RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kb78bq/RM_5407.SunJan140154202024 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: 1705226058 Database = /dev/shm/rModeler.kb78bq/GCA_031893025.1_aLepFus1.hap1 - Sequences = 2266 - Bases = 2307711212 - N50 = 258304867 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 348941299-373864851 | [ 1 ] 324017748-348941299 | [ ] 299094197-324017748 | [ ] 274170646-299094197 | [ 1 ] 249247095-274170646 | [ 1 ] 224323543-249247094 | [ 2 ] 199399992-224323543 | [ ] 174476441-199399992 | [ 1 ] 149552890-174476441 | [ 1 ] 124629339-149552890 | [ ] 99705787-124629338 | [ ] 74782236-99705787 | [ 4 ] 49858685-74782236 | [ ] 24935134-49858685 | [ ] 11583-24935134 |************************************************** [ 2255 ] Storage Throughput = excellent ( 1121.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40186321 bp ( 40019732 non ambiguous ) - Num Contigs Represented = 120 - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:27 (hh:mm:ss) Elapsed Time Round Time: 00:52:04 (hh:mm:ss) Elapsed Time : 624 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15605 repeats masked totaling 3327354 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10059852 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10007971 bp After Masking: 4538074 bp Masked: 54.66 % -- Input Database Coverage: 10059852 bp out of 2307711212 bp ( 0.44 % ) Sampling Time: 00:07:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:10:59 (hh:mm:ss) Elapsed Time, 102427 HSPs Collected Number of families returned by RECON: 1340 Round Time: 00:19:44 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49152 repeats masked totaling 10179826 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30126389 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 30011681 bp After Masking: 12829326 bp Masked: 57.25 % -- Input Database Coverage: 40186241 bp out of 2307711212 bp ( 1.74 % ) Sampling Time: 00:20:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299151 Comparison Time: 00:29:00 (hh:mm:ss) Elapsed Time, 426356 HSPs Collected Number of families returned by RECON: 4116 Round Time: 00:51:48 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:10:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168173 repeats masked totaling 33941348 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90406857 bp Num Contigs Represented = 220 Non ambiguous bp: Initial: 90035344 bp After Masking: 37311730 bp Masked: 58.56 % -- Input Database Coverage: 130593098 bp out of 2307711212 bp ( 5.66 % ) Sampling Time: 00:53:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2650753 Comparison Time: 02:56:22 (hh:mm:ss) Elapsed Time, 2598988 HSPs Collected Number of families returned by RECON: 11339 Round Time: 04:01:22 (hh:mm:ss) Elapsed Time : 440 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:30:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:11:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 568235 repeats masked totaling 113845001 bp(s). - TE Masking time 00:09:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271330143 bp Num Contigs Represented = 589 Non ambiguous bp: Initial: 270036499 bp After Masking: 98285725 bp Masked: 63.60 % -- Input Database Coverage: 401923241 bp out of 2307711212 bp ( 17.42 % ) Sampling Time: 02:52:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23849871 Comparison Time: 20:50:34 (hh:mm:ss) Elapsed Time, 21940977 HSPs Collected Number of families returned by RECON: 30194 Round Time: 24:46:08 (hh:mm:ss) Elapsed Time : 999 families discovered. RepeatScout/RECON discovery complete: 2238 families found Classification Time: 01:20:46 (hh:mm:ss) Elapsed Time Program Time: 32:11:52 (hh:mm:ss) Elapsed Time