RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hBWs2I/RM_27257.TueJul21423472024 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: 1719955426 Database = /dev/shm/rModeler.hBWs2I/GCA_038024135.1_fCypVen1.hap2 - Sequences = 413 - Bases = 928717837 - N50 = 36068944 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 55170718-59110519 | [ 2 ] 51230917-55170717 | [ ] 47291116-51230916 | [ 1 ] 43351316-47291116 | [ 1 ] 39411515-43351315 | [ 1 ] 35471714-39411514 | [ 5 ] 31531913-35471713 | [ 5 ] 27592113-31531913 |* [ 8 ] 23652312-27592112 | [ ] 19712511-23652311 | [ 2 ] 15772710-19712510 | [ ] 11832910-15772710 | [ ] 7893109-11832909 | [ ] 3953308-7893108 | [ ] 13508-3953308 |************************************************** [ 388 ] Storage Throughput = excellent ( 1032.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044245 bp ( 40039045 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:02 (hh:mm:ss) Elapsed Time Round Time: 00:50:33 (hh:mm:ss) Elapsed Time : 855 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 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12954 repeats masked totaling 2749612 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035607 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10034607 bp After Masking: 5903047 bp Masked: 41.17 % -- Input Database Coverage: 10035607 bp out of 928717837 bp ( 1.08 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:34:32 (hh:mm:ss) Elapsed Time, 48715 HSPs Collected Number of families returned by RECON: 1393 Round Time: 00:39:49 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40088 repeats masked totaling 8475858 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008558 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30004358 bp After Masking: 17015500 bp Masked: 43.29 % -- Input Database Coverage: 40044165 bp out of 928717837 bp ( 4.31 % ) Sampling Time: 00:06:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 01:51:45 (hh:mm:ss) Elapsed Time, 52244 HSPs Collected Number of families returned by RECON: 4759 Round Time: 02:02:40 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128140 repeats masked totaling 26571561 bp(s). - TE Masking time 00:03:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035497 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 90023165 bp After Masking: 49768618 bp Masked: 44.72 % -- Input Database Coverage: 130079662 bp out of 928717837 bp ( 14.01 % ) Sampling Time: 00:20:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 06:51:28 (hh:mm:ss) Elapsed Time, 321671 HSPs Collected Number of families returned by RECON: 14461 Round Time: 07:26:41 (hh:mm:ss) Elapsed Time : 594 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 452701 repeats masked totaling 92988780 bp(s). - TE Masking time 00:16:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270049325 bp Num Contigs Represented = 207 Non ambiguous bp: Initial: 270009827 bp After Masking: 135274150 bp Masked: 49.90 % -- Input Database Coverage: 400128987 bp out of 928717837 bp ( 43.08 % ) Sampling Time: 01:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 21:24:08 (hh:mm:ss) Elapsed Time, 1486212 HSPs Collected Number of families returned by RECON: 42232 Round Time: 23:52:14 (hh:mm:ss) Elapsed Time : 1294 families discovered. RepeatScout/RECON discovery complete: 2877 families found Classification Time: 02:03:00 (hh:mm:ss) Elapsed Time Program Time: 36:54:57 (hh:mm:ss) Elapsed Time