RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.U44YQm/RM_1530509.WedDec41745562024 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: 1733363155 Database = /scratch/tmp/rModeler.U44YQm/GCA_964234825.1_rPodMel1.hap2.1 - Sequences = 200 - Bases = 1437044901 - N50 = 99688005 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 126496238-135531613 | [ 1 ] 117460864-126496238 | [ 2 ] 108425490-117460864 | [ ] 99390116-108425490 | [ 3 ] 90354742-99390116 | [ 2 ] 81319367-90354741 | [ ] 72283993-81319367 | [ 2 ] 63248619-72283993 | [ 1 ] 54213245-63248619 | [ 2 ] 45177871-54213245 | [ 1 ] 36142496-45177870 | [ 3 ] 27107122-36142496 | [ ] 18071748-27107122 | [ ] 9036374-18071748 | [ 1 ] 1000-9036374 |************************************************** [ 182 ] Storage Throughput = excellent ( 1452.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019074 bp ( 40014874 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:06 (hh:mm:ss) Elapsed Time Round Time: 00:10:15 (hh:mm:ss) Elapsed Time : 541 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 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17290 repeats masked totaling 2983723 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015792 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10014792 bp After Masking: 6635516 bp Masked: 33.74 % -- Input Database Coverage: 10015792 bp out of 1437044901 bp ( 0.70 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:48 (hh:mm:ss) Elapsed Time, 8943 HSPs Collected Number of families returned by RECON: 1319 Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 24 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 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52500 repeats masked totaling 9159757 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003202 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30000002 bp After Masking: 19313225 bp Masked: 35.62 % -- Input Database Coverage: 40018994 bp out of 1437044901 bp ( 2.78 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:11:53 (hh:mm:ss) Elapsed Time, 48683 HSPs Collected Number of families returned by RECON: 4317 Round Time: 00:15:12 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 173312 repeats masked totaling 30193408 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024556 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90012956 bp After Masking: 55412267 bp Masked: 38.44 % -- Input Database Coverage: 130043550 bp out of 1437044901 bp ( 9.05 % ) Sampling Time: 00:07:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:04:32 (hh:mm:ss) Elapsed Time, 221009 HSPs Collected Number of families returned by RECON: 13662 Round Time: 01:16:18 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 583214 repeats masked totaling 101483105 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053051 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 270026651 bp After Masking: 155733372 bp Masked: 42.33 % -- Input Database Coverage: 400096601 bp out of 1437044901 bp ( 27.84 % ) Sampling Time: 00:22:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 07:20:17 (hh:mm:ss) Elapsed Time, 1140695 HSPs Collected Number of families returned by RECON: 47858 Round Time: 08:10:54 (hh:mm:ss) Elapsed Time : 1045 families discovered. RepeatScout/RECON discovery complete: 2146 families found Classification Time: 00:30:19 (hh:mm:ss) Elapsed Time Program Time: 10:26:46 (hh:mm:ss) Elapsed Time