RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GMq3X0/RM_32556.WedJan101934562024 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: 1704944096 Database = /dev/shm/rModeler.GMq3X0/GCA_014706295.1_ASM1470629v1 - Sequences = 1695 - Bases = 1107771238 - N50 = 74275243 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142061734-152208986 | [ 1 ] 131914482-142061733 | [ ] 121767230-131914481 | [ ] 111619979-121767230 | [ 1 ] 101472727-111619978 | [ 1 ] 91325475-101472726 | [ ] 81178223-91325474 | [ ] 71030972-81178223 | [ 3 ] 60883720-71030971 | [ 1 ] 50736468-60883719 | [ ] 40589216-50736467 | [ ] 30441965-40589216 | [ 3 ] 20294713-30441964 | [ 5 ] 10147461-20294712 | [ 8 ] 210-10147461 |************************************************** [ 1672 ] Storage Throughput = excellent ( 1140.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40283087 bp ( 40022247 non ambiguous ) - Num Contigs Represented = 97 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:22 (hh:mm:ss) Elapsed Time Round Time: 00:25:48 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2799 repeats masked totaling 821444 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10083809 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10012626 bp After Masking: 9068404 bp Masked: 9.43 % -- Input Database Coverage: 10083809 bp out of 1107771238 bp ( 0.91 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 693 HSPs Collected Number of families returned by RECON: 273 Round Time: 00:06:52 (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 : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8024 repeats masked totaling 2277569 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30199274 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 30009617 bp After Masking: 27348738 bp Masked: 8.87 % -- Input Database Coverage: 40283083 bp out of 1107771238 bp ( 3.64 % ) Sampling Time: 00:02:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 308505 Comparison Time: 00:35:34 (hh:mm:ss) Elapsed Time, 8912 HSPs Collected Number of families returned by RECON: 1535 Round Time: 00:39:01 (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 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24093 repeats masked totaling 6865247 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90554444 bp Num Contigs Represented = 171 Non ambiguous bp: Initial: 90029966 bp After Masking: 82178392 bp Masked: 8.72 % -- Input Database Coverage: 130837527 bp out of 1107771238 bp ( 11.81 % ) Sampling Time: 00:07:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2745996 Comparison Time: 04:33:11 (hh:mm:ss) Elapsed Time, 51095 HSPs Collected Number of families returned by RECON: 9785 Round Time: 04:51:26 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84236 repeats masked totaling 24697713 bp(s). - TE Masking time 00:04:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271417186 bp Num Contigs Represented = 487 Non ambiguous bp: Initial: 270031825 bp After Masking: 241973915 bp Masked: 10.39 % -- Input Database Coverage: 402254713 bp out of 1107771238 bp ( 36.31 % ) Sampling Time: 00:23:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24981846 Comparison Time: 39:30:30 (hh:mm:ss) Elapsed Time, 251822 HSPs Collected Number of families returned by RECON: 66497 Round Time: 41:12:24 (hh:mm:ss) Elapsed Time : 282 families discovered. RepeatScout/RECON discovery complete: 510 families found Classification Time: 00:44:00 (hh:mm:ss) Elapsed Time Program Time: 47:59:31 (hh:mm:ss) Elapsed Time