RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Ba40Tv/RM_102021.SunJan150826342023 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: 1673799992 Database = /dev/shm/rModeler.Ba40Tv/GCF_009769535.1_rThaEle1.pri - Sequences = 365 - Bases = 1672190305 - N50 = 142845885 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 174276995-186725308 | [ 2 ] 161828682-174276994 | [ ] 149380369-161828681 | [ 1 ] 136932056-149380368 | [ 2 ] 124483744-136932056 | [ ] 112035431-124483743 | [ ] 99587118-112035430 | [ 1 ] 87138805-99587117 | [ 1 ] 74690492-87138804 | [ 3 ] 62242180-74690492 | [ 2 ] 49793867-62242179 | [ 2 ] 37345554-49793866 | [ 3 ] 24897241-37345553 | [ ] 12448928-24897240 | [ 1 ] 616-12448928 |************************************************** [ 347 ] Storage Throughput = excellent ( 1690.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40851939 bp ( 40006044 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:21 (hh:mm:ss) Elapsed Time Round Time: 00:18:29 (hh:mm:ss) Elapsed Time : 688 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18682 repeats masked totaling 3742052 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10270967 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10029046 bp After Masking: 5951706 bp Masked: 40.66 % -- Input Database Coverage: 10270967 bp out of 1672190305 bp ( 0.61 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:06:30 (hh:mm:ss) Elapsed Time, 10016 HSPs Collected Number of families returned by RECON: 991 Round Time: 00:08:21 (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 : 00:01:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59665 repeats masked totaling 12023373 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30620963 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30016989 bp After Masking: 16951830 bp Masked: 43.53 % -- Input Database Coverage: 40891930 bp out of 1672190305 bp ( 2.45 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:24:43 (hh:mm:ss) Elapsed Time, 33786 HSPs Collected Number of families returned by RECON: 3120 Round Time: 00:29:28 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 184295 repeats masked totaling 36706825 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91667405 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90009920 bp After Masking: 50510272 bp Masked: 43.88 % -- Input Database Coverage: 132559335 bp out of 1672190305 bp ( 7.93 % ) Sampling Time: 00:11:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 02:06:25 (hh:mm:ss) Elapsed Time, 168473 HSPs Collected Number of families returned by RECON: 9753 Round Time: 02:21:59 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 603573 repeats masked totaling 119577137 bp(s). - TE Masking time 00:05:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276127812 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 270010699 bp After Masking: 142308850 bp Masked: 47.30 % -- Input Database Coverage: 408687147 bp out of 1672190305 bp ( 24.44 % ) Sampling Time: 00:40:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24050580 Comparison Time: 13:39:50 (hh:mm:ss) Elapsed Time, 534254 HSPs Collected Number of families returned by RECON: 32825 Round Time: 14:47:00 (hh:mm:ss) Elapsed Time : 829 families discovered. RepeatScout/RECON discovery complete: 1960 families found Classification Time: 00:51:20 (hh:mm:ss) Elapsed Time Program Time: 18:56:37 (hh:mm:ss) Elapsed Time