RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WGg6F2/RM_1831.TueDec52332192023 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: 1701847938 Database = /dev/shm/rModeler.WGg6F2/GCA_949316205.1_fPlaFle2.1 - Sequences = 109 - Bases = 597138466 - N50 = 26771016 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29241421-31329391 |* [ 2 ] 27153452-29241421 |**** [ 7 ] 25065483-27153452 |* [ 3 ] 22977514-25065483 |** [ 4 ] 20889545-22977514 |** [ 4 ] 18801576-20889545 | [ 1 ] 16713607-18801576 | [ 1 ] 14625638-16713607 |* [ 2 ] 12537669-14625638 | [ ] 10449700-12537669 | [ ] 8361731-10449700 | [ ] 6273762-8361731 | [ ] 4185793-6273762 | [ ] 2097824-4185793 | [ ] 9855-2097824 |************************************************** [ 85 ] Storage Throughput = excellent ( 1089.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014632 bp ( 40009632 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:34 (hh:mm:ss) Elapsed Time Round Time: 00:28:06 (hh:mm:ss) Elapsed Time : 304 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6104 repeats masked totaling 1172059 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032852 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10031452 bp After Masking: 8479396 bp Masked: 15.47 % -- Input Database Coverage: 10032852 bp out of 597138466 bp ( 1.68 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:42 (hh:mm:ss) Elapsed Time, 7584 HSPs Collected Number of families returned by RECON: 1173 Round Time: 00:06:59 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19503 repeats masked totaling 3592036 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021760 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30018160 bp After Masking: 25493383 bp Masked: 15.07 % -- Input Database Coverage: 40054612 bp out of 597138466 bp ( 6.71 % ) Sampling Time: 00:02:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:33:10 (hh:mm:ss) Elapsed Time, 36986 HSPs Collected Number of families returned by RECON: 4888 Round Time: 00:37:00 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:15 (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... 67018 repeats masked totaling 11598493 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031128 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90017328 bp After Masking: 75757945 bp Masked: 15.84 % -- Input Database Coverage: 130085740 bp out of 597138466 bp ( 21.78 % ) Sampling Time: 00:07:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 04:04:11 (hh:mm:ss) Elapsed Time, 234198 HSPs Collected Number of families returned by RECON: 19110 Round Time: 04:25:22 (hh:mm:ss) Elapsed Time : 370 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 249075 repeats masked totaling 45925955 bp(s). - TE Masking time 00:09:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270069965 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270026565 bp After Masking: 215754059 bp Masked: 20.10 % -- Input Database Coverage: 400155705 bp out of 597138466 bp ( 67.01 % ) Sampling Time: 00:27:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 33:09:25 (hh:mm:ss) Elapsed Time, 883492 HSPs Collected Number of families returned by RECON: 77451 Round Time: 35:58:35 (hh:mm:ss) Elapsed Time : 820 families discovered. RepeatScout/RECON discovery complete: 1589 families found Classification Time: 01:27:15 (hh:mm:ss) Elapsed Time Program Time: 43:03:17 (hh:mm:ss) Elapsed Time