RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ZcksrY/RM_8525.SatDec71555572024 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: 1733615756 Database = /scratch/tmp/rModeler.ZcksrY/GCA_038021265.1_fCypVen1.hap1 - Sequences = 673 - Bases = 918162819 - N50 = 36646589 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 53672334-57505201 | [ 2 ] 49839467-53672333 | [ ] 46006601-49839467 | [ 1 ] 42173734-46006600 | [ 1 ] 38340868-42173734 | [ 2 ] 34508001-38340867 | [ 7 ] 30675135-34508001 | [ 4 ] 26842268-30675134 | [ 5 ] 23009402-26842268 | [ 3 ] 19176535-23009401 | [ ] 15343669-19176535 | [ ] 11510802-15343668 | [ ] 7677936-11510802 | [ ] 3845069-7677935 | [ ] 12203-3845069 |************************************************** [ 648 ] Storage Throughput = fair ( 603.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044595 bp ( 40037795 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:06 (hh:mm:ss) Elapsed Time Round Time: 00:36:24 (hh:mm:ss) Elapsed Time : 799 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13516 repeats masked totaling 2753556 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038798 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10037298 bp After Masking: 5968533 bp Masked: 40.54 % -- Input Database Coverage: 10038798 bp out of 918162819 bp ( 1.09 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 16217 HSPs Collected Number of families returned by RECON: 1435 Round Time: 00:08:03 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40534 repeats masked totaling 8171427 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005786 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30000486 bp After Masking: 17357930 bp Masked: 42.14 % -- Input Database Coverage: 40044584 bp out of 918162819 bp ( 4.36 % ) Sampling Time: 00:06:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:26:59 (hh:mm:ss) Elapsed Time, 48691 HSPs Collected Number of families returned by RECON: 4955 Round Time: 00:37:22 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129170 repeats masked totaling 24740111 bp(s). - TE Masking time 00:02:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012954 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90000817 bp After Masking: 50773151 bp Masked: 43.59 % -- Input Database Coverage: 130057538 bp out of 918162819 bp ( 14.16 % ) Sampling Time: 00:18:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 03:00:28 (hh:mm:ss) Elapsed Time, 364197 HSPs Collected Number of families returned by RECON: 14593 Round Time: 03:46:28 (hh:mm:ss) Elapsed Time : 603 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 468312 repeats masked totaling 91097220 bp(s). - TE Masking time 00:16:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270067948 bp Num Contigs Represented = 266 Non ambiguous bp: Initial: 270029918 bp After Masking: 140500320 bp Masked: 47.97 % -- Input Database Coverage: 400125486 bp out of 918162819 bp ( 43.58 % ) Sampling Time: 01:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23423590 Comparison Time: 22:27:16 (hh:mm:ss) Elapsed Time, 1056353 HSPs Collected Number of families returned by RECON: 45457 Round Time: 26:03:25 (hh:mm:ss) Elapsed Time : 1358 families discovered. RepeatScout/RECON discovery complete: 2888 families found Classification Time: 02:08:56 (hh:mm:ss) Elapsed Time Program Time: 33:20:38 (hh:mm:ss) Elapsed Time