RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2EbsT6/RM_3903837.MonMar251950572024 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: 1711421457 Database = /dev/shm/rModeler.2EbsT6/GCA_963422515.1_fBleOce1.1 - Sequences = 525 - Bases = 728745255 - N50 = 29778139 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35092247-37598765 | [ 1 ] 32585729-35092246 | [ 3 ] 30079212-32585729 | [ 5 ] 27572694-30079211 | [ 6 ] 25066176-27572693 | [ 4 ] 22559659-25066176 | [ 1 ] 20053141-22559658 | [ 2 ] 17546623-20053140 | [ 1 ] 15040106-17546623 | [ 1 ] 12533588-15040105 | [ ] 10027070-12533587 | [ ] 7520553-10027070 | [ ] 5014035-7520552 | [ ] 2507517-5014034 | [ 1 ] 1000-2507517 |************************************************** [ 500 ] Storage Throughput = excellent ( 1396.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022139 bp ( 40001999 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:51 (hh:mm:ss) Elapsed Time Round Time: 00:21:54 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5987 repeats masked totaling 859009 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024502 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10019446 bp After Masking: 8111678 bp Masked: 19.04 % -- Input Database Coverage: 10024502 bp out of 728745255 bp ( 1.38 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:47 (hh:mm:ss) Elapsed Time, 9539 HSPs Collected Number of families returned by RECON: 1126 Round Time: 00:09:32 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19267 repeats masked totaling 3256854 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037557 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30022473 bp After Masking: 23122324 bp Masked: 22.98 % -- Input Database Coverage: 40062059 bp out of 728745255 bp ( 5.50 % ) Sampling Time: 00:09:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:32:27 (hh:mm:ss) Elapsed Time, 37397 HSPs Collected Number of families returned by RECON: 4068 Round Time: 00:43:30 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63428 repeats masked totaling 11065841 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90067045 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 90030651 bp After Masking: 68028619 bp Masked: 24.44 % -- Input Database Coverage: 130129104 bp out of 728745255 bp ( 17.86 % ) Sampling Time: 00:29:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 03:39:11 (hh:mm:ss) Elapsed Time, 187196 HSPs Collected Number of families returned by RECON: 15625 Round Time: 04:16:11 (hh:mm:ss) Elapsed Time : 335 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:18:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 244126 repeats masked totaling 42503784 bp(s). - TE Masking time 00:07:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270121012 bp Num Contigs Represented = 292 Non ambiguous bp: Initial: 270000171 bp After Masking: 194488499 bp Masked: 27.97 % -- Input Database Coverage: 400250116 bp out of 728745255 bp ( 54.92 % ) Sampling Time: 01:30:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23512653 Comparison Time: 26:20:13 (hh:mm:ss) Elapsed Time, 635079 HSPs Collected Number of families returned by RECON: 62589 Round Time: 29:08:19 (hh:mm:ss) Elapsed Time : 907 families discovered. RepeatScout/RECON discovery complete: 1763 families found Classification Time: 01:20:48 (hh:mm:ss) Elapsed Time Program Time: 36:00:14 (hh:mm:ss) Elapsed Time