RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.VzWBSZ/RM_3762957.MonApr210709052025 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: 1745244545 Database = /data/tmp/rModeler.VzWBSZ/GCA_026230055.1_mCorTow1.0.hap1 - Sequences = 391 - Bases = 2104912948 - N50 = 188654229 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217898478-233461832 | [ 3 ] 202335125-217898478 | [ ] 186771772-202335125 | [ 1 ] 171208418-186771771 | [ 2 ] 155645065-171208418 | [ 2 ] 140081712-155645065 | [ 1 ] 124518359-140081712 | [ 1 ] 108955005-124518358 | [ ] 93391652-108955005 | [ ] 77828299-93391652 | [ ] 62264946-77828299 | [ ] 46701592-62264945 | [ 2 ] 31138239-46701592 | [ 1 ] 15574886-31138239 | [ 3 ] 11533-15574886 |************************************************** [ 375 ] Storage Throughput = excellent ( 1197.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040367 bp ( 40039667 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:03:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:26 (hh:mm:ss) Elapsed Time Round Time: 00:26:57 (hh:mm:ss) Elapsed Time : 346 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15002 repeats masked totaling 2805198 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026747 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10026447 bp After Masking: 7030921 bp Masked: 29.88 % -- Input Database Coverage: 10026747 bp out of 2104912948 bp ( 0.48 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 4900 HSPs Collected Number of families returned by RECON: 737 Round Time: 00:07:53 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46391 repeats masked totaling 9098022 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013619 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30013219 bp After Masking: 20303714 bp Masked: 32.35 % -- Input Database Coverage: 40040366 bp out of 2104912948 bp ( 1.90 % ) Sampling Time: 00:05:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:24:44 (hh:mm:ss) Elapsed Time, 24685 HSPs Collected Number of families returned by RECON: 2732 Round Time: 00:34:22 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151377 repeats masked totaling 29565121 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023753 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90023153 bp After Masking: 58705697 bp Masked: 34.79 % -- Input Database Coverage: 130064119 bp out of 2104912948 bp ( 6.18 % ) Sampling Time: 00:17:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:57:10 (hh:mm:ss) Elapsed Time, 115744 HSPs Collected Number of families returned by RECON: 8739 Round Time: 03:33:11 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:26:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 501155 repeats masked totaling 98030522 bp(s). - TE Masking time 00:06:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270006548 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 270003548 bp After Masking: 167401906 bp Masked: 38.00 % -- Input Database Coverage: 400070667 bp out of 2104912948 bp ( 19.01 % ) Sampling Time: 00:48:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 20:17:21 (hh:mm:ss) Elapsed Time, 320013 HSPs Collected Number of families returned by RECON: 33939 Round Time: 22:19:27 (hh:mm:ss) Elapsed Time : 455 families discovered. RepeatScout/RECON discovery complete: 1098 families found Classification Time: 00:43:20 (hh:mm:ss) Elapsed Time Program Time: 27:45:10 (hh:mm:ss) Elapsed Time