RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ABPaQ7/RM_5611.WedDec61036532023 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: 1701887812 Database = /dev/shm/rModeler.ABPaQ7/GCA_949316345.1_fPunPun2.1 - Sequences = 175 - Bases = 480450674 - N50 = 21811056 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33362094-35745030 | [ 2 ] 30979159-33362094 | [ ] 28596224-30979159 | [ 1 ] 26213288-28596223 | [ ] 23830353-26213288 | [ 2 ] 21447418-23830353 |* [ 4 ] 19064482-21447417 |* [ 6 ] 16681547-19064482 |* [ 5 ] 14298612-16681547 | [ 1 ] 11915676-14298611 | [ ] 9532741-11915676 | [ ] 7149806-9532741 | [ ] 4766870-7149805 | [ ] 2383935-4766870 | [ ] 1000-2383935 |************************************************** [ 154 ] Storage Throughput = excellent ( 1109.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015691 bp ( 40003891 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:23 (hh:mm:ss) Elapsed Time Round Time: 00:33:42 (hh:mm:ss) Elapsed Time : 289 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3101 repeats masked totaling 816232 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004737 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10002537 bp After Masking: 8256074 bp Masked: 17.46 % -- Input Database Coverage: 10004737 bp out of 480450674 bp ( 2.08 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:40 (hh:mm:ss) Elapsed Time, 6043 HSPs Collected Number of families returned by RECON: 924 Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10613 repeats masked totaling 2636797 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010923 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30001323 bp After Masking: 24838337 bp Masked: 17.21 % -- Input Database Coverage: 40015660 bp out of 480450674 bp ( 8.33 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:38:11 (hh:mm:ss) Elapsed Time, 44354 HSPs Collected Number of families returned by RECON: 3999 Round Time: 00:42:35 (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 : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37688 repeats masked totaling 9083910 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040694 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 90011494 bp After Masking: 74174093 bp Masked: 17.59 % -- Input Database Coverage: 130056354 bp out of 480450674 bp ( 27.07 % ) Sampling Time: 00:08:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 04:38:17 (hh:mm:ss) Elapsed Time, 228845 HSPs Collected Number of families returned by RECON: 18054 Round Time: 04:59:27 (hh:mm:ss) Elapsed Time : 305 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 146222 repeats masked totaling 34513716 bp(s). - TE Masking time 00:07:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270115330 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270030330 bp After Masking: 214648918 bp Masked: 20.51 % -- Input Database Coverage: 400171684 bp out of 480450674 bp ( 83.29 % ) Sampling Time: 00:31:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 35:49:59 (hh:mm:ss) Elapsed Time, 839401 HSPs Collected Number of families returned by RECON: 76086 Round Time: 38:35:50 (hh:mm:ss) Elapsed Time : 748 families discovered. RepeatScout/RECON discovery complete: 1405 families found Classification Time: 01:26:25 (hh:mm:ss) Elapsed Time Program Time: 46:26:24 (hh:mm:ss) Elapsed Time