RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/002/335/545/GCA_002335545.1_Aspe_assembly01/trackData/repeatModeler/RM_286909.SatMay40131272024 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: 1714811479 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/002/335/545/GCA_002335545.1_Aspe_assembly01/trackData/repeatModeler/GCA_002335545.1_Aspe_assembly01 - Sequences = 336123 - Bases = 3494278632 - N50 = 49032 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 6138522-6576926 | [ 1 ] 5700119-6138522 | [ ] 5261716-5700119 | [ ] 4823313-5261716 | [ ] 4384910-4823313 | [ ] 3946507-4384910 | [ 1 ] 3508104-3946507 | [ 2 ] 3069701-3508104 | [ ] 2631298-3069701 | [ 4 ] 2192895-2631298 | [ 5 ] 1754492-2192895 | [ 6 ] 1316089-1754492 | [ 11 ] 877686-1316089 | [ 19 ] 439283-877686 | [ 113 ] 880-439283 |************************************************** [ 335961 ] Storage Throughput = good ( 706.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 68270858 bp ( 40001391 non ambiguous ) - Num Contigs Represented = 7395 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:06 (hh:mm:ss) Elapsed Time Round Time: 00:09:40 (hh:mm:ss) Elapsed Time : 217 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10944 repeats masked totaling 2059307 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 17404133 bp Num Contigs Represented = 1838 Non ambiguous bp: Initial: 10017388 bp After Masking: 7778999 bp Masked: 22.35 % -- Input Database Coverage: 17404133 bp out of 3494278632 bp ( 0.50 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1695561 Comparison Time: 00:32:06 (hh:mm:ss) Elapsed Time, 13141 HSPs Collected Number of families returned by RECON: 972 Round Time: 00:36:33 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37943 repeats masked totaling 7464543 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 50918685 bp Num Contigs Represented = 5577 Non ambiguous bp: Initial: 30003257 bp After Masking: 22009362 bp Masked: 26.64 % -- Input Database Coverage: 68322818 bp out of 3494278632 bp ( 1.96 % ) Sampling Time: 00:01:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 15682800 Comparison Time: 01:44:23 (hh:mm:ss) Elapsed Time, 26887 HSPs Collected Number of families returned by RECON: 2534 Round Time: 01:52:03 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125021 repeats masked totaling 24143963 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 156644841 bp Num Contigs Represented = 16805 Non ambiguous bp: Initial: 90003243 bp After Masking: 64322779 bp Masked: 28.53 % -- Input Database Coverage: 224967659 bp out of 3494278632 bp ( 6.44 % ) Sampling Time: 00:04:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 144746605 Comparison Time: 07:10:22 (hh:mm:ss) Elapsed Time, 93901 HSPs Collected Number of families returned by RECON: 9054 Round Time: 07:35:09 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 427800 repeats masked totaling 79673439 bp(s). - TE Masking time 00:02:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 467068161 bp Num Contigs Represented = 48882 Non ambiguous bp: Initial: 270002380 bp After Masking: 185872007 bp Masked: 31.16 % -- Input Database Coverage: 692035820 bp out of 3494278632 bp ( 19.80 % ) Sampling Time: 00:11:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1266126681 Comparison Time: 39:36:32 (hh:mm:ss) Elapsed Time, 235510 HSPs Collected Number of families returned by RECON: 39398 Round Time: 41:34:00 (hh:mm:ss) Elapsed Time : 412 families discovered. RepeatScout/RECON discovery complete: 889 families found Classification Time: 00:19:26 (hh:mm:ss) Elapsed Time Program Time: 52:06:51 (hh:mm:ss) Elapsed Time