RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.iuDZxL/RM_21812.WedNov290333592023 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: 1701257638 Database = /dev/shm/rModeler.iuDZxL/GCA_028372415.1_mMacEug1.pri - Sequences = 315 - Bases = 3448908279 - N50 = 539575378 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 711411000-762225844 | [ 1 ] 660596156-711410999 | [ ] 609781312-660596155 | [ ] 558966468-609781311 | [ ] 508151625-558966468 | [ 1 ] 457336781-508151624 | [ 3 ] 406521937-457336780 | [ ] 355707093-406521936 | [ 1 ] 304892249-355707092 | [ ] 254077406-304892249 | [ ] 203262562-254077405 | [ ] 152447718-203262561 | [ 1 ] 101632874-152447717 | [ 1 ] 50818030-101632873 | [ ] 3187-50818030 |************************************************** [ 307 ] Storage Throughput = excellent ( 1119.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40052531 bp ( 40011007 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:10:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:34 (hh:mm:ss) Elapsed Time Round Time: 00:40:51 (hh:mm:ss) Elapsed Time : 303 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20556 repeats masked totaling 3766607 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003137 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 10001638 bp After Masking: 6104521 bp Masked: 38.96 % -- Input Database Coverage: 10003137 bp out of 3448908279 bp ( 0.29 % ) Sampling Time: 00:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 25289 HSPs Collected Number of families returned by RECON: 1212 Round Time: 00:10:22 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67316 repeats masked totaling 13131381 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30049314 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30009289 bp After Masking: 16292140 bp Masked: 45.71 % -- Input Database Coverage: 40052451 bp out of 3448908279 bp ( 1.16 % ) Sampling Time: 00:10:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:31:14 (hh:mm:ss) Elapsed Time, 45788 HSPs Collected Number of families returned by RECON: 2888 Round Time: 00:43:13 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:23:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 214835 repeats masked totaling 41819053 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90157454 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90008828 bp After Masking: 46093152 bp Masked: 48.79 % -- Input Database Coverage: 130209905 bp out of 3448908279 bp ( 3.78 % ) Sampling Time: 00:31:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:20:50 (hh:mm:ss) Elapsed Time, 210037 HSPs Collected Number of families returned by RECON: 9523 Round Time: 03:57:47 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:10:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 698573 repeats masked totaling 135533876 bp(s). - TE Masking time 00:08:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270479897 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 270003968 bp After Masking: 129882214 bp Masked: 51.90 % -- Input Database Coverage: 400689802 bp out of 3448908279 bp ( 11.62 % ) Sampling Time: 01:38:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 25:04:23 (hh:mm:ss) Elapsed Time, 1363884 HSPs Collected Number of families returned by RECON: 33915 Round Time: 27:18:38 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatScout/RECON discovery complete: 1063 families found Classification Time: 00:40:56 (hh:mm:ss) Elapsed Time Program Time: 33:31:47 (hh:mm:ss) Elapsed Time