 55966352-69953692 | [ 1 ] 41979012-55966352 | [ 2 ] 27991671-41979011 |* [ 5 ] 14004330-27991670 |* [ 6 ] 16990-14004330 |************************************************* [ 224 ] Storage Throughput = fair ( 617.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40130746 bp ( 40038941 non ambiguous ) - Num Contigs Represented = 71 - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:34 (hh:mm:ss) Elapsed Time Round Time: 00:29:43 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3887 repeats masked totaling 1102061 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005571 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10005071 bp After Masking: 8299998 bp Masked: 17.04 % -- Input Database Coverage: 10005571 bp out of 1153503718 bp ( 0.87 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:30 (hh:mm:ss) Elapsed Time, 460 HSPs Collected Number of families returned by RECON: 219 Round Time: 00:06:51 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10438 repeats masked totaling 3103025 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30125098 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30033793 bp After Masking: 24802730 bp Masked: 17.42 % -- Input Database Coverage: 40130669 bp out of 1153503718 bp ( 3.48 % ) Sampling Time: 00:04:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:31:40 (hh:mm:ss) Elapsed Time, 4124 HSPs Collected Number of families returned by RECON: 1176 Round Time: 00:35:53 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31555 repeats masked totaling 9252288 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90519007 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 90016818 bp After Masking: 74740070 bp Masked: 16.97 % -- Input Database Coverage: 130649676 bp out of 1153503718 bp ( 11.33 % ) Sampling Time: 00:11:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 03:58:54 (hh:mm:ss) Elapsed Time, 44777 HSPs Collected Number of families returned by RECON: 7796 Round Time: 04:14:52 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111512 repeats masked totaling 32047814 bp(s). - TE Masking time 00:04:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270857833 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 270013081 bp After Masking: 219422423 bp Masked: 18.74 % -- Input Database Coverage: 401507509 bp out of 1153503718 bp ( 34.81 % ) Sampling Time: 00:37:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 32:25:04 (hh:mm:ss) Elapsed Time, 191861 HSPs Collected Number of families returned by RECON: 53602 Round Time: 34:01:19 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatScout/RECON discovery complete: 400 families found Classification Time: 00:36:18 (hh:mm:ss) Elapsed Time Program Time: 40:04:56 (hh:mm:ss) Elapsed Time