RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RDgQFk/RM_2830686.SatMay130920532023 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: 1683994852 Database = /dev/shm/rModeler.RDgQFk/GCA_900634625.2_fParRan2.2 - Sequences = 157 - Bases = 551029983 - N50 = 23963493 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 43590407-46703924 | [ 1 ] 40476890-43590406 | [ ] 37363373-40476889 | [ ] 34249856-37363372 | [ ] 31136340-34249856 | [ 1 ] 28022823-31136339 | [ ] 24909306-28022822 |* [ 3 ] 21795789-24909305 |*** [ 10 ] 18682272-21795788 |* [ 3 ] 15568756-18682272 |* [ 3 ] 12455239-15568755 | [ 1 ] 9341722-12455238 | [ 1 ] 6228205-9341721 | [ ] 3114688-6228204 | [ 2 ] 1172-3114688 |************************************************** [ 132 ] Storage Throughput = excellent ( 1313.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40576496 bp ( 40026803 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:13 (hh:mm:ss) Elapsed Time Round Time: 00:22:42 (hh:mm:ss) Elapsed Time : 401 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5587 repeats masked totaling 1309132 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10097983 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10033857 bp After Masking: 8566775 bp Masked: 14.62 % -- Input Database Coverage: 10097983 bp out of 551029983 bp ( 1.83 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:31 (hh:mm:ss) Elapsed Time, 4152 HSPs Collected Number of families returned by RECON: 1142 Round Time: 00:07:53 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16750 repeats masked totaling 4142620 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30518366 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30032799 bp After Masking: 25356593 bp Masked: 15.57 % -- Input Database Coverage: 40616349 bp out of 551029983 bp ( 7.37 % ) Sampling Time: 00:02:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:34:09 (hh:mm:ss) Elapsed Time, 26838 HSPs Collected Number of families returned by RECON: 4824 Round Time: 00:38:41 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53928 repeats masked totaling 12436109 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92257041 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90032886 bp After Masking: 75880278 bp Masked: 15.72 % -- Input Database Coverage: 132873390 bp out of 551029983 bp ( 24.11 % ) Sampling Time: 00:09:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2685403 Comparison Time: 03:58:09 (hh:mm:ss) Elapsed Time, 198360 HSPs Collected Number of families returned by RECON: 20496 Round Time: 04:20:43 (hh:mm:ss) Elapsed Time : 280 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 197463 repeats masked totaling 45701580 bp(s). - TE Masking time 00:10:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275490933 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 270024237 bp After Masking: 219870209 bp Masked: 18.57 % -- Input Database Coverage: 408364323 bp out of 551029983 bp ( 74.11 % ) Sampling Time: 00:29:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23988201 Comparison Time: 29:09:07 (hh:mm:ss) Elapsed Time, 897173 HSPs Collected Number of families returned by RECON: 90427 Round Time: 32:41:50 (hh:mm:ss) Elapsed Time : 830 families discovered. RepeatScout/RECON discovery complete: 1564 families found Classification Time: 02:27:22 (hh:mm:ss) Elapsed Time Program Time: 40:39:11 (hh:mm:ss) Elapsed Time