RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JaUFq3/RM_22007.SunNov101023252024 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: 1731263003 Database = /dev/shm/rModeler.JaUFq3/GCA_964194405.1_rVipBer3.hap2.1 - Sequences = 348 - Bases = 1476666783 - N50 = 288144837 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 338784060-362982850 | [ 1 ] 314585270-338784060 | [ ] 290386480-314585270 | [ ] 266187690-290386480 | [ 1 ] 241988900-266187690 | [ ] 217790110-241988900 | [ ] 193591320-217790110 | [ 1 ] 169392530-193591320 | [ ] 145193740-169392530 | [ ] 120994950-145193740 | [ 1 ] 96796160-120994950 | [ 1 ] 72597370-96796160 | [ 2 ] 48398580-72597370 | [ ] 24199790-48398580 | [ 2 ] 1000-24199790 |************************************************** [ 339 ] Storage Throughput = excellent ( 1032.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044172 bp ( 40039972 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:04:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:54 (hh:mm:ss) Elapsed Time Round Time: 00:30:58 (hh:mm:ss) Elapsed Time : 483 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14708 repeats masked totaling 3811164 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013074 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10011674 bp After Masking: 5863054 bp Masked: 41.44 % -- Input Database Coverage: 10013074 bp out of 1476666783 bp ( 0.68 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 4421 HSPs Collected Number of families returned by RECON: 846 Round Time: 00:07:18 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46128 repeats masked totaling 11594903 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031018 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30028218 bp After Masking: 17361153 bp Masked: 42.18 % -- Input Database Coverage: 40044092 bp out of 1476666783 bp ( 2.71 % ) Sampling Time: 00:05:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:25:52 (hh:mm:ss) Elapsed Time, 24256 HSPs Collected Number of families returned by RECON: 2780 Round Time: 00:33:06 (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 : 00:09:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143115 repeats masked totaling 34923455 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016171 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90006171 bp After Masking: 51126561 bp Masked: 43.20 % -- Input Database Coverage: 130060263 bp out of 1476666783 bp ( 8.81 % ) Sampling Time: 00:18:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:56:05 (hh:mm:ss) Elapsed Time, 134303 HSPs Collected Number of families returned by RECON: 9145 Round Time: 03:26:04 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:29:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 480619 repeats masked totaling 116583056 bp(s). - TE Masking time 00:09:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043193 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 270011647 bp After Masking: 142757294 bp Masked: 47.13 % -- Input Database Coverage: 400103456 bp out of 1476666783 bp ( 27.10 % ) Sampling Time: 00:56:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 22:31:57 (hh:mm:ss) Elapsed Time, 392362 HSPs Collected Number of families returned by RECON: 31317 Round Time: 24:05:18 (hh:mm:ss) Elapsed Time : 665 families discovered. RepeatScout/RECON discovery complete: 1508 families found Classification Time: 01:05:11 (hh:mm:ss) Elapsed Time Program Time: 29:47:55 (hh:mm:ss) Elapsed Time