RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zRnYik/RM_31382.SunJul210706392024 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: 1721570798 Database = /dev/shm/rModeler.zRnYik/GCF_016745375.1_EPA_FHM_2.0 - Sequences = 911 - Bases = 1066429022 - N50 = 12863486 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 55804978-59790976 | [ 1 ] 51818980-55804977 | [ ] 47832982-51818979 | [ ] 43846984-47832981 | [ ] 39860986-43846983 | [ 1 ] 35874988-39860985 | [ 1 ] 31888990-35874987 | [ 1 ] 27902992-31888989 | [ ] 23916994-27902991 | [ 3 ] 19930996-23916993 | [ 6 ] 15944998-19930995 | [ 5 ] 11959000-15944997 | [ 4 ] 7973002-11958999 | [ 12 ] 3987004-7973001 |* [ 32 ] 1007-3987004 |************************************************** [ 845 ] Storage Throughput = good ( 996.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 45544182 bp ( 40025124 non ambiguous ) - Num Contigs Represented = 223 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:41 (hh:mm:ss) Elapsed Time Round Time: 00:32:34 (hh:mm:ss) Elapsed Time : 1083 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16244 repeats masked totaling 3296889 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11360461 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 10026745 bp After Masking: 6108409 bp Masked: 39.08 % -- Input Database Coverage: 11360461 bp out of 1066429022 bp ( 1.07 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42778 Comparison Time: 00:07:04 (hh:mm:ss) Elapsed Time, 8608 HSPs Collected Number of families returned by RECON: 1618 Round Time: 00:08:56 (hh:mm:ss) Elapsed Time : 9 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 00:02:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48061 repeats masked totaling 9808033 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 34223721 bp Num Contigs Represented = 186 Non ambiguous bp: Initial: 30037879 bp After Masking: 18652192 bp Masked: 37.90 % -- Input Database Coverage: 45584182 bp out of 1066429022 bp ( 4.27 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 377146 Comparison Time: 00:38:42 (hh:mm:ss) Elapsed Time, 53627 HSPs Collected Number of families returned by RECON: 5419 Round Time: 00:45:58 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155322 repeats masked totaling 30894750 bp(s). - TE Masking time 00:04:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 103071730 bp Num Contigs Represented = 318 Non ambiguous bp: Initial: 90014673 bp After Masking: 54135350 bp Masked: 39.86 % -- Input Database Coverage: 148655912 bp out of 1066429022 bp ( 13.94 % ) Sampling Time: 00:14:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3433510 Comparison Time: 05:03:39 (hh:mm:ss) Elapsed Time, 347898 HSPs Collected Number of families returned by RECON: 16433 Round Time: 05:40:28 (hh:mm:ss) Elapsed Time : 701 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 549928 repeats masked totaling 110055261 bp(s). - TE Masking time 00:22:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 313201208 bp Num Contigs Represented = 513 Non ambiguous bp: Initial: 270002962 bp After Masking: 145677234 bp Masked: 46.05 % -- Input Database Coverage: 461857120 bp out of 1066429022 bp ( 43.31 % ) Sampling Time: 00:48:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31852171 Comparison Time: 44:37:41 (hh:mm:ss) Elapsed Time, 974895 HSPs Collected Number of families returned by RECON: 49314 Round Time: 48:09:04 (hh:mm:ss) Elapsed Time : 1516 families discovered. RepeatScout/RECON discovery complete: 3451 families found Classification Time: 02:36:29 (hh:mm:ss) Elapsed Time Program Time: 57:53:29 (hh:mm:ss) Elapsed Time