RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Rjb47K/RM_2647337.FriMar221633442024 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: 1711150423 Database = /dev/shm/rModeler.Rjb47K/GCA_036417895.1_bPasDom1.hap2 - Sequences = 482 - Bases = 1260479385 - N50 = 77871685 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 151314557-162122669 | [ 1 ] 140506446-151314557 | [ ] 129698335-140506446 | [ ] 118890223-129698334 | [ 2 ] 108082112-118890223 | [ ] 97274001-108082112 | [ ] 86465890-97274001 | [ ] 75657778-86465889 | [ 2 ] 64849667-75657778 | [ 2 ] 54041556-64849667 | [ 2 ] 43233445-54041556 | [ 1 ] 32425333-43233444 | [ 1 ] 21617222-32425333 | [ 1 ] 10809111-21617222 | [ 9 ] 1000-10809111 |************************************************** [ 461 ] Storage Throughput = excellent ( 1454.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041485 bp ( 40039485 non ambiguous ) - Num Contigs Represented = 92 - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:19 (hh:mm:ss) Elapsed Time Round Time: 00:27:20 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3700 repeats masked totaling 1430539 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027622 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10027022 bp After Masking: 7747768 bp Masked: 22.73 % -- Input Database Coverage: 10027622 bp out of 1260479385 bp ( 0.80 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:08:00 (hh:mm:ss) Elapsed Time, 79821 HSPs Collected Number of families returned by RECON: 285 Round Time: 00:11:27 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9609 repeats masked totaling 3374254 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013852 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30012452 bp After Masking: 24000323 bp Masked: 20.03 % -- Input Database Coverage: 40041474 bp out of 1260479385 bp ( 3.18 % ) Sampling Time: 00:06:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:07:25 (hh:mm:ss) Elapsed Time, 4290076 HSPs Collected Number of families returned by RECON: 1320 Round Time: 01:16:31 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30886 repeats masked totaling 10816583 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019468 bp Num Contigs Represented = 150 Non ambiguous bp: Initial: 90015868 bp After Masking: 69923391 bp Masked: 22.32 % -- Input Database Coverage: 130060942 bp out of 1260479385 bp ( 10.32 % ) Sampling Time: 00:27:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 06:55:21 (hh:mm:ss) Elapsed Time, 25068604 HSPs Collected Number of families returned by RECON: 8479 Round Time: 07:44:13 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104628 repeats masked totaling 40199650 bp(s). - TE Masking time 00:07:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036732 bp Num Contigs Represented = 289 Non ambiguous bp: Initial: 270028932 bp After Masking: 203506441 bp Masked: 24.64 % -- Input Database Coverage: 400097674 bp out of 1260479385 bp ( 31.74 % ) Sampling Time: 01:22:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23273253 Comparison Time: 49:52:16 (hh:mm:ss) Elapsed Time, 270403698 HSPs Collected Number of families returned by RECON: 54622 Round Time: 56:53:43 (hh:mm:ss) Elapsed Time : 265 families discovered. RepeatScout/RECON discovery complete: 541 families found Classification Time: 00:57:57 (hh:mm:ss) Elapsed Time Program Time: 67:31:11 (hh:mm:ss) Elapsed Time