RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Yvim1y/RM_347316.SunMar51352532023 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: 1678053172 Database = /dev/shm/rModeler.Yvim1y/GCF_027579735.1_aBomBom1.pri - Sequences = 2467 - Bases = 10019663791 - N50 = 1296922325 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1494886879-1601664463 | [ 1 ] 1388109296-1494886879 | [ 1 ] 1281331712-1388109295 | [ 1 ] 1174554129-1281331712 | [ 1 ] 1067776545-1174554128 | [ 2 ] 960998962-1067776545 | [ ] 854221378-960998961 | [ ] 747443795-854221378 | [ ] 640666211-747443794 | [ 1 ] 533888628-640666211 | [ ] 427111044-533888627 | [ ] 320333461-427111044 | [ 1 ] 213555877-320333460 | [ 2 ] 106778294-213555877 | [ 2 ] 711-106778294 |************************************************** [ 2455 ] Storage Throughput = excellent ( 1227.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40743694 bp ( 40031118 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:21:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:02 (hh:mm:ss) Elapsed Time Round Time: 00:50:03 (hh:mm:ss) Elapsed Time : 676 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15688 repeats masked totaling 5615424 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10157175 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10019002 bp After Masking: 3541961 bp Masked: 64.65 % -- Input Database Coverage: 10157175 bp out of 10019663791 bp ( 0.10 % ) Sampling Time: 00:07:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 10752 HSPs Collected Number of families returned by RECON: 1045 Round Time: 00:13:31 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:14:07 (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... 46260 repeats masked totaling 17233770 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30586439 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30012036 bp After Masking: 10056476 bp Masked: 66.49 % -- Input Database Coverage: 40743614 bp out of 10019663791 bp ( 0.41 % ) Sampling Time: 00:19:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:20:30 (hh:mm:ss) Elapsed Time, 44946 HSPs Collected Number of families returned by RECON: 3497 Round Time: 00:40:36 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:41:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145835 repeats masked totaling 52883084 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92628506 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90014974 bp After Masking: 29428717 bp Masked: 67.31 % -- Input Database Coverage: 133372120 bp out of 10019663791 bp ( 1.33 % ) Sampling Time: 00:59:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2708628 Comparison Time: 01:29:50 (hh:mm:ss) Elapsed Time, 305964 HSPs Collected Number of families returned by RECON: 10729 Round Time: 02:35:03 (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 : 02:22:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 478230 repeats masked totaling 173112379 bp(s). - TE Masking time 00:07:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275231789 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 270000282 bp After Masking: 73752315 bp Masked: 72.68 % -- Input Database Coverage: 408603909 bp out of 10019663791 bp ( 4.08 % ) Sampling Time: 03:12:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23822253 Comparison Time: 08:10:59 (hh:mm:ss) Elapsed Time, 896736 HSPs Collected Number of families returned by RECON: 28643 Round Time: 11:53:40 (hh:mm:ss) Elapsed Time : 962 families discovered. RepeatScout/RECON discovery complete: 2051 families found Classification Time: 01:08:55 (hh:mm:ss) Elapsed Time Program Time: 17:21:48 (hh:mm:ss) Elapsed Time