RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.q91I8M/RM_1095004.WedNov130637182024 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: 1731508638 Database = /scratch/tmp/rModeler.q91I8M/GCA_037893015.1_bilby.v1.9.chrom.fasta - Sequences = 609 - Bases = 3655732635 - N50 = 934355481 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 872066279-934355481 | [ 1 ] 809777077-872066278 | [ ] 747487876-809777077 | [ ] 685198674-747487875 | [ 1 ] 622909473-685198674 | [ ] 560620271-622909472 | [ ] 498331069-560620270 | [ ] 436041868-498331069 | [ ] 373752666-436041867 | [ ] 311463465-373752666 | [ 1 ] 249174263-311463464 | [ 3 ] 186885061-249174262 | [ 3 ] 124595860-186885061 | [ ] 62306658-124595859 | [ ] 17457-62306658 |************************************************** [ 600 ] Storage Throughput = excellent ( 1443.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40101612 bp ( 40007460 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:05:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:45 (hh:mm:ss) Elapsed Time Round Time: 00:16:35 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17971 repeats masked totaling 3340112 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10045977 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10010904 bp After Masking: 6033605 bp Masked: 39.73 % -- Input Database Coverage: 10045977 bp out of 3655732635 bp ( 0.27 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:34 (hh:mm:ss) Elapsed Time, 50026 HSPs Collected Number of families returned by RECON: 1174 Round Time: 00:06:02 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57720 repeats masked totaling 11540056 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30095556 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30036477 bp After Masking: 17014766 bp Masked: 43.35 % -- Input Database Coverage: 40141533 bp out of 3655732635 bp ( 1.10 % ) Sampling Time: 00:05:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:13:05 (hh:mm:ss) Elapsed Time, 66198 HSPs Collected Number of families returned by RECON: 3208 Round Time: 00:19:40 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191106 repeats masked totaling 38344663 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90430853 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 90024486 bp After Masking: 47024109 bp Masked: 47.77 % -- Input Database Coverage: 130572386 bp out of 3655732635 bp ( 3.57 % ) Sampling Time: 00:17:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:12:59 (hh:mm:ss) Elapsed Time, 1039375 HSPs Collected Number of families returned by RECON: 9791 Round Time: 01:32:38 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:35:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 637194 repeats masked totaling 123446164 bp(s). - TE Masking time 00:02:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271102339 bp Num Contigs Represented = 229 Non ambiguous bp: Initial: 270023981 bp After Masking: 134038011 bp Masked: 50.36 % -- Input Database Coverage: 401674725 bp out of 3655732635 bp ( 10.99 % ) Sampling Time: 00:54:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 08:01:34 (hh:mm:ss) Elapsed Time, 4162763 HSPs Collected Number of families returned by RECON: 36319 Round Time: 09:10:31 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatScout/RECON discovery complete: 956 families found Classification Time: 00:16:22 (hh:mm:ss) Elapsed Time Program Time: 11:41:48 (hh:mm:ss) Elapsed Time