RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BYuk3X/RM_19463.SunMar300201162025 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: 1743325275 Database = /dev/shm/rModeler.BYuk3X/GCA_048569125.1_fDirArg3.hap1 - Sequences = 5504 - Bases = 1517026147 - N50 = 43051431 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52731306-56497672 | [ 2 ] 48964940-52731305 | [ 2 ] 45198574-48964939 | [ 8 ] 41432208-45198573 | [ 4 ] 37665842-41432207 | [ 5 ] 33899476-37665841 | [ ] 30133110-33899475 | [ 1 ] 26366745-30133110 | [ 1 ] 22600379-26366744 | [ 1 ] 18834013-22600378 | [ ] 15067647-18834012 | [ ] 11301281-15067646 | [ ] 7534915-11301280 | [ ] 3768549-7534914 | [ ] 2184-3768549 |************************************************** [ 5480 ] Storage Throughput = excellent ( 1853.50 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031701 bp ( 40009978 non ambiguous ) - Num Contigs Represented = 376 - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:47 (hh:mm:ss) Elapsed Time Round Time: 00:14:21 (hh:mm:ss) Elapsed Time : 878 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10434 repeats masked totaling 2528992 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031003 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 10025003 bp After Masking: 5266887 bp Masked: 47.46 % -- Input Database Coverage: 10031003 bp out of 1517026147 bp ( 0.66 % ) Sampling Time: 00:02:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36585 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 7687 HSPs Collected Number of families returned by RECON: 1381 Round Time: 00:05:31 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31382 repeats masked totaling 7355366 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040767 bp Num Contigs Represented = 284 Non ambiguous bp: Initial: 30025044 bp After Masking: 15555707 bp Masked: 48.19 % -- Input Database Coverage: 40071770 bp out of 1517026147 bp ( 2.64 % ) Sampling Time: 00:07:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 322806 Comparison Time: 00:11:30 (hh:mm:ss) Elapsed Time, 67078 HSPs Collected Number of families returned by RECON: 5348 Round Time: 00:19:38 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102810 repeats masked totaling 22698109 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90076299 bp Num Contigs Represented = 761 Non ambiguous bp: Initial: 90038157 bp After Masking: 45785622 bp Masked: 49.15 % -- Input Database Coverage: 130148069 bp out of 1517026147 bp ( 8.58 % ) Sampling Time: 00:23:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2982903 Comparison Time: 00:58:59 (hh:mm:ss) Elapsed Time, 439175 HSPs Collected Number of families returned by RECON: 15030 Round Time: 01:28:25 (hh:mm:ss) Elapsed Time : 680 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 385191 repeats masked totaling 87312143 bp(s). - TE Masking time 00:05:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270150215 bp Num Contigs Represented = 1737 Non ambiguous bp: Initial: 270032065 bp After Masking: 118344842 bp Masked: 56.17 % -- Input Database Coverage: 400298284 bp out of 1517026147 bp ( 26.39 % ) Sampling Time: 01:12:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26721705 Comparison Time: 05:29:39 (hh:mm:ss) Elapsed Time, 1397521 HSPs Collected Number of families returned by RECON: 39588 Round Time: 07:14:36 (hh:mm:ss) Elapsed Time : 1802 families discovered. RepeatScout/RECON discovery complete: 3465 families found Classification Time: 01:32:01 (hh:mm:ss) Elapsed Time Program Time: 10:54:32 (hh:mm:ss) Elapsed Time