RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.STQrYa/RM_416407.WedApr231215002025 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: 1745435697 Database = /dev/shm/rModeler.STQrYa/GCA_048772815.1_mCalLat2.hap1 - Sequences = 8087 - Bases = 4646974320 - N50 = 109147636 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 210136520-225145741 | [ 2 ] 195127299-210136519 | [ 1 ] 180118079-195127299 | [ ] 165108858-180118078 | [ 2 ] 150099638-165108858 | [ 1 ] 135090417-150099637 | [ 3 ] 120081196-135090416 | [ 3 ] 105071976-120081196 | [ 3 ] 90062755-105071975 | [ 2 ] 75053535-90062755 | [ 1 ] 60044314-75053534 | [ 1 ] 45035093-60044313 | [ ] 30025873-45035093 | [ 1 ] 15016652-30025872 | [ 3 ] 7432-15016652 |************************************************** [ 8064 ] Storage Throughput = excellent ( 1719.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029230 bp ( 40026712 non ambiguous ) - Num Contigs Represented = 410 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:33 (hh:mm:ss) Elapsed Time Round Time: 00:17:03 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8997 repeats masked totaling 4110766 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001490 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 10000490 bp After Masking: 5099309 bp Masked: 49.01 % -- Input Database Coverage: 10001490 bp out of 4646974320 bp ( 0.22 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:41 (hh:mm:ss) Elapsed Time, 3955 HSPs Collected Number of families returned by RECON: 510 Round Time: 00:03:44 (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 : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26708 repeats masked totaling 12321968 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027739 bp Num Contigs Represented = 327 Non ambiguous bp: Initial: 30026221 bp After Masking: 14773730 bp Masked: 50.80 % -- Input Database Coverage: 40029229 bp out of 4646974320 bp ( 0.86 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:15:05 (hh:mm:ss) Elapsed Time, 30510 HSPs Collected Number of families returned by RECON: 1698 Round Time: 00:17:12 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 83959 repeats masked totaling 38761372 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035755 bp Num Contigs Represented = 804 Non ambiguous bp: Initial: 90030255 bp After Masking: 42981543 bp Masked: 52.26 % -- Input Database Coverage: 130064984 bp out of 4646974320 bp ( 2.80 % ) Sampling Time: 00:05:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2701650 Comparison Time: 00:59:25 (hh:mm:ss) Elapsed Time, 108812 HSPs Collected Number of families returned by RECON: 5249 Round Time: 01:06:25 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 286777 repeats masked totaling 119167487 bp(s). - TE Masking time 00:03:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055224 bp Num Contigs Represented = 1808 Non ambiguous bp: Initial: 270036442 bp After Masking: 124821702 bp Masked: 53.78 % -- Input Database Coverage: 400120208 bp out of 4646974320 bp ( 8.61 % ) Sampling Time: 00:17:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24419566 Comparison Time: 06:20:45 (hh:mm:ss) Elapsed Time, 961810 HSPs Collected Number of families returned by RECON: 21990 Round Time: 06:51:11 (hh:mm:ss) Elapsed Time : 307 families discovered. RepeatScout/RECON discovery complete: 650 families found Classification Time: 00:33:54 (hh:mm:ss) Elapsed Time Program Time: 09:09:29 (hh:mm:ss) Elapsed Time