RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.zNRzuj/RM_3408366.SunDec80820482024 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: 1733674848 Database = /scratch/tmp/rModeler.zNRzuj/GCA_964106925.2_mVulVul1.hap2.2 - Sequences = 350 - Bases = 2398532178 - N50 = 140023408 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 184724482-197919017 | [ 2 ] 171529948-184724482 | [ ] 158335413-171529947 | [ 2 ] 145140879-158335413 | [ 2 ] 131946344-145140878 | [ 3 ] 118751810-131946344 | [ 3 ] 105557275-118751809 | [ 2 ] 92362741-105557275 | [ 3 ] 79168206-92362740 | [ ] 65973672-79168206 | [ ] 52779137-65973671 | [ ] 39584603-52779137 | [ ] 26390068-39584602 | [ ] 13195534-26390068 | [ ] 1000-13195534 |************************************************** [ 333 ] Storage Throughput = excellent ( 1412.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019451 bp ( 40015051 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:33 (hh:mm:ss) Elapsed Time Round Time: 00:12:04 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10954 repeats masked totaling 2143266 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008481 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10007681 bp After Masking: 7766388 bp Masked: 22.40 % -- Input Database Coverage: 10008481 bp out of 2398532178 bp ( 0.42 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 14394 HSPs Collected Number of families returned by RECON: 802 Round Time: 00:04:11 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39958 repeats masked totaling 7357667 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010890 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30007290 bp After Masking: 22341516 bp Masked: 25.55 % -- Input Database Coverage: 40019371 bp out of 2398532178 bp ( 1.67 % ) Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:02 (hh:mm:ss) Elapsed Time, 39100 HSPs Collected Number of families returned by RECON: 2303 Round Time: 00:15:34 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128653 repeats masked totaling 25125001 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039512 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90030512 bp After Masking: 63789023 bp Masked: 29.15 % -- Input Database Coverage: 130058883 bp out of 2398532178 bp ( 5.42 % ) Sampling Time: 00:06:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:15:29 (hh:mm:ss) Elapsed Time, 64757 HSPs Collected Number of families returned by RECON: 8411 Round Time: 01:23:35 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 427885 repeats masked totaling 84057677 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066142 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 270021364 bp After Masking: 182347865 bp Masked: 32.47 % -- Input Database Coverage: 400125025 bp out of 2398532178 bp ( 16.68 % ) Sampling Time: 00:20:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 09:19:52 (hh:mm:ss) Elapsed Time, 199482 HSPs Collected Number of families returned by RECON: 37192 Round Time: 09:54:42 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatScout/RECON discovery complete: 723 families found Classification Time: 00:16:59 (hh:mm:ss) Elapsed Time Program Time: 12:07:05 (hh:mm:ss) Elapsed Time