RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hxSTyn/RM_13972.FriJan121636382024 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: 1705106195 Database = /dev/shm/rModeler.hxSTyn/GCA_031877795.1_bStrAlu1.hap1 - Sequences = 203 - Bases = 1414802443 - N50 = 132253835 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 161540517-173077747 | [ 1 ] 150003287-161540516 | [ ] 138466057-150003286 | [ ] 126928827-138466056 | [ 3 ] 115391597-126928826 | [ ] 103854367-115391596 | [ ] 92317137-103854366 | [ 1 ] 80779907-92317136 | [ 1 ] 69242677-80779906 | [ ] 57705447-69242676 | [ ] 46168217-57705446 | [ 1 ] 34630987-46168216 | [ 3 ] 23093757-34630986 |* [ 6 ] 11556527-23093756 |** [ 9 ] 19298-11556527 |************************************************** [ 178 ] Storage Throughput = excellent ( 1077.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40150988 bp ( 40026060 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:49 (hh:mm:ss) Elapsed Time Round Time: 00:32:13 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1396 repeats masked totaling 631603 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082692 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10037964 bp After Masking: 8235883 bp Masked: 17.95 % -- Input Database Coverage: 10082692 bp out of 1414802443 bp ( 0.71 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:40:01 (hh:mm:ss) Elapsed Time, 15193 HSPs Collected Number of families returned by RECON: 240 Round Time: 00:42:02 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4455 repeats masked totaling 1997419 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30108293 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30028093 bp After Masking: 25068806 bp Masked: 16.52 % -- Input Database Coverage: 40190985 bp out of 1414802443 bp ( 2.84 % ) Sampling Time: 00:08:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 01:27:05 (hh:mm:ss) Elapsed Time, 7573 HSPs Collected Number of families returned by RECON: 1267 Round Time: 01:35:49 (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 : 00:04:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14666 repeats masked totaling 6169010 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90289980 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 90033535 bp After Masking: 74870633 bp Masked: 16.84 % -- Input Database Coverage: 130480965 bp out of 1414802443 bp ( 9.22 % ) Sampling Time: 00:22:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 06:26:00 (hh:mm:ss) Elapsed Time, 192161 HSPs Collected Number of families returned by RECON: 7782 Round Time: 06:52:40 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59272 repeats masked totaling 22450127 bp(s). - TE Masking time 00:02:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270995178 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 270000573 bp After Masking: 221507173 bp Masked: 17.96 % -- Input Database Coverage: 401476143 bp out of 1414802443 bp ( 28.38 % ) Sampling Time: 01:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 43:43:34 (hh:mm:ss) Elapsed Time, 1434679 HSPs Collected Number of families returned by RECON: 48008 Round Time: 45:27:11 (hh:mm:ss) Elapsed Time : 261 families discovered. RepeatScout/RECON discovery complete: 446 families found Classification Time: 00:43:38 (hh:mm:ss) Elapsed Time Program Time: 55:53:33 (hh:mm:ss) Elapsed Time