RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.4DjjvQ/RM_790424.MonDec91757352024 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: 1733795854 Database = /scratch/tmp/rModeler.4DjjvQ/GCA_040954845.1_fLepOcu1.hap1 - Sequences = 831 - Bases = 1110649520 - N50 = 54398919 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 73757163-79024862 | [ 3 ] 68489464-73757162 | [ ] 63221765-68489463 | [ 1 ] 57954066-63221764 | [ 3 ] 52686368-57954066 | [ 1 ] 47418669-52686367 | [ ] 42150970-47418668 | [ 3 ] 36883271-42150969 | [ 3 ] 31615572-36883270 | [ 1 ] 26347874-31615572 | [ ] 21080175-26347873 | [ 3 ] 15812476-21080174 | [ 5 ] 10544777-15812475 | [ 5 ] 5277078-10544776 | [ 1 ] 9380-5277078 |************************************************** [ 802 ] Storage Throughput = excellent ( 1268.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035052 bp ( 40034452 non ambiguous ) - Num Contigs Represented = 94 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:55 (hh:mm:ss) Elapsed Time Round Time: 00:12:32 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7842 repeats masked totaling 1856888 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033731 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10033731 bp After Masking: 7532869 bp Masked: 24.92 % -- Input Database Coverage: 10033731 bp out of 1110649520 bp ( 0.90 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 5727 HSPs Collected Number of families returned by RECON: 912 Round Time: 00:03:36 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25930 repeats masked totaling 6168034 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001316 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 30000716 bp After Masking: 21552836 bp Masked: 28.16 % -- Input Database Coverage: 40035047 bp out of 1110649520 bp ( 3.60 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:12:52 (hh:mm:ss) Elapsed Time, 31542 HSPs Collected Number of families returned by RECON: 2795 Round Time: 00:15:45 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84536 repeats masked totaling 20469379 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004171 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 90002971 bp After Masking: 63142857 bp Masked: 29.84 % -- Input Database Coverage: 130039218 bp out of 1110649520 bp ( 11.71 % ) Sampling Time: 00:04:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 01:09:33 (hh:mm:ss) Elapsed Time, 238462 HSPs Collected Number of families returned by RECON: 9350 Round Time: 01:17:16 (hh:mm:ss) Elapsed Time : 271 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 301045 repeats masked totaling 73388918 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022811 bp Num Contigs Represented = 337 Non ambiguous bp: Initial: 270019611 bp After Masking: 178440409 bp Masked: 33.92 % -- Input Database Coverage: 400062029 bp out of 1110649520 bp ( 36.02 % ) Sampling Time: 00:13:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23389380 Comparison Time: 08:20:44 (hh:mm:ss) Elapsed Time, 629056 HSPs Collected Number of families returned by RECON: 33584 Round Time: 08:48:24 (hh:mm:ss) Elapsed Time : 672 families discovered. RepeatScout/RECON discovery complete: 1387 families found Classification Time: 00:36:37 (hh:mm:ss) Elapsed Time Program Time: 11:14:10 (hh:mm:ss) Elapsed Time