RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.xPTlHi/RM_4047607.FriNov150659592024 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: 1731682798 Database = /scratch/tmp/rModeler.xPTlHi/GCA_964270895.1_rPodFil1.hap1.1 - Sequences = 349 - Bases = 1506966124 - N50 = 99614481 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 127297423-136390025 | [ 1 ] 118204821-127297422 | [ 2 ] 109112220-118204821 | [ ] 100019618-109112219 | [ 2 ] 90927016-100019617 | [ 2 ] 81834415-90927016 | [ 1 ] 72741813-81834414 | [ 2 ] 63649211-72741812 | [ ] 54556610-63649211 | [ 2 ] 45464008-54556609 | [ 3 ] 36371406-45464007 | [ 4 ] 27278805-36371406 | [ ] 18186203-27278804 | [ ] 9093601-18186202 | [ 1 ] 1000-9093601 |************************************************** [ 329 ] Storage Throughput = excellent ( 1448.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005641 bp ( 40002041 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:39 (hh:mm:ss) Elapsed Time Round Time: 00:10:47 (hh:mm:ss) Elapsed Time : 583 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17628 repeats masked totaling 3159692 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007820 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10007020 bp After Masking: 6566164 bp Masked: 34.38 % -- Input Database Coverage: 10007820 bp out of 1506966124 bp ( 0.66 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 10335 HSPs Collected Number of families returned by RECON: 1367 Round Time: 00:03:57 (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 : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57306 repeats masked totaling 10331572 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037741 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30034941 bp After Masking: 18913043 bp Masked: 37.03 % -- Input Database Coverage: 40045561 bp out of 1506966124 bp ( 2.66 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:12:40 (hh:mm:ss) Elapsed Time, 41151 HSPs Collected Number of families returned by RECON: 4087 Round Time: 00:14:56 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179442 repeats masked totaling 32039316 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047504 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90036304 bp After Masking: 55036836 bp Masked: 38.87 % -- Input Database Coverage: 130093065 bp out of 1506966124 bp ( 8.63 % ) Sampling Time: 00:04:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:12:26 (hh:mm:ss) Elapsed Time, 388143 HSPs Collected Number of families returned by RECON: 13352 Round Time: 01:21:28 (hh:mm:ss) Elapsed Time : 443 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 610272 repeats masked totaling 107940853 bp(s). - TE Masking time 00:03:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041261 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 270009261 bp After Masking: 153976977 bp Masked: 42.97 % -- Input Database Coverage: 400134326 bp out of 1506966124 bp ( 26.55 % ) Sampling Time: 00:15:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 07:38:33 (hh:mm:ss) Elapsed Time, 648682 HSPs Collected Number of families returned by RECON: 47168 Round Time: 08:24:11 (hh:mm:ss) Elapsed Time : 1080 families discovered. RepeatScout/RECON discovery complete: 2254 families found Classification Time: 00:35:51 (hh:mm:ss) Elapsed Time Program Time: 10:51:10 (hh:mm:ss) Elapsed Time