RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uobwGb/RM_1286274.TueApr151805502025 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: 1744765548 Database = /dev/shm/rModeler.uobwGb/GCA_043880285.1_ASM4388028v1 - Sequences = 66 - Bases = 2390604663 Storage Throughput = excellent ( 1802.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015774 bp ( 40012554 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:31 (hh:mm:ss) Elapsed Time Round Time: 00:11:38 (hh:mm:ss) Elapsed Time : 273 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 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12129 repeats masked totaling 2996193 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028597 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10028097 bp After Masking: 6902641 bp Masked: 31.17 % -- Input Database Coverage: 10028597 bp out of 2390604663 bp ( 0.42 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:47 (hh:mm:ss) Elapsed Time, 11062 HSPs Collected Number of families returned by RECON: 821 Round Time: 00:03:45 (hh:mm:ss) Elapsed Time : 20 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 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37237 repeats masked totaling 9219187 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027177 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30024457 bp After Masking: 20450774 bp Masked: 31.89 % -- Input Database Coverage: 40055774 bp out of 2390604663 bp ( 1.68 % ) Sampling Time: 00:02:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:31 (hh:mm:ss) Elapsed Time, 18997 HSPs Collected Number of families returned by RECON: 2406 Round Time: 00:14:52 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123129 repeats masked totaling 30848386 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008158 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90005718 bp After Masking: 58209186 bp Masked: 35.33 % -- Input Database Coverage: 130063932 bp out of 2390604663 bp ( 5.44 % ) Sampling Time: 00:06:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:07:21 (hh:mm:ss) Elapsed Time, 84462 HSPs Collected Number of families returned by RECON: 8418 Round Time: 01:14:51 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 403546 repeats masked totaling 98897856 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043576 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270026196 bp After Masking: 168088145 bp Masked: 37.75 % -- Input Database Coverage: 400107508 bp out of 2390604663 bp ( 16.74 % ) Sampling Time: 00:18:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 07:57:39 (hh:mm:ss) Elapsed Time, 223675 HSPs Collected Number of families returned by RECON: 33992 Round Time: 08:25:27 (hh:mm:ss) Elapsed Time : 406 families discovered. RepeatScout/RECON discovery complete: 931 families found Classification Time: 00:21:59 (hh:mm:ss) Elapsed Time Program Time: 10:32:32 (hh:mm:ss) Elapsed Time