RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yGHvx3/RM_25672.WedDec61351532023 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: 1701899511 Database = /dev/shm/rModeler.yGHvx3/GCA_949357725.1_fHypImm3.1 - Sequences = 1568 - Bases = 797804280 - N50 = 31445268 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36034542-38608367 | [ 3 ] 33460718-36034542 | [ 5 ] 30886893-33460717 | [ 4 ] 28313069-30886893 | [ 5 ] 25739244-28313068 | [ 3 ] 23165420-25739244 | [ 1 ] 20591595-23165419 | [ 2 ] 18017771-20591595 | [ ] 15443946-18017770 | [ ] 12870122-15443946 | [ 1 ] 10296297-12870121 | [ ] 7722473-10296297 | [ ] 5148648-7722472 | [ ] 2574824-5148648 | [ ] 1000-2574824 |************************************************** [ 1544 ] Storage Throughput = excellent ( 1089.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40046640 bp ( 40034752 non ambiguous ) - Num Contigs Represented = 137 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:46 (hh:mm:ss) Elapsed Time Round Time: 00:32:49 (hh:mm:ss) Elapsed Time : 656 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10436 repeats masked totaling 2796129 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010005 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10007117 bp After Masking: 6674860 bp Masked: 33.30 % -- Input Database Coverage: 10010005 bp out of 797804280 bp ( 1.25 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:06:30 (hh:mm:ss) Elapsed Time, 4445 HSPs Collected Number of families returned by RECON: 1069 Round Time: 00:08:11 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31797 repeats masked totaling 8494387 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036555 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 30027555 bp After Masking: 19850175 bp Masked: 33.89 % -- Input Database Coverage: 40046560 bp out of 797804280 bp ( 5.02 % ) Sampling Time: 00:04:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:36:50 (hh:mm:ss) Elapsed Time, 39954 HSPs Collected Number of families returned by RECON: 3495 Round Time: 00:42:32 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99077 repeats masked totaling 25962847 bp(s). - TE Masking time 00:03:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90060454 bp Num Contigs Represented = 277 Non ambiguous bp: Initial: 90030243 bp After Masking: 58700032 bp Masked: 34.80 % -- Input Database Coverage: 130107014 bp out of 797804280 bp ( 16.31 % ) Sampling Time: 00:13:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2785980 Comparison Time: 03:30:55 (hh:mm:ss) Elapsed Time, 252277 HSPs Collected Number of families returned by RECON: 12267 Round Time: 03:56:00 (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 : 00:04:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 340135 repeats masked totaling 87135524 bp(s). - TE Masking time 00:15:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270101195 bp Num Contigs Represented = 717 Non ambiguous bp: Initial: 270021795 bp After Masking: 166021861 bp Masked: 38.52 % -- Input Database Coverage: 400208209 bp out of 797804280 bp ( 50.16 % ) Sampling Time: 00:45:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25066740 Comparison Time: 24:39:19 (hh:mm:ss) Elapsed Time, 664307 HSPs Collected Number of families returned by RECON: 44581 Round Time: 26:31:50 (hh:mm:ss) Elapsed Time : 1041 families discovered. RepeatScout/RECON discovery complete: 2199 families found Classification Time: 01:54:37 (hh:mm:ss) Elapsed Time Program Time: 33:45:59 (hh:mm:ss) Elapsed Time