RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RtmMjY/RM_29120.SatJun291913482024 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: 1719713627 Database = /dev/shm/rModeler.RtmMjY/GCA_019721115.1_AMEX_1.1 - Sequences = 195 - Bases = 1378811567 - N50 = 53013356 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 125040366-133971750 | [ 1 ] 116108983-125040366 | [ ] 107177600-116108983 | [ ] 98246216-107177599 | [ ] 89314833-98246216 | [ ] 80383450-89314833 | [ 1 ] 71452066-80383449 | [ ] 62520683-71452066 | [ 1 ] 53589300-62520683 |* [ 6 ] 44657916-53589299 |** [ 10 ] 35726533-44657916 |* [ 4 ] 26795150-35726533 | [ 2 ] 17863766-26795149 | [ ] 8932383-17863766 | [ ] 1000-8932383 |************************************************** [ 170 ] Storage Throughput = excellent ( 1152.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026066 bp ( 40020066 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:00 (hh:mm:ss) Elapsed Time Round Time: 00:32:25 (hh:mm:ss) Elapsed Time : 856 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17749 repeats masked totaling 3029550 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037009 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10036009 bp After Masking: 6161429 bp Masked: 38.61 % -- Input Database Coverage: 10037009 bp out of 1378811567 bp ( 0.73 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:46 (hh:mm:ss) Elapsed Time, 22615 HSPs Collected Number of families returned by RECON: 1759 Round Time: 00:10:39 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55112 repeats masked totaling 9893078 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029057 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30024057 bp After Masking: 17673123 bp Masked: 41.14 % -- Input Database Coverage: 40066066 bp out of 1378811567 bp ( 2.91 % ) Sampling Time: 00:08:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:30:23 (hh:mm:ss) Elapsed Time, 138175 HSPs Collected Number of families returned by RECON: 5404 Round Time: 00:41:52 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181744 repeats masked totaling 31261270 bp(s). - TE Masking time 00:03:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009906 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90001881 bp After Masking: 50232628 bp Masked: 44.19 % -- Input Database Coverage: 130075972 bp out of 1378811567 bp ( 9.43 % ) Sampling Time: 00:26:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:29:29 (hh:mm:ss) Elapsed Time, 1154056 HSPs Collected Number of families returned by RECON: 15798 Round Time: 04:24:58 (hh:mm:ss) Elapsed Time : 525 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 638998 repeats masked totaling 109681598 bp(s). - TE Masking time 00:19:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063891 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 270032448 bp After Masking: 137022270 bp Masked: 49.26 % -- Input Database Coverage: 400139863 bp out of 1378811567 bp ( 29.02 % ) Sampling Time: 01:32:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 25:02:07 (hh:mm:ss) Elapsed Time, 5456950 HSPs Collected Number of families returned by RECON: 47563 Round Time: 28:10:21 (hh:mm:ss) Elapsed Time : 1269 families discovered. RepeatScout/RECON discovery complete: 2836 families found Classification Time: 02:02:04 (hh:mm:ss) Elapsed Time Program Time: 36:02:19 (hh:mm:ss) Elapsed Time