RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.frtYOZ/RM_28839.SatNov160525022024 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: 1731763501 Database = /scratch/tmp/rModeler.frtYOZ/GCA_964252035.1_rPodErh1.hap1.1 - Sequences = 326 - Bases = 1495994634 - N50 = 101020263 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130766602-140107003 | [ 1 ] 121426202-130766602 | [ 2 ] 112085802-121426202 | [ ] 102745402-112085802 | [ 1 ] 93405002-102745402 | [ 4 ] 84064601-93405001 | [ ] 74724201-84064601 | [ 2 ] 65383801-74724201 | [ ] 56043401-65383801 | [ 2 ] 46703001-56043401 | [ 3 ] 37362600-46703000 | [ 2 ] 28022200-37362600 | [ 2 ] 18681800-28022200 | [ ] 9341400-18681800 | [ 1 ] 1000-9341400 |************************************************** [ 306 ] Storage Throughput = fair ( 594.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007859 bp ( 40003459 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:55 (hh:mm:ss) Elapsed Time Round Time: 00:30:43 (hh:mm:ss) Elapsed Time : 561 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (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... 17644 repeats masked totaling 3415986 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032658 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10031858 bp After Masking: 6476711 bp Masked: 35.44 % -- Input Database Coverage: 10032658 bp out of 1495994634 bp ( 0.67 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 8903 HSPs Collected Number of families returned by RECON: 1310 Round Time: 00:06:22 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55051 repeats masked totaling 10439329 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015121 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30011521 bp After Masking: 18890291 bp Masked: 37.06 % -- Input Database Coverage: 40047779 bp out of 1495994634 bp ( 2.68 % ) Sampling Time: 00:03:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:25:43 (hh:mm:ss) Elapsed Time, 42287 HSPs Collected Number of families returned by RECON: 4113 Round Time: 00:30:41 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177209 repeats masked totaling 33706017 bp(s). - TE Masking time 00:02:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047855 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90039055 bp After Masking: 54163263 bp Masked: 39.84 % -- Input Database Coverage: 130095634 bp out of 1495994634 bp ( 8.70 % ) Sampling Time: 00:09:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:52:01 (hh:mm:ss) Elapsed Time, 191362 HSPs Collected Number of families returned by RECON: 13428 Round Time: 03:14:34 (hh:mm:ss) Elapsed Time : 404 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 600423 repeats masked totaling 109957483 bp(s). - TE Masking time 00:09:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046996 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270018511 bp After Masking: 154322552 bp Masked: 42.85 % -- Input Database Coverage: 400142630 bp out of 1495994634 bp ( 26.75 % ) Sampling Time: 00:31:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 22:04:18 (hh:mm:ss) Elapsed Time, 539052 HSPs Collected Number of families returned by RECON: 49009 Round Time: 24:37:04 (hh:mm:ss) Elapsed Time : 1090 families discovered. RepeatScout/RECON discovery complete: 2195 families found Classification Time: 01:14:27 (hh:mm:ss) Elapsed Time Program Time: 30:13:51 (hh:mm:ss) Elapsed Time