RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EQmpM6/RM_32574.TueJan160915352024 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: 1705425328 Database = /dev/shm/rModeler.EQmpM6/GCA_963514085.1_fCheLab1.1 - Sequences = 363 - Bases = 717420143 - N50 = 30521011 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36876735-39510717 | [ 1 ] 34242754-36876735 | [ 1 ] 31608773-34242754 | [ 2 ] 28974792-31608773 |* [ 11 ] 26340811-28974792 | [ 3 ] 23706830-26340811 | [ 4 ] 21072849-23706830 | [ 1 ] 18438867-21072848 | [ ] 15804886-18438867 | [ ] 13170905-15804886 | [ 1 ] 10536924-13170905 | [ ] 7902943-10536924 | [ ] 5268962-7902943 | [ ] 2634981-5268962 | [ ] 1000-2634981 |************************************************** [ 339 ] Storage Throughput = excellent ( 1097.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024008 bp ( 40018408 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:35 (hh:mm:ss) Elapsed Time Round Time: 00:29:26 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8009 repeats masked totaling 1402279 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020113 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10018913 bp After Masking: 7922658 bp Masked: 20.92 % -- Input Database Coverage: 10020113 bp out of 717420143 bp ( 1.40 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:09:34 (hh:mm:ss) Elapsed Time, 5414 HSPs Collected Number of families returned by RECON: 1073 Round Time: 00:11:45 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25393 repeats masked totaling 4447252 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30043815 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30039415 bp After Masking: 24577571 bp Masked: 18.18 % -- Input Database Coverage: 40063928 bp out of 717420143 bp ( 5.58 % ) Sampling Time: 00:02:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:54:43 (hh:mm:ss) Elapsed Time, 32222 HSPs Collected Number of families returned by RECON: 4384 Round Time: 00:59:45 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 82862 repeats masked totaling 14733399 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018183 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 90003013 bp After Masking: 72036799 bp Masked: 19.96 % -- Input Database Coverage: 130082111 bp out of 717420143 bp ( 18.13 % ) Sampling Time: 00:07:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 04:58:20 (hh:mm:ss) Elapsed Time, 257193 HSPs Collected Number of families returned by RECON: 16685 Round Time: 05:27:41 (hh:mm:ss) Elapsed Time : 397 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 302533 repeats masked totaling 56239233 bp(s). - TE Masking time 00:10:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270065660 bp Num Contigs Represented = 215 Non ambiguous bp: Initial: 270018921 bp After Masking: 205486821 bp Masked: 23.90 % -- Input Database Coverage: 400147771 bp out of 717420143 bp ( 55.78 % ) Sampling Time: 00:27:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 32:48:33 (hh:mm:ss) Elapsed Time, 901986 HSPs Collected Number of families returned by RECON: 64856 Round Time: 35:32:48 (hh:mm:ss) Elapsed Time : 1116 families discovered. RepeatScout/RECON discovery complete: 2077 families found Classification Time: 02:06:27 (hh:mm:ss) Elapsed Time Program Time: 44:47:52 (hh:mm:ss) Elapsed Time