RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NZ85pC/RM_14176.WedJul170342222024 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: 1721212934 Database = /dev/shm/rModeler.NZ85pC/GCF_013103735.1_CSU_Ecrag_1.0 - Sequences = 4664 - Bases = 643078674 - N50 = 28644895 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32172035-34469967 | [ 1 ] 29874104-32172035 | [ 4 ] 27576173-29874104 | [ 6 ] 25278242-27576173 | [ 3 ] 22980311-25278242 | [ 5 ] 20682380-22980311 | [ 2 ] 18384449-20682380 | [ 2 ] 16086517-18384448 | [ ] 13788586-16086517 | [ ] 11490655-13788586 | [ 1 ] 9192724-11490655 | [ ] 6894793-9192724 | [ ] 4596862-6894793 | [ ] 2298931-4596862 | [ ] 1000-2298931 |************************************************** [ 4640 ] Storage Throughput = good ( 993.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40221681 bp ( 40002309 non ambiguous ) - Num Contigs Represented = 337 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:34 (hh:mm:ss) Elapsed Time Round Time: 00:37:29 (hh:mm:ss) Elapsed Time : 745 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11310 repeats masked totaling 1475856 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10090570 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 10029790 bp After Masking: 8220959 bp Masked: 18.03 % -- Input Database Coverage: 10090570 bp out of 643078674 bp ( 1.57 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 58653 Comparison Time: 00:44:04 (hh:mm:ss) Elapsed Time, 8967 HSPs Collected Number of families returned by RECON: 1836 Round Time: 00:46:30 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35407 repeats masked totaling 4583456 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30175647 bp Num Contigs Represented = 234 Non ambiguous bp: Initial: 30017045 bp After Masking: 24516817 bp Masked: 18.32 % -- Input Database Coverage: 40266217 bp out of 643078674 bp ( 6.26 % ) Sampling Time: 00:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 448878 Comparison Time: 02:18:02 (hh:mm:ss) Elapsed Time, 63962 HSPs Collected Number of families returned by RECON: 6253 Round Time: 02:27:46 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117180 repeats masked totaling 15744802 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90472395 bp Num Contigs Represented = 698 Non ambiguous bp: Initial: 90025143 bp After Masking: 71707651 bp Masked: 20.35 % -- Input Database Coverage: 130738612 bp out of 643078674 bp ( 20.33 % ) Sampling Time: 00:07:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4171716 Comparison Time: 07:54:28 (hh:mm:ss) Elapsed Time, 298639 HSPs Collected Number of families returned by RECON: 19530 Round Time: 08:28:51 (hh:mm:ss) Elapsed Time : 616 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 426898 repeats masked totaling 62685719 bp(s). - TE Masking time 00:11:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271396301 bp Num Contigs Represented = 2019 Non ambiguous bp: Initial: 270005530 bp After Masking: 199574353 bp Masked: 26.09 % -- Input Database Coverage: 402134913 bp out of 643078674 bp ( 62.53 % ) Sampling Time: 00:27:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37406925 Comparison Time: 50:36:25 (hh:mm:ss) Elapsed Time, 776691 HSPs Collected Number of families returned by RECON: 67447 Round Time: 53:40:24 (hh:mm:ss) Elapsed Time : 1421 families discovered. RepeatScout/RECON discovery complete: 2971 families found Classification Time: 01:35:07 (hh:mm:ss) Elapsed Time Program Time: 67:36:07 (hh:mm:ss) Elapsed Time