RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NFmM7F/RM_17718.WedNov291706212023 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: 1701306379 Database = /dev/shm/rModeler.NFmM7F/GCA_029493135.1_aHylSar1.hap2 - Sequences = 2802 - Bases = 4080080015 - N50 = 419944051 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 565038853-605398700 | [ 1 ] 524679006-565038852 | [ ] 484319160-524679006 | [ 1 ] 443959313-484319159 | [ 1 ] 403599466-443959312 | [ 1 ] 363239620-403599466 | [ 1 ] 322879773-363239619 | [ ] 282519926-322879772 | [ 1 ] 242160080-282519926 | [ ] 201800233-242160079 | [ 2 ] 161440386-201800232 | [ 1 ] 121080540-161440386 | [ 1 ] 80720693-121080539 | [ 2 ] 40360846-80720692 | [ 1 ] 1000-40360846 |************************************************** [ 2789 ] Storage Throughput = excellent ( 1189.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029584 bp ( 40026984 non ambiguous ) - Num Contigs Represented = 141 - Sequence extraction : 00:07:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:37 (hh:mm:ss) Elapsed Time Round Time: 00:52:01 (hh:mm:ss) Elapsed Time : 942 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19839 repeats masked totaling 5310491 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031469 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10030669 bp After Masking: 3642976 bp Masked: 63.68 % -- Input Database Coverage: 10031469 bp out of 4080080015 bp ( 0.25 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:06:06 (hh:mm:ss) Elapsed Time, 38629 HSPs Collected Number of families returned by RECON: 1262 Round Time: 00:10:53 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60750 repeats masked totaling 16352297 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038035 bp Num Contigs Represented = 109 Non ambiguous bp: Initial: 30036235 bp After Masking: 9734054 bp Masked: 67.59 % -- Input Database Coverage: 40069504 bp out of 4080080015 bp ( 0.98 % ) Sampling Time: 00:14:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:20:45 (hh:mm:ss) Elapsed Time, 53307 HSPs Collected Number of families returned by RECON: 3558 Round Time: 00:37:29 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:16:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191440 repeats masked totaling 50973828 bp(s). - TE Masking time 00:04:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049067 bp Num Contigs Represented = 226 Non ambiguous bp: Initial: 90037867 bp After Masking: 27502698 bp Masked: 69.45 % -- Input Database Coverage: 130118571 bp out of 4080080015 bp ( 3.19 % ) Sampling Time: 00:44:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 01:55:03 (hh:mm:ss) Elapsed Time, 258945 HSPs Collected Number of families returned by RECON: 10312 Round Time: 02:50:03 (hh:mm:ss) Elapsed Time : 451 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:47:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:07:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 638987 repeats masked totaling 165622103 bp(s). - TE Masking time 00:18:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039185 bp Num Contigs Represented = 566 Non ambiguous bp: Initial: 270009585 bp After Masking: 71237471 bp Masked: 73.62 % -- Input Database Coverage: 400157756 bp out of 4080080015 bp ( 9.81 % ) Sampling Time: 02:14:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23293725 Comparison Time: 11:48:24 (hh:mm:ss) Elapsed Time, 842016 HSPs Collected Number of families returned by RECON: 25640 Round Time: 14:57:20 (hh:mm:ss) Elapsed Time : 1168 families discovered. RepeatScout/RECON discovery complete: 2687 families found Classification Time: 01:39:31 (hh:mm:ss) Elapsed Time Program Time: 21:07:17 (hh:mm:ss) Elapsed Time