RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.U3z1Ku/RM_18782.MonMay81022162023 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: 1683566534 Database = /dev/shm/rModeler.U3z1Ku/GCA_027477595.1_bHaeMex1.pri - Sequences = 183 - Bases = 1148216196 - N50 = 89315722 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 148685719-159305015 | [ 1 ] 138066424-148685719 | [ ] 127447129-138066424 | [ ] 116827834-127447129 | [ 2 ] 106208539-116827834 | [ ] 95589244-106208539 | [ ] 84969949-95589244 | [ 1 ] 74350654-84969949 | [ 2 ] 63731359-74350654 | [ 1 ] 53112064-63731359 | [ ] 42492769-53112064 | [ 1 ] 31873474-42492769 | [ ] 21254179-31873474 |* [ 6 ] 10634884-21254179 |** [ 9 ] 15589-10634884 |************************************************** [ 160 ] Storage Throughput = excellent ( 1211.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40394999 bp ( 40031948 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:22 (hh:mm:ss) Elapsed Time Round Time: 00:37:59 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2725 repeats masked totaling 862392 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10048247 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10007547 bp After Masking: 8684040 bp Masked: 13.23 % -- Input Database Coverage: 10048247 bp out of 1148216196 bp ( 0.88 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:11:07 (hh:mm:ss) Elapsed Time, 2058 HSPs Collected Number of families returned by RECON: 317 Round Time: 00:12:44 (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 : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7571 repeats masked totaling 2473814 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30346672 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30024321 bp After Masking: 26087717 bp Masked: 13.11 % -- Input Database Coverage: 40394919 bp out of 1148216196 bp ( 3.52 % ) Sampling Time: 00:03:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:52:16 (hh:mm:ss) Elapsed Time, 12631 HSPs Collected Number of families returned by RECON: 1727 Round Time: 00:56:57 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23919 repeats masked totaling 7435174 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91003550 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90037754 bp After Masking: 77385436 bp Masked: 14.05 % -- Input Database Coverage: 131398469 bp out of 1148216196 bp ( 11.44 % ) Sampling Time: 00:12:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 05:15:54 (hh:mm:ss) Elapsed Time, 80342 HSPs Collected Number of families returned by RECON: 11192 Round Time: 05:50:11 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84179 repeats masked totaling 27794302 bp(s). - TE Masking time 00:06:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272448156 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 270009725 bp After Masking: 228829717 bp Masked: 15.25 % -- Input Database Coverage: 403846625 bp out of 1148216196 bp ( 35.17 % ) Sampling Time: 00:39:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23293725 Comparison Time: 38:06:34 (hh:mm:ss) Elapsed Time, 244896 HSPs Collected Number of families returned by RECON: 74651 Round Time: 40:16:59 (hh:mm:ss) Elapsed Time : 280 families discovered. RepeatScout/RECON discovery complete: 518 families found Classification Time: 00:51:39 (hh:mm:ss) Elapsed Time Program Time: 48:46:29 (hh:mm:ss) Elapsed Time