RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.O20kfB/RM_1443019.SatJul191223242025 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: 1752953002 Database = /dev/shm/rModeler.O20kfB/GCA_048544215.1_fCoiMys1.hap1 - Sequences = 180 - Bases = 803134922 - N50 = 34963122 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35839565-38399463 |** [ 7 ] 33279667-35839564 |*** [ 11 ] 30719770-33279667 | [ 3 ] 28159872-30719769 | [ 2 ] 25599975-28159872 | [ ] 23040077-25599974 | [ ] 20480180-23040077 | [ ] 17920282-20480179 | [ ] 15360385-17920282 | [ ] 12800487-15360384 | [ ] 10240590-12800487 | [ ] 7680692-10240589 | [ ] 5120795-7680692 | [ ] 2560897-5120794 | [ ] 1000-2560897 |************************************************** [ 157 ] Storage Throughput = excellent ( 1677.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037303 bp ( 40031503 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:40 (hh:mm:ss) Elapsed Time Round Time: 00:17:39 (hh:mm:ss) Elapsed Time : 470 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8550 repeats masked totaling 1402459 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021455 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10019855 bp After Masking: 7230678 bp Masked: 27.84 % -- Input Database Coverage: 10021455 bp out of 803134922 bp ( 1.25 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:16 (hh:mm:ss) Elapsed Time, 7317 HSPs Collected Number of families returned by RECON: 1158 Round Time: 00:05:08 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26393 repeats masked totaling 4317022 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015828 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30011628 bp After Masking: 21519225 bp Masked: 28.30 % -- Input Database Coverage: 40037283 bp out of 803134922 bp ( 4.99 % ) Sampling Time: 00:04:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:14:45 (hh:mm:ss) Elapsed Time, 38306 HSPs Collected Number of families returned by RECON: 4240 Round Time: 00:19:58 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84385 repeats masked totaling 14234839 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015015 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90002615 bp After Masking: 63661151 bp Masked: 29.27 % -- Input Database Coverage: 130052298 bp out of 803134922 bp ( 16.19 % ) Sampling Time: 00:14:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:26:54 (hh:mm:ss) Elapsed Time, 244987 HSPs Collected Number of families returned by RECON: 16244 Round Time: 01:45:40 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 308312 repeats masked totaling 53589706 bp(s). - TE Masking time 00:04:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062069 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 270020514 bp After Masking: 178824671 bp Masked: 33.77 % -- Input Database Coverage: 400114367 bp out of 803134922 bp ( 49.82 % ) Sampling Time: 00:45:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 10:20:17 (hh:mm:ss) Elapsed Time, 847299 HSPs Collected Number of families returned by RECON: 59979 Round Time: 11:41:27 (hh:mm:ss) Elapsed Time : 1037 families discovered. RepeatScout/RECON discovery complete: 2009 families found Classification Time: 00:45:28 (hh:mm:ss) Elapsed Time Program Time: 14:55:20 (hh:mm:ss) Elapsed Time