RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CVr562/RM_3445010.ThuMar210558462024 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: 1711025926 Database = /dev/shm/rModeler.CVr562/GCA_036417435.1_mIniGeo1.hap1 - Sequences = 903 - Bases = 2749362370 - N50 = 120325874 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 178992940-191777932 | [ 4 ] 166207949-178992940 | [ ] 153422958-166207949 | [ ] 140637967-153422958 | [ 2 ] 127852976-140637967 | [ 1 ] 115067984-127852975 | [ 2 ] 102282993-115067984 | [ 4 ] 89498002-102282993 | [ 3 ] 76713011-89498002 | [ 3 ] 63928020-76713011 | [ 2 ] 51143028-63928019 | [ ] 38358037-51143028 | [ ] 25573046-38358037 | [ 1 ] 12788055-25573046 | [ 1 ] 3064-12788055 |************************************************* [ 880 ] Storage Throughput = excellent ( 1433.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003482 bp ( 40003082 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:42 (hh:mm:ss) Elapsed Time Round Time: 00:32:08 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11309 repeats masked totaling 3212594 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010968 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10010968 bp After Masking: 6449051 bp Masked: 35.58 % -- Input Database Coverage: 10010968 bp out of 2749362370 bp ( 0.36 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:47 (hh:mm:ss) Elapsed Time, 19483 HSPs Collected Number of families returned by RECON: 768 Round Time: 00:07:38 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36178 repeats masked totaling 10664624 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032434 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30032034 bp After Masking: 18116532 bp Masked: 39.68 % -- Input Database Coverage: 40043402 bp out of 2749362370 bp ( 1.46 % ) Sampling Time: 00:04:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:28:19 (hh:mm:ss) Elapsed Time, 27970 HSPs Collected Number of families returned by RECON: 2020 Round Time: 00:34:07 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114764 repeats masked totaling 34371725 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030526 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 90028726 bp After Masking: 51336575 bp Masked: 42.98 % -- Input Database Coverage: 130073928 bp out of 2749362370 bp ( 4.73 % ) Sampling Time: 00:12:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:25:38 (hh:mm:ss) Elapsed Time, 134964 HSPs Collected Number of families returned by RECON: 6836 Round Time: 02:40:26 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 380231 repeats masked totaling 109095386 bp(s). - TE Masking time 00:04:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270007324 bp Num Contigs Represented = 308 Non ambiguous bp: Initial: 270000124 bp After Masking: 150989445 bp Masked: 44.08 % -- Input Database Coverage: 400081252 bp out of 2749362370 bp ( 14.55 % ) Sampling Time: 00:34:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 17:07:52 (hh:mm:ss) Elapsed Time, 586903 HSPs Collected Number of families returned by RECON: 29898 Round Time: 18:04:13 (hh:mm:ss) Elapsed Time : 311 families discovered. RepeatScout/RECON discovery complete: 755 families found Classification Time: 00:28:39 (hh:mm:ss) Elapsed Time Program Time: 22:27:11 (hh:mm:ss) Elapsed Time