RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.us1Hw7/RM_28813.FriDec82254052023 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: 1702104844 Database = /dev/shm/rModeler.us1Hw7/GCA_951799975.1_fGobNig1.1 - Sequences = 298 - Bases = 870572126 - N50 = 38085758 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 71401683-76501732 | [ 1 ] 66301634-71401682 | [ ] 61201585-66301633 | [ ] 56101536-61201584 | [ ] 51001488-56101536 | [ ] 45901439-51001487 | [ 1 ] 40801390-45901438 | [ 4 ] 35701341-40801389 | [ 4 ] 30601292-35701340 |* [ 6 ] 25501244-30601292 | [ 5 ] 20401195-25501243 | [ 1 ] 15301146-20401194 | [ 2 ] 10201097-15301145 | [ ] 5101048-10201096 | [ ] 1000-5101048 |************************************************* [ 274 ] Storage Throughput = excellent ( 1104.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039862 bp ( 40034862 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:29 (hh:mm:ss) Elapsed Time Round Time: 00:25:32 (hh:mm:ss) Elapsed Time : 897 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18006 repeats masked totaling 3006377 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010441 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10009241 bp After Masking: 6133535 bp Masked: 38.72 % -- Input Database Coverage: 10010441 bp out of 870572126 bp ( 1.15 % ) Sampling Time: 00:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 7322 HSPs Collected Number of families returned by RECON: 1383 Round Time: 00:08:35 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56340 repeats masked totaling 9386219 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029400 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30025600 bp After Masking: 18205130 bp Masked: 39.37 % -- Input Database Coverage: 40039841 bp out of 870572126 bp ( 4.60 % ) Sampling Time: 00:06:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:35 (hh:mm:ss) Elapsed Time, 45420 HSPs Collected Number of families returned by RECON: 4677 Round Time: 00:34:06 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 178698 repeats masked totaling 29413336 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037990 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90026990 bp After Masking: 52779023 bp Masked: 41.37 % -- Input Database Coverage: 130077831 bp out of 870572126 bp ( 14.94 % ) Sampling Time: 00:22:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 02:46:58 (hh:mm:ss) Elapsed Time, 265146 HSPs Collected Number of families returned by RECON: 13692 Round Time: 03:23:23 (hh:mm:ss) Elapsed Time : 589 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 613823 repeats masked totaling 101061171 bp(s). - TE Masking time 00:12:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047019 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 270005219 bp After Masking: 145214137 bp Masked: 46.22 % -- Input Database Coverage: 400124850 bp out of 870572126 bp ( 45.96 % ) Sampling Time: 01:18:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 20:08:21 (hh:mm:ss) Elapsed Time, 639972 HSPs Collected Number of families returned by RECON: 41096 Round Time: 22:41:18 (hh:mm:ss) Elapsed Time : 1247 families discovered. RepeatScout/RECON discovery complete: 2891 families found Classification Time: 01:52:18 (hh:mm:ss) Elapsed Time Program Time: 29:05:12 (hh:mm:ss) Elapsed Time