RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rQArpm/RM_1125055.WedJul171454172024 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: 1721253252 Database = /dev/shm/rModeler.rQArpm/GCF_024256425.1_CGAR_prim_01v2 - Sequences = 48 - Bases = 969620777 Storage Throughput = good ( 832.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000480 bp ( 40000480 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:34 (hh:mm:ss) Elapsed Time Round Time: 00:29:46 (hh:mm:ss) Elapsed Time : 679 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15449 repeats masked totaling 2764881 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032138 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10032138 bp After Masking: 6850128 bp Masked: 31.72 % -- Input Database Coverage: 10032138 bp out of 969620777 bp ( 1.03 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:24:02 (hh:mm:ss) Elapsed Time, 6054 HSPs Collected Number of families returned by RECON: 1309 Round Time: 00:26:22 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47462 repeats masked totaling 8924868 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008263 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30008263 bp After Masking: 19638074 bp Masked: 34.56 % -- Input Database Coverage: 40040401 bp out of 969620777 bp ( 4.13 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 01:17:03 (hh:mm:ss) Elapsed Time, 49637 HSPs Collected Number of families returned by RECON: 4960 Round Time: 01:24:40 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155211 repeats masked totaling 28229491 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025662 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90025662 bp After Masking: 58469544 bp Masked: 35.05 % -- Input Database Coverage: 130066063 bp out of 969620777 bp ( 13.41 % ) Sampling Time: 00:10:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 11:51:40 (hh:mm:ss) Elapsed Time, 274447 HSPs Collected Number of families returned by RECON: 16191 Round Time: 13:26:29 (hh:mm:ss) Elapsed Time : 494 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 541504 repeats masked totaling 101618413 bp(s). - TE Masking time 00:12:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023301 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 270023301 bp After Masking: 157926072 bp Masked: 41.51 % -- Input Database Coverage: 400089364 bp out of 969620777 bp ( 41.26 % ) Sampling Time: 00:39:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 36:16:55 (hh:mm:ss) Elapsed Time, 817289 HSPs Collected Number of families returned by RECON: 52550 Round Time: 38:19:02 (hh:mm:ss) Elapsed Time : 1050 families discovered. RepeatScout/RECON discovery complete: 2339 families found Classification Time: 01:43:22 (hh:mm:ss) Elapsed Time Program Time: 55:49:41 (hh:mm:ss) Elapsed Time