RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ZWUYxZ/RM_3921248.MonDec21732262024 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: 1733189546 Database = /scratch/tmp/rModeler.ZWUYxZ/GCF_032444005.1_aRanImi1.pri - Sequences = 1672 - Bases = 5956610564 - N50 = 847732560 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1169848561-1253408930 | [ 1 ] 1086288192-1169848560 | [ ] 1002727824-1086288192 | [ ] 919167455-1002727823 | [ ] 835607087-919167455 | [ 2 ] 752046718-835607086 | [ ] 668486349-752046717 | [ 2 ] 584925981-668486349 | [ ] 501365612-584925980 | [ 1 ] 417805244-501365612 | [ ] 334244875-417805243 | [ ] 250684506-334244874 | [ ] 167124138-250684506 | [ 2 ] 83563769-167124137 | [ 2 ] 3401-83563769 |************************************************** [ 1662 ] Storage Throughput = excellent ( 1413.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023092 bp ( 40022692 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:07:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:38 (hh:mm:ss) Elapsed Time Round Time: 00:22:17 (hh:mm:ss) Elapsed Time : 809 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14816 repeats masked totaling 5412468 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027611 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10027511 bp After Masking: 2903391 bp Masked: 71.05 % -- Input Database Coverage: 10027611 bp out of 5956610564 bp ( 0.17 % ) Sampling Time: 00:03:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 30918 HSPs Collected Number of families returned by RECON: 1014 Round Time: 00:06:43 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48652 repeats masked totaling 16995606 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035401 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30035101 bp After Masking: 7924859 bp Masked: 73.61 % -- Input Database Coverage: 40063012 bp out of 5956610564 bp ( 0.67 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:10:30 (hh:mm:ss) Elapsed Time, 46593 HSPs Collected Number of families returned by RECON: 3126 Round Time: 00:21:46 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:18:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149574 repeats masked totaling 51519439 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013262 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90012589 bp After Masking: 21619109 bp Masked: 75.98 % -- Input Database Coverage: 130076274 bp out of 5956610564 bp ( 2.18 % ) Sampling Time: 00:34:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 00:40:23 (hh:mm:ss) Elapsed Time, 227674 HSPs Collected Number of families returned by RECON: 7596 Round Time: 01:18:20 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:53:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:49:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 500863 repeats masked totaling 167349453 bp(s). - TE Masking time 00:04:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009454 bp Num Contigs Represented = 258 Non ambiguous bp: Initial: 270005869 bp After Masking: 51507896 bp Masked: 80.92 % -- Input Database Coverage: 400085728 bp out of 5956610564 bp ( 6.72 % ) Sampling Time: 01:48:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 04:06:43 (hh:mm:ss) Elapsed Time, 697777 HSPs Collected Number of families returned by RECON: 16924 Round Time: 06:07:10 (hh:mm:ss) Elapsed Time : 946 families discovered. RepeatScout/RECON discovery complete: 2323 families found Classification Time: 00:45:54 (hh:mm:ss) Elapsed Time Program Time: 09:02:10 (hh:mm:ss) Elapsed Time