RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.jreQit/RM_2442895.TueDec31429072024 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: 1733264944 Database = /scratch/tmp/rModeler.jreQit/GCA_964276395.1_fGasAcu3.hap1.1 - Sequences = 130 - Bases = 511155287 - N50 = 22127121 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33748106-36158614 | [ 1 ] 31337598-33748105 | [ 2 ] 28927091-31337598 | [ ] 26516583-28927090 | [ ] 24106076-26516583 | [ 2 ] 21695568-24106075 |** [ 6 ] 19285060-21695567 |** [ 5 ] 16874553-19285060 |** [ 6 ] 14464045-16874552 | [ ] 12053538-14464045 | [ ] 9643030-12053537 | [ ] 7232522-9643029 | [ ] 4822015-7232522 | [ ] 2411507-4822014 | [ ] 1000-2411507 |************************************************** [ 108 ] Storage Throughput = excellent ( 1497.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011838 bp ( 40006838 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:11 (hh:mm:ss) Elapsed Time Round Time: 00:09:51 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3522 repeats masked totaling 825296 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022539 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10021539 bp After Masking: 8673730 bp Masked: 13.45 % -- Input Database Coverage: 10022539 bp out of 511155287 bp ( 1.96 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:47 (hh:mm:ss) Elapsed Time, 15617 HSPs Collected Number of families returned by RECON: 878 Round Time: 00:03:24 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10638 repeats masked totaling 2571124 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029299 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30025299 bp After Masking: 25316192 bp Masked: 15.68 % -- Input Database Coverage: 40051838 bp out of 511155287 bp ( 7.84 % ) Sampling Time: 00:03:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:15 (hh:mm:ss) Elapsed Time, 28472 HSPs Collected Number of families returned by RECON: 3723 Round Time: 00:15:59 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36703 repeats masked totaling 8992897 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011009 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90000815 bp After Masking: 74548098 bp Masked: 17.17 % -- Input Database Coverage: 130062847 bp out of 511155287 bp ( 25.44 % ) Sampling Time: 00:06:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 01:16:22 (hh:mm:ss) Elapsed Time, 341501 HSPs Collected Number of families returned by RECON: 15826 Round Time: 01:29:06 (hh:mm:ss) Elapsed Time : 298 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 146569 repeats masked totaling 35519226 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270077575 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 270038691 bp After Masking: 215680198 bp Masked: 20.13 % -- Input Database Coverage: 400140422 bp out of 511155287 bp ( 78.28 % ) Sampling Time: 00:22:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23021505 Comparison Time: 09:33:17 (hh:mm:ss) Elapsed Time, 2707095 HSPs Collected Number of families returned by RECON: 66379 Round Time: 10:34:40 (hh:mm:ss) Elapsed Time : 746 families discovered. RepeatScout/RECON discovery complete: 1394 families found Classification Time: 00:42:31 (hh:mm:ss) Elapsed Time Program Time: 13:15:31 (hh:mm:ss) Elapsed Time