RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0fXwKN/RM_9060.SunJul142048132024 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: 1721015293 Database = /dev/shm/rModeler.0fXwKN/GCF_006386435.1_YSFRI_EMoa_1.0 - Sequences = 4563 - Bases = 1030477684 - N50 = 45153007 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 49238791-52755815 | [ 2 ] 45721767-49238790 | [ 4 ] 42204743-45721766 | [ 9 ] 38687719-42204742 | [ 4 ] 35170695-38687718 | [ 2 ] 31653671-35170694 | [ 2 ] 28136647-31653670 | [ ] 24619623-28136646 | [ ] 21102599-24619622 | [ ] 17585575-21102598 | [ 1 ] 14068551-17585574 | [ ] 10551527-14068550 | [ ] 7034503-10551526 | [ ] 3517479-7034502 | [ ] 456-3517479 |************************************************** [ 4539 ] Storage Throughput = excellent ( 1005.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41205201 bp ( 40033892 non ambiguous ) - Num Contigs Represented = 200 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:58 (hh:mm:ss) Elapsed Time Round Time: 00:25:15 (hh:mm:ss) Elapsed Time : 1098 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (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... 18855 repeats masked totaling 2653468 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10315371 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 10035221 bp After Masking: 7239289 bp Masked: 27.86 % -- Input Database Coverage: 10315371 bp out of 1030477684 bp ( 1.00 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 45451 Comparison Time: 00:06:52 (hh:mm:ss) Elapsed Time, 10280 HSPs Collected Number of families returned by RECON: 2146 Round Time: 00:08:05 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55198 repeats masked totaling 7751257 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30929752 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 30038592 bp After Masking: 21726767 bp Masked: 27.67 % -- Input Database Coverage: 41245123 bp out of 1030477684 bp ( 4.00 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 394716 Comparison Time: 00:34:27 (hh:mm:ss) Elapsed Time, 80513 HSPs Collected Number of families returned by RECON: 6783 Round Time: 00:40:33 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189774 repeats masked totaling 27687034 bp(s). - TE Masking time 00:02:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92779578 bp Num Contigs Represented = 450 Non ambiguous bp: Initial: 90008107 bp After Masking: 60785945 bp Masked: 32.47 % -- Input Database Coverage: 134024701 bp out of 1030477684 bp ( 13.01 % ) Sampling Time: 00:08:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3670695 Comparison Time: 03:38:12 (hh:mm:ss) Elapsed Time, 401776 HSPs Collected Number of families returned by RECON: 19044 Round Time: 04:09:09 (hh:mm:ss) Elapsed Time : 812 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 671041 repeats masked totaling 102283419 bp(s). - TE Masking time 00:16:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 278464609 bp Num Contigs Represented = 1243 Non ambiguous bp: Initial: 270018062 bp After Masking: 163287875 bp Masked: 39.53 % -- Input Database Coverage: 412489310 bp out of 1030477684 bp ( 40.03 % ) Sampling Time: 00:33:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32663403 Comparison Time: 30:02:57 (hh:mm:ss) Elapsed Time, 894969 HSPs Collected Number of families returned by RECON: 58771 Round Time: 33:14:37 (hh:mm:ss) Elapsed Time : 1636 families discovered. RepeatScout/RECON discovery complete: 3811 families found Classification Time: 02:10:54 (hh:mm:ss) Elapsed Time Program Time: 40:48:33 (hh:mm:ss) Elapsed Time