RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yQV5Ix/RM_3027782.SunJul201306552025 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: 1753042015 Database = /dev/shm/rModeler.yQV5Ix/GCA_965140265.1_rLepKem1.hap2 - Sequences = 88 - Bases = 2204769334 Storage Throughput = excellent ( 1752.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032822 bp ( 40031622 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:39 (hh:mm:ss) Elapsed Time Round Time: 00:12:04 (hh:mm:ss) Elapsed Time : 556 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14007 repeats masked totaling 3150409 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003122 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10002722 bp After Masking: 6684497 bp Masked: 33.17 % -- Input Database Coverage: 10003122 bp out of 2204769334 bp ( 0.45 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 11707 HSPs Collected Number of families returned by RECON: 1465 Round Time: 00:03:58 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45933 repeats masked totaling 9882534 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029695 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30028895 bp After Masking: 19781803 bp Masked: 34.12 % -- Input Database Coverage: 40032817 bp out of 2204769334 bp ( 1.82 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:01 (hh:mm:ss) Elapsed Time, 55045 HSPs Collected Number of families returned by RECON: 4536 Round Time: 00:14:46 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153786 repeats masked totaling 32912957 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021791 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90019391 bp After Masking: 55648903 bp Masked: 38.18 % -- Input Database Coverage: 130054608 bp out of 2204769334 bp ( 5.90 % ) Sampling Time: 00:06:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:04:46 (hh:mm:ss) Elapsed Time, 220472 HSPs Collected Number of families returned by RECON: 13233 Round Time: 01:15:24 (hh:mm:ss) Elapsed Time : 445 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 525850 repeats masked totaling 114485059 bp(s). - TE Masking time 00:03:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046654 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270039254 bp After Masking: 151453157 bp Masked: 43.91 % -- Input Database Coverage: 400101262 bp out of 2204769334 bp ( 18.15 % ) Sampling Time: 00:21:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 06:46:50 (hh:mm:ss) Elapsed Time, 667445 HSPs Collected Number of families returned by RECON: 41791 Round Time: 07:28:57 (hh:mm:ss) Elapsed Time : 988 families discovered. RepeatScout/RECON discovery complete: 2145 families found Classification Time: 00:41:57 (hh:mm:ss) Elapsed Time Program Time: 09:57:06 (hh:mm:ss) Elapsed Time