RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MdqLcO/RM_128658.SatJan71551482023 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: 1673135507 Database = /dev/shm/rModeler.MdqLcO/GCF_020740725.1_bCorHaw1.pri.cur - Sequences = 188 - Bases = 1151611379 - N50 = 79826082 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 115221464-123451405 | [ 2 ] 106991523-115221463 | [ ] 98761583-106991523 | [ 1 ] 90531642-98761582 | [ ] 82301702-90531642 | [ ] 74071761-82301701 | [ 3 ] 65841821-74071761 | [ 1 ] 57611880-65841820 | [ ] 49381940-57611880 | [ ] 41151999-49381939 | [ 1 ] 32922059-41151999 | [ 3 ] 24692118-32922058 | [ 1 ] 16462178-24692118 |** [ 8 ] 8232237-16462177 |* [ 6 ] 2297-8232237 |************************************************** [ 162 ] Storage Throughput = excellent ( 1104.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40067817 bp ( 40024969 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:59 (hh:mm:ss) Elapsed Time Round Time: 00:27:28 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2623 repeats masked totaling 858980 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009237 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10008965 bp After Masking: 8845303 bp Masked: 11.63 % -- Input Database Coverage: 10009237 bp out of 1151611379 bp ( 0.87 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:28 (hh:mm:ss) Elapsed Time, 837 HSPs Collected Number of families returned by RECON: 233 Round Time: 00:08:18 (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 : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7487 repeats masked totaling 2537892 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30058500 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30015924 bp After Masking: 26615064 bp Masked: 11.33 % -- Input Database Coverage: 40067737 bp out of 1151611379 bp ( 3.48 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:35:34 (hh:mm:ss) Elapsed Time, 335248 HSPs Collected Number of families returned by RECON: 1414 Round Time: 00:40:58 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26807 repeats masked totaling 9703994 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90083212 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90024940 bp After Masking: 77768659 bp Masked: 13.61 % -- Input Database Coverage: 130150949 bp out of 1151611379 bp ( 11.30 % ) Sampling Time: 00:11:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:51:28 (hh:mm:ss) Elapsed Time, 45367 HSPs Collected Number of families returned by RECON: 8888 Round Time: 04:11:19 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92643 repeats masked totaling 31734383 bp(s). - TE Masking time 00:03:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270575800 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270018827 bp After Masking: 231138695 bp Masked: 14.40 % -- Input Database Coverage: 400726749 bp out of 1151611379 bp ( 34.80 % ) Sampling Time: 00:40:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 29:36:06 (hh:mm:ss) Elapsed Time, 214376 HSPs Collected Number of families returned by RECON: 62945 Round Time: 31:00:25 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 413 families found Classification Time: 00:34:42 (hh:mm:ss) Elapsed Time Program Time: 37:03:10 (hh:mm:ss) Elapsed Time