RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.RAgzN4/RM_2725066.TueMar41041262025 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: 1741113685 Database = /data/tmp/rModeler.RAgzN4/GCA_048127205.1_SpiSpi1_v1.hap2 - Sequences = 52 - Bases = 406020468 Storage Throughput = excellent ( 1114.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022793 bp ( 40020593 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:29 (hh:mm:ss) Elapsed Time Round Time: 00:12:52 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1683 repeats masked totaling 245889 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003141 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10002641 bp After Masking: 8824506 bp Masked: 11.78 % -- Input Database Coverage: 10003141 bp out of 406020468 bp ( 2.46 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:04 (hh:mm:ss) Elapsed Time, 3582 HSPs Collected Number of families returned by RECON: 842 Round Time: 00:05:26 (hh:mm:ss) Elapsed Time : 4 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 00:02:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5497 repeats masked totaling 872713 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019572 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30017872 bp After Masking: 26934761 bp Masked: 10.27 % -- Input Database Coverage: 40022713 bp out of 406020468 bp ( 9.86 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:17:03 (hh:mm:ss) Elapsed Time, 31503 HSPs Collected Number of families returned by RECON: 3829 Round Time: 00:19:56 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20642 repeats masked totaling 3292793 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008155 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90001455 bp After Masking: 79763273 bp Masked: 11.38 % -- Input Database Coverage: 130030868 bp out of 406020468 bp ( 32.03 % ) Sampling Time: 00:07:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:54:47 (hh:mm:ss) Elapsed Time, 176329 HSPs Collected Number of families returned by RECON: 16385 Round Time: 02:06:10 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92801 repeats masked totaling 15757443 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028006 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 270009806 bp After Masking: 233223706 bp Masked: 13.62 % -- Input Database Coverage: 400058874 bp out of 406020468 bp ( 98.53 % ) Sampling Time: 00:25:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 13:28:41 (hh:mm:ss) Elapsed Time, 919416 HSPs Collected Number of families returned by RECON: 72472 Round Time: 14:48:37 (hh:mm:ss) Elapsed Time : 587 families discovered. RepeatScout/RECON discovery complete: 983 families found Classification Time: 00:23:32 (hh:mm:ss) Elapsed Time Program Time: 17:56:33 (hh:mm:ss) Elapsed Time