RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lWvXxy/RM_29514.MonJun241450492024 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: 1719265848 Database = /dev/shm/rModeler.lWvXxy/GCF_011100685.1_UU_Cfam_GSD_1.0 - Sequences = 2197 - Bases = 2481983352 - N50 = 64676183 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116660100-124992030 | [ 2 ] 108328170-116660099 | [ ] 99996240-108328169 | [ ] 91664311-99996240 | [ 1 ] 83332381-91664310 | [ 3 ] 75000451-83332380 | [ 3 ] 66668521-75000450 | [ 3 ] 58336592-66668521 | [ 8 ] 50004662-58336591 | [ 5 ] 41672732-50004661 | [ 5 ] 33340802-41672731 | [ 4 ] 25008873-33340802 | [ 4 ] 16676943-25008872 | [ 1 ] 8345013-16676942 | [ ] 13084-8345013 |************************************************** [ 2158 ] Storage Throughput = excellent ( 1062.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028804 bp ( 40027958 non ambiguous ) - Num Contigs Represented = 116 - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:22 (hh:mm:ss) Elapsed Time Round Time: 00:29:59 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11336 repeats masked totaling 2312694 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027144 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10027044 bp After Masking: 7537156 bp Masked: 24.83 % -- Input Database Coverage: 10027144 bp out of 2481983352 bp ( 0.40 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:06:07 (hh:mm:ss) Elapsed Time, 12669 HSPs Collected Number of families returned by RECON: 844 Round Time: 00:07:35 (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 : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36923 repeats masked totaling 7535345 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001648 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 30000902 bp After Masking: 22004918 bp Masked: 26.65 % -- Input Database Coverage: 40028792 bp out of 2481983352 bp ( 1.61 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:51:00 (hh:mm:ss) Elapsed Time, 913459 HSPs Collected Number of families returned by RECON: 2478 Round Time: 00:55:07 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121746 repeats masked totaling 25167338 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040768 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 90039468 bp After Masking: 63543028 bp Masked: 29.43 % -- Input Database Coverage: 130069560 bp out of 2481983352 bp ( 5.24 % ) Sampling Time: 00:08:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 04:30:06 (hh:mm:ss) Elapsed Time, 3117885 HSPs Collected Number of families returned by RECON: 9128 Round Time: 04:43:49 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 396126 repeats masked totaling 82177524 bp(s). - TE Masking time 00:06:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039864 bp Num Contigs Represented = 455 Non ambiguous bp: Initial: 270033664 bp After Masking: 183486232 bp Masked: 32.05 % -- Input Database Coverage: 400109424 bp out of 2481983352 bp ( 16.12 % ) Sampling Time: 00:29:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23588146 Comparison Time: 41:55:25 (hh:mm:ss) Elapsed Time, 53233073 HSPs Collected Number of families returned by RECON: 39294 Round Time: 43:31:21 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatScout/RECON discovery complete: 763 families found Classification Time: 00:30:07 (hh:mm:ss) Elapsed Time Program Time: 50:17:58 (hh:mm:ss) Elapsed Time