RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8UC8sm/RM_31678.TueSep171300222024 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: 1726603220 Database = /dev/shm/rModeler.8UC8sm/GCA_902651635.1_mastiga_genome_v5.1 - Sequences = 1925 - Bases = 57266623 - N50 = 442786 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1865037-1998111 | [ 1 ] 1731963-1865036 | [ 1 ] 1598889-1731962 | [ ] 1465815-1598888 | [ ] 1332741-1465814 | [ ] 1199667-1332740 | [ 3 ] 1066593-1199666 | [ 3 ] 933520-1066593 | [ 1 ] 800446-933519 | [ 5 ] 667372-800445 | [ 4 ] 534298-667371 | [ 8 ] 401224-534297 | [ 14 ] 268150-401223 | [ 19 ] 135076-268149 |* [ 43 ] 2003-135076 |************************************************** [ 1823 ] Storage Throughput = excellent ( 1116.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42504609 bp ( 40005346 non ambiguous ) - Num Contigs Represented = 1470 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:31 (hh:mm:ss) Elapsed Time Round Time: 00:31:53 (hh:mm:ss) Elapsed Time : 447 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5423 repeats masked totaling 1924502 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10621545 bp Num Contigs Represented = 489 Non ambiguous bp: Initial: 10026162 bp After Masking: 8055200 bp Masked: 19.66 % -- Input Database Coverage: 10621545 bp out of 57266623 bp ( 18.55 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 189420 Comparison Time: 00:25:06 (hh:mm:ss) Elapsed Time, 4580 HSPs Collected Number of families returned by RECON: 1348 Round Time: 00:26:37 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14645 repeats masked totaling 5394526 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31937660 bp Num Contigs Represented = 1078 Non ambiguous bp: Initial: 30022475 bp After Masking: 24453023 bp Masked: 18.55 % -- Input Database Coverage: 42559205 bp out of 57266623 bp ( 74.32 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1408681 Comparison Time: 03:10:23 (hh:mm:ss) Elapsed Time, 36107 HSPs Collected Number of families returned by RECON: 6200 Round Time: 03:15:35 (hh:mm:ss) Elapsed Time : 35 families discovered. - Increasing sample size to include end piece now = 106645078 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 106645078 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6960 repeats masked totaling 2678693 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 14707148 bp Num Contigs Represented = 568 Non ambiguous bp: Initial: 13900931 bp After Masking: 11146798 bp Masked: 19.81 % -- Input Database Coverage: 57266353 bp out of 57266623 bp ( 100.00 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 309291 Comparison Time: 00:39:38 (hh:mm:ss) Elapsed Time, 7523 HSPs Collected Number of families returned by RECON: 2279 Round Time: 00:41:41 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatScout/RECON discovery complete: 488 families found Classification Time: 00:19:03 (hh:mm:ss) Elapsed Time Program Time: 05:14:49 (hh:mm:ss) Elapsed Time