RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fWFlFP/RM_3055897.ThuNov300626042023 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: 1701354363 Database = /dev/shm/rModeler.fWFlFP/GCF_029499605.1_aHylSar1.hap1 - Sequences = 3474 - Bases = 4142159359 - N50 = 420026731 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 579386958-620771670 | [ 1 ] 538002247-579386958 | [ ] 496617536-538002247 | [ 1 ] 455232824-496617535 | [ ] 413848113-455232824 | [ 2 ] 372463402-413848113 | [ 1 ] 331078690-372463401 | [ ] 289693979-331078690 | [ 1 ] 248309268-289693979 | [ ] 206924556-248309267 | [ 2 ] 165539845-206924556 | [ 1 ] 124155134-165539845 | [ 1 ] 82770422-124155133 | [ 2 ] 41385711-82770422 | [ 1 ] 1000-41385711 |************************************************** [ 3461 ] Storage Throughput = good ( 863.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013900 bp ( 40011500 non ambiguous ) - Num Contigs Represented = 109 - Sequence extraction : 00:07:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:00 (hh:mm:ss) Elapsed Time Round Time: 00:42:30 (hh:mm:ss) Elapsed Time : 957 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19962 repeats masked totaling 5360539 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038446 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10038046 bp After Masking: 3474593 bp Masked: 65.39 % -- Input Database Coverage: 10038446 bp out of 4142159359 bp ( 0.24 % ) Sampling Time: 00:04:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:55 (hh:mm:ss) Elapsed Time, 10326 HSPs Collected Number of families returned by RECON: 1152 Round Time: 00:10:06 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62280 repeats masked totaling 16294039 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015454 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 30013454 bp After Masking: 10012642 bp Masked: 66.64 % -- Input Database Coverage: 40053900 bp out of 4142159359 bp ( 0.97 % ) Sampling Time: 00:14:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:21:28 (hh:mm:ss) Elapsed Time, 80295 HSPs Collected Number of families returned by RECON: 3758 Round Time: 00:38:07 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:15:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191005 repeats masked totaling 49646788 bp(s). - TE Masking time 00:03:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021956 bp Num Contigs Represented = 262 Non ambiguous bp: Initial: 90011756 bp After Masking: 28416679 bp Masked: 68.43 % -- Input Database Coverage: 130075856 bp out of 4142159359 bp ( 3.14 % ) Sampling Time: 00:43:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2634660 Comparison Time: 01:50:13 (hh:mm:ss) Elapsed Time, 308597 HSPs Collected Number of families returned by RECON: 10281 Round Time: 02:41:56 (hh:mm:ss) Elapsed Time : 446 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:46:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:11:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 627924 repeats masked totaling 165559247 bp(s). - TE Masking time 00:12:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032984 bp Num Contigs Represented = 631 Non ambiguous bp: Initial: 270003584 bp After Masking: 71061673 bp Masked: 73.68 % -- Input Database Coverage: 400108840 bp out of 4142159359 bp ( 9.66 % ) Sampling Time: 02:11:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23444128 Comparison Time: 10:42:25 (hh:mm:ss) Elapsed Time, 866834 HSPs Collected Number of families returned by RECON: 25993 Round Time: 13:32:02 (hh:mm:ss) Elapsed Time : 1194 families discovered. RepeatScout/RECON discovery complete: 2718 families found Classification Time: 01:22:45 (hh:mm:ss) Elapsed Time Program Time: 19:07:26 (hh:mm:ss) Elapsed Time