RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gCBPzP/RM_2938730.MonJul80259252024 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: 1720432764 Database = /dev/shm/rModeler.gCBPzP/GCF_031168955.1_ASM3116895v1 - Sequences = 24 - Bases = 555697652 Storage Throughput = good ( 855.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045335 bp ( 40014235 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:50 (hh:mm:ss) Elapsed Time Round Time: 00:23:48 (hh:mm:ss) Elapsed Time : 660 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7374 repeats masked totaling 1572464 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041267 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10033267 bp After Masking: 7398745 bp Masked: 26.26 % -- Input Database Coverage: 10041267 bp out of 555697652 bp ( 1.81 % ) Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 5076 HSPs Collected Number of families returned by RECON: 1215 Round Time: 00:08:11 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23899 repeats masked totaling 5374837 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30043922 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30020822 bp After Masking: 21558422 bp Masked: 28.19 % -- Input Database Coverage: 40085189 bp out of 555697652 bp ( 7.21 % ) Sampling Time: 00:06:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:27:55 (hh:mm:ss) Elapsed Time, 44979 HSPs Collected Number of families returned by RECON: 4293 Round Time: 00:35:18 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74355 repeats masked totaling 15799836 bp(s). - TE Masking time 00:02:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90090747 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90008957 bp After Masking: 64593326 bp Masked: 28.24 % -- Input Database Coverage: 130175936 bp out of 555697652 bp ( 23.43 % ) Sampling Time: 00:18:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:59:39 (hh:mm:ss) Elapsed Time, 306949 HSPs Collected Number of families returned by RECON: 15277 Round Time: 03:28:12 (hh:mm:ss) Elapsed Time : 477 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 279686 repeats masked totaling 63142193 bp(s). - TE Masking time 00:10:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270258051 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270027662 bp After Masking: 177829920 bp Masked: 34.14 % -- Input Database Coverage: 400433987 bp out of 555697652 bp ( 72.06 % ) Sampling Time: 00:56:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 21:23:50 (hh:mm:ss) Elapsed Time, 1042194 HSPs Collected Number of families returned by RECON: 52096 Round Time: 23:26:53 (hh:mm:ss) Elapsed Time : 1243 families discovered. RepeatScout/RECON discovery complete: 2447 families found Classification Time: 02:05:07 (hh:mm:ss) Elapsed Time Program Time: 30:07:29 (hh:mm:ss) Elapsed Time