RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.muveVd/RM_1431004.SatNov160524002024 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: 1731763439 Database = /scratch/tmp/rModeler.muveVd/GCA_037962945.1_bSarPap1.hap1 - Sequences = 124 - Bases = 1543950730 - N50 = 96980784 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 219162758-234816392 | [ 1 ] 203509125-219162758 | [ ] 187855492-203509125 | [ 1 ] 172201858-187855491 | [ ] 156548225-172201858 | [ ] 140894592-156548225 | [ 1 ] 125240958-140894591 | [ ] 109587325-125240958 | [ ] 93933692-109587325 | [ 2 ] 78280058-93933691 | [ 1 ] 62626425-78280058 | [ ] 46972792-62626425 |* [ 3 ] 31319158-46972791 |* [ 4 ] 15665525-31319158 |*** [ 7 ] 11892-15665525 |************************************************** [ 104 ] Storage Throughput = excellent ( 1426.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018421 bp ( 40017421 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:07 (hh:mm:ss) Elapsed Time Round Time: 00:16:27 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1664 repeats masked totaling 566309 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002149 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10002149 bp After Masking: 7894478 bp Masked: 21.07 % -- Input Database Coverage: 10002149 bp out of 1543950730 bp ( 0.65 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 927 HSPs Collected Number of families returned by RECON: 215 Round Time: 00:04:08 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4442 repeats masked totaling 1834790 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016192 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30015192 bp After Masking: 22607536 bp Masked: 24.68 % -- Input Database Coverage: 40018341 bp out of 1543950730 bp ( 2.59 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:14:18 (hh:mm:ss) Elapsed Time, 4673 HSPs Collected Number of families returned by RECON: 1158 Round Time: 00:17:14 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17486 repeats masked totaling 6512386 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003069 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90001069 bp After Masking: 69767372 bp Masked: 22.48 % -- Input Database Coverage: 130021410 bp out of 1543950730 bp ( 8.42 % ) Sampling Time: 00:06:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:24:23 (hh:mm:ss) Elapsed Time, 37291 HSPs Collected Number of families returned by RECON: 6722 Round Time: 01:34:33 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57824 repeats masked totaling 22465451 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030198 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 270025398 bp After Masking: 207328659 bp Masked: 23.22 % -- Input Database Coverage: 400051608 bp out of 1543950730 bp ( 25.91 % ) Sampling Time: 00:20:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 10:00:48 (hh:mm:ss) Elapsed Time, 187578 HSPs Collected Number of families returned by RECON: 41877 Round Time: 10:33:29 (hh:mm:ss) Elapsed Time : 258 families discovered. RepeatScout/RECON discovery complete: 390 families found Classification Time: 00:23:53 (hh:mm:ss) Elapsed Time Program Time: 13:09:44 (hh:mm:ss) Elapsed Time