RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BVy24R/RM_17213.SunNov261810342023 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: 1701051033 Database = /dev/shm/rModeler.BVy24R/GCA_026419925.1_bHarHar1 - Sequences = 5968 - Bases = 1185324778 - N50 = 731539 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 4258567-4561956 | [ 2 ] 3955178-4258567 | [ 3 ] 3651789-3955178 | [ 2 ] 3348400-3651789 | [ 2 ] 3045011-3348400 | [ 3 ] 2741622-3045011 | [ 12 ] 2438233-2741622 | [ 11 ] 2134844-2438233 | [ 16 ] 1831455-2134844 | [ 27 ] 1528066-1831455 | [ 38 ] 1224677-1528066 | [ 80 ] 921288-1224677 |* [ 123 ] 617899-921288 |* [ 199 ] 314510-617899 |**** [ 425 ] 11121-314510 |************************************************** [ 5025 ] Storage Throughput = excellent ( 1170.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001750 bp ( 40001750 non ambiguous ) - Num Contigs Represented = 820 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:39 (hh:mm:ss) Elapsed Time Round Time: 00:42:08 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1892 repeats masked totaling 1129606 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028052 bp Num Contigs Represented = 251 Non ambiguous bp: Initial: 10028052 bp After Masking: 8506533 bp Masked: 15.17 % -- Input Database Coverage: 10028052 bp out of 1185324778 bp ( 0.85 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36585 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 777 HSPs Collected Number of families returned by RECON: 268 Round Time: 00:06:47 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5303 repeats masked totaling 3263230 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013539 bp Num Contigs Represented = 657 Non ambiguous bp: Initial: 30013539 bp After Masking: 25567818 bp Masked: 14.81 % -- Input Database Coverage: 40041591 bp out of 1185324778 bp ( 3.38 % ) Sampling Time: 00:02:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 348195 Comparison Time: 00:34:20 (hh:mm:ss) Elapsed Time, 5892 HSPs Collected Number of families returned by RECON: 1395 Round Time: 00:37:30 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17062 repeats masked totaling 9356233 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032575 bp Num Contigs Represented = 1426 Non ambiguous bp: Initial: 90032575 bp After Masking: 76218356 bp Masked: 15.34 % -- Input Database Coverage: 130074166 bp out of 1185324778 bp ( 10.97 % ) Sampling Time: 00:07:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2975580 Comparison Time: 04:45:19 (hh:mm:ss) Elapsed Time, 83070 HSPs Collected Number of families returned by RECON: 8078 Round Time: 05:00:51 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63323 repeats masked totaling 33280212 bp(s). - TE Masking time 00:07:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019354 bp Num Contigs Represented = 2887 Non ambiguous bp: Initial: 270019354 bp After Masking: 221389974 bp Masked: 18.01 % -- Input Database Coverage: 400093520 bp out of 1185324778 bp ( 33.75 % ) Sampling Time: 00:28:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27147396 Comparison Time: 37:11:46 (hh:mm:ss) Elapsed Time, 1100218 HSPs Collected Number of families returned by RECON: 48472 Round Time: 38:22:24 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatScout/RECON discovery complete: 472 families found Classification Time: 01:02:22 (hh:mm:ss) Elapsed Time Program Time: 45:52:02 (hh:mm:ss) Elapsed Time