RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.khFAHy/RM_3250125.ThuApr101848382025 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: 1744336116 Database = /dev/shm/rModeler.khFAHy/GCA_965140295.1_rLepOli2.hap1 - Sequences = 44 - Bases = 2206585630 Storage Throughput = excellent ( 1662.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007252 bp ( 40007152 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:39 (hh:mm:ss) Elapsed Time Round Time: 00:11:29 (hh:mm:ss) Elapsed Time : 533 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13198 repeats masked totaling 2981927 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000585 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000585 bp After Masking: 6912856 bp Masked: 30.88 % -- Input Database Coverage: 10000585 bp out of 2206585630 bp ( 0.45 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 13660 HSPs Collected Number of families returned by RECON: 1547 Round Time: 00:03:50 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (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... 42960 repeats masked totaling 9594849 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006665 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30006565 bp After Masking: 19899237 bp Masked: 33.68 % -- Input Database Coverage: 40007250 bp out of 2206585630 bp ( 1.81 % ) Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:24 (hh:mm:ss) Elapsed Time, 63051 HSPs Collected Number of families returned by RECON: 4978 Round Time: 00:15:17 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149096 repeats masked totaling 32611431 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023452 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90022939 bp After Masking: 56061417 bp Masked: 37.73 % -- Input Database Coverage: 130030702 bp out of 2206585630 bp ( 5.89 % ) Sampling Time: 00:06:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:05:59 (hh:mm:ss) Elapsed Time, 265705 HSPs Collected Number of families returned by RECON: 13340 Round Time: 01:16:47 (hh:mm:ss) Elapsed Time : 425 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 514309 repeats masked totaling 112420607 bp(s). - TE Masking time 00:03:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270139137 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270031759 bp After Masking: 152847943 bp Masked: 43.40 % -- Input Database Coverage: 400169839 bp out of 2206585630 bp ( 18.14 % ) Sampling Time: 00:20:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 06:56:59 (hh:mm:ss) Elapsed Time, 610039 HSPs Collected Number of families returned by RECON: 43467 Round Time: 07:42:05 (hh:mm:ss) Elapsed Time : 1028 families discovered. RepeatScout/RECON discovery complete: 2168 families found Classification Time: 00:40:14 (hh:mm:ss) Elapsed Time Program Time: 10:09:42 (hh:mm:ss) Elapsed Time