RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nKRiv5/RM_11672.MonJan90114272023 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: 1673255666 Database = /dev/shm/rModeler.nKRiv5/GCF_015476345.1_ZJU1.0 - Sequences = 756 - Bases = 1188533289 - N50 = 120086012 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193422715-207238429 | [ 1 ] 179607001-193422714 | [ ] 165791288-179607001 | [ ] 151975574-165791287 | [ 1 ] 138159861-151975574 | [ ] 124344147-138159860 | [ ] 110528433-124344146 | [ 1 ] 96712720-110528433 | [ ] 82897006-96712719 | [ 1 ] 69081293-82897006 | [ 1 ] 55265579-69081292 | [ 1 ] 41449865-55265578 | [ ] 27634152-41449865 | [ 3 ] 13818438-27634151 | [ 10 ] 2725-13818438 |************************************************** [ 737 ] Storage Throughput = excellent ( 1100.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40242730 bp ( 40008746 non ambiguous ) - Num Contigs Represented = 95 - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:35 (hh:mm:ss) Elapsed Time Round Time: 00:35:16 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2101 repeats masked totaling 827422 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10097554 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10036771 bp After Masking: 8761378 bp Masked: 12.71 % -- Input Database Coverage: 10097554 bp out of 1188533289 bp ( 0.85 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:08:01 (hh:mm:ss) Elapsed Time, 1184 HSPs Collected Number of families returned by RECON: 263 Round Time: 00:09:39 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6039 repeats masked totaling 2352544 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30185183 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30011982 bp After Masking: 26611851 bp Masked: 11.33 % -- Input Database Coverage: 40282737 bp out of 1188533289 bp ( 3.39 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:50:16 (hh:mm:ss) Elapsed Time, 106001 HSPs Collected Number of families returned by RECON: 1602 Round Time: 00:54:58 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19473 repeats masked totaling 7225980 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90369037 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 90019711 bp After Masking: 79057945 bp Masked: 12.18 % -- Input Database Coverage: 130651774 bp out of 1188533289 bp ( 10.99 % ) Sampling Time: 00:12:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 05:44:19 (hh:mm:ss) Elapsed Time, 117898 HSPs Collected Number of families returned by RECON: 9603 Round Time: 05:59:20 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65010 repeats masked totaling 23335551 bp(s). - TE Masking time 00:03:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270684307 bp Num Contigs Represented = 327 Non ambiguous bp: Initial: 270007634 bp After Masking: 237068137 bp Masked: 12.20 % -- Input Database Coverage: 401336081 bp out of 1188533289 bp ( 33.77 % ) Sampling Time: 00:36:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23403061 Comparison Time: 47:43:41 (hh:mm:ss) Elapsed Time, 1250117 HSPs Collected Number of families returned by RECON: 62996 Round Time: 49:22:15 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatScout/RECON discovery complete: 394 families found Classification Time: 00:28:56 (hh:mm:ss) Elapsed Time Program Time: 57:30:24 (hh:mm:ss) Elapsed Time