RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rBq3HV/RM_7298.WedJul31131342024 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: 1720031493 Database = /dev/shm/rModeler.rBq3HV/GCF_000239375.1_PunNye1.0 - Sequences = 7233 - Bases = 830129318 - N50 = 2534605 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 11775833-12616905 | [ 1 ] 10934762-11775833 | [ ] 10093691-10934762 | [ 1 ] 9252620-10093691 | [ 1 ] 8411549-9252620 | [ 2 ] 7570477-8411548 | [ 2 ] 6729406-7570477 | [ 6 ] 5888335-6729406 | [ 2 ] 5047264-5888335 | [ 13 ] 4206193-5047264 | [ 12 ] 3365121-4206192 | [ 20 ] 2524050-3365121 | [ 33 ] 1682979-2524050 | [ 49 ] 841908-1682979 | [ 104 ] 837-841908 |************************************************** [ 6987 ] Storage Throughput = excellent ( 1028.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 47055805 bp ( 40010489 non ambiguous ) - Num Contigs Represented = 786 - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:44 (hh:mm:ss) Elapsed Time Round Time: 00:23:11 (hh:mm:ss) Elapsed Time : 521 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9375 repeats masked totaling 1332525 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11935257 bp Num Contigs Represented = 288 Non ambiguous bp: Initial: 10016390 bp After Masking: 8631020 bp Masked: 13.83 % -- Input Database Coverage: 11935257 bp out of 830129318 bp ( 1.44 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 79003 Comparison Time: 00:07:02 (hh:mm:ss) Elapsed Time, 7594 HSPs Collected Number of families returned by RECON: 1465 Round Time: 00:07:48 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29453 repeats masked totaling 4148211 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 35160468 bp Num Contigs Represented = 640 Non ambiguous bp: Initial: 30033252 bp After Masking: 25732422 bp Masked: 14.32 % -- Input Database Coverage: 47095725 bp out of 830129318 bp ( 5.67 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 657231 Comparison Time: 00:38:51 (hh:mm:ss) Elapsed Time, 49620 HSPs Collected Number of families returned by RECON: 5130 Round Time: 00:41:54 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104119 repeats masked totaling 15391624 bp(s). - TE Masking time 00:01:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 107597925 bp Num Contigs Represented = 1429 Non ambiguous bp: Initial: 90028011 bp After Masking: 74176502 bp Masked: 17.61 % -- Input Database Coverage: 154693650 bp out of 830129318 bp ( 18.63 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 6133753 Comparison Time: 04:44:52 (hh:mm:ss) Elapsed Time, 243923 HSPs Collected Number of families returned by RECON: 17837 Round Time: 05:02:59 (hh:mm:ss) Elapsed Time : 460 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 380482 repeats masked totaling 58034398 bp(s). - TE Masking time 00:09:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 320574826 bp Num Contigs Represented = 3231 Non ambiguous bp: Initial: 270038584 bp After Masking: 210657228 bp Masked: 21.99 % -- Input Database Coverage: 475268476 bp out of 830129318 bp ( 57.25 % ) Sampling Time: 00:17:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 53587128 Comparison Time: 36:54:05 (hh:mm:ss) Elapsed Time, 643772 HSPs Collected Number of families returned by RECON: 68440 Round Time: 39:13:50 (hh:mm:ss) Elapsed Time : 1045 families discovered. RepeatScout/RECON discovery complete: 2165 families found Classification Time: 01:17:23 (hh:mm:ss) Elapsed Time Program Time: 46:47:05 (hh:mm:ss) Elapsed Time