RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1Pl83V/RM_3413.FriDec82235282023 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: 1702103726 Database = /dev/shm/rModeler.1Pl83V/GCA_951799395.1_fArgSil1.1 - Sequences = 1024 - Bases = 670765936 - N50 = 24665992 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 50490211-54096584 | [ 2 ] 46883839-50490211 | [ ] 43277467-46883839 | [ ] 39671094-43277466 | [ ] 36064722-39671094 | [ 1 ] 32458350-36064722 | [ 2 ] 28851978-32458350 | [ ] 25245605-28851977 | [ 2 ] 21639233-25245605 | [ 7 ] 18032861-21639233 | [ 6 ] 14426489-18032861 | [ 3 ] 10820116-14426488 | [ 1 ] 7213744-10820116 | [ ] 3607372-7213744 | [ ] 1000-3607372 |************************************************** [ 1000 ] Storage Throughput = excellent ( 1163.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40048151 bp ( 40027258 non ambiguous ) - Num Contigs Represented = 109 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:27 (hh:mm:ss) Elapsed Time Round Time: 00:36:12 (hh:mm:ss) Elapsed Time : 533 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8655 repeats masked totaling 1840752 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032751 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10027058 bp After Masking: 6659535 bp Masked: 33.58 % -- Input Database Coverage: 10032751 bp out of 670765936 bp ( 1.50 % ) Sampling Time: 00:02:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:06:17 (hh:mm:ss) Elapsed Time, 64664 HSPs Collected Number of families returned by RECON: 1066 Round Time: 00:10:01 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28061 repeats masked totaling 6003449 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015320 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 30000120 bp After Masking: 20064777 bp Masked: 33.12 % -- Input Database Coverage: 40048071 bp out of 670765936 bp ( 5.97 % ) Sampling Time: 00:08:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:30:13 (hh:mm:ss) Elapsed Time, 42741 HSPs Collected Number of families returned by RECON: 4249 Round Time: 00:39:48 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86024 repeats masked totaling 16792549 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90085294 bp Num Contigs Represented = 225 Non ambiguous bp: Initial: 90035133 bp After Masking: 61165498 bp Masked: 32.06 % -- Input Database Coverage: 130133365 bp out of 670765936 bp ( 19.40 % ) Sampling Time: 00:24:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2724945 Comparison Time: 03:36:21 (hh:mm:ss) Elapsed Time, 262870 HSPs Collected Number of families returned by RECON: 15974 Round Time: 04:14:37 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 308694 repeats masked totaling 61433789 bp(s). - TE Masking time 00:11:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270180935 bp Num Contigs Represented = 496 Non ambiguous bp: Initial: 270038239 bp After Masking: 171904561 bp Masked: 36.34 % -- Input Database Coverage: 400314300 bp out of 670765936 bp ( 59.68 % ) Sampling Time: 01:21:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24440536 Comparison Time: 27:29:02 (hh:mm:ss) Elapsed Time, 839190 HSPs Collected Number of families returned by RECON: 60114 Round Time: 30:38:15 (hh:mm:ss) Elapsed Time : 979 families discovered. RepeatScout/RECON discovery complete: 2010 families found Classification Time: 01:45:30 (hh:mm:ss) Elapsed Time Program Time: 38:04:23 (hh:mm:ss) Elapsed Time