RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qv3rF9/RM_571.SunJul71926422024 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: 1720405599 Database = /dev/shm/rModeler.qv3rF9/GCF_001515625.1_SAMN03320098_v1.1 - Sequences = 164172 - Bases = 1655785943 - N50 = 945973 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 4700018-5035720 | [ 2 ] 4364317-4700018 | [ 1 ] 4028616-4364317 | [ 4 ] 3692914-4028615 | [ 5 ] 3357213-3692914 | [ 12 ] 3021512-3357213 | [ 16 ] 2685810-3021511 | [ 16 ] 2350109-2685810 | [ 27 ] 2014408-2350109 | [ 34 ] 1678706-2014407 | [ 63 ] 1343005-1678706 | [ 99 ] 1007304-1343005 | [ 161 ] 671602-1007303 | [ 266 ] 335901-671602 | [ 577 ] 200-335901 |************************************************** [ 162889 ] Storage Throughput = excellent ( 1159.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43557062 bp ( 40034158 non ambiguous ) - Num Contigs Represented = 4961 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:55 (hh:mm:ss) Elapsed Time Round Time: 00:27:42 (hh:mm:ss) Elapsed Time : 1295 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19507 repeats masked totaling 2572408 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10955494 bp Num Contigs Represented = 1252 Non ambiguous bp: Initial: 10015243 bp After Masking: 7283367 bp Masked: 27.28 % -- Input Database Coverage: 10955494 bp out of 1655785943 bp ( 0.66 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 809628 Comparison Time: 00:10:45 (hh:mm:ss) Elapsed Time, 17176 HSPs Collected Number of families returned by RECON: 2086 Round Time: 00:12:41 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59891 repeats masked totaling 7939370 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32601504 bp Num Contigs Represented = 3791 Non ambiguous bp: Initial: 30018851 bp After Masking: 21630100 bp Masked: 27.94 % -- Input Database Coverage: 43556998 bp out of 1655785943 bp ( 2.63 % ) Sampling Time: 00:02:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7866561 Comparison Time: 00:49:30 (hh:mm:ss) Elapsed Time, 67645 HSPs Collected Number of families returned by RECON: 6773 Round Time: 00:55:38 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 193582 repeats masked totaling 25967999 bp(s). - TE Masking time 00:03:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 98088385 bp Num Contigs Represented = 10780 Non ambiguous bp: Initial: 90029371 bp After Masking: 62673655 bp Masked: 30.39 % -- Input Database Coverage: 141645383 bp out of 1655785943 bp ( 8.55 % ) Sampling Time: 00:08:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 70395045 Comparison Time: 05:06:27 (hh:mm:ss) Elapsed Time, 390619 HSPs Collected Number of families returned by RECON: 20491 Round Time: 05:38:28 (hh:mm:ss) Elapsed Time : 774 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 683146 repeats masked totaling 94541229 bp(s). - TE Masking time 00:21:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 293607556 bp Num Contigs Represented = 30496 Non ambiguous bp: Initial: 270000355 bp After Masking: 171470008 bp Masked: 36.49 % -- Input Database Coverage: 435252939 bp out of 1655785943 bp ( 26.29 % ) Sampling Time: 00:35:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 628156290 Comparison Time: 36:31:51 (hh:mm:ss) Elapsed Time, 938005 HSPs Collected Number of families returned by RECON: 70662 Round Time: 39:48:16 (hh:mm:ss) Elapsed Time : 1531 families discovered. RepeatScout/RECON discovery complete: 3782 families found Classification Time: 02:03:29 (hh:mm:ss) Elapsed Time Program Time: 49:06:14 (hh:mm:ss) Elapsed Time