RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lTJVdQ/RM_4052530.TueMay161803242023 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: 1684285403 Database = /dev/shm/rModeler.lTJVdQ/GCF_027406575.1_mNycCou1.pri - Sequences = 84 - Bases = 2917154053 Storage Throughput = excellent ( 1167.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043723 bp ( 40035371 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:42 (hh:mm:ss) Elapsed Time Round Time: 00:27:31 (hh:mm:ss) Elapsed Time : 264 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13675 repeats masked totaling 3375180 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041218 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10039250 bp After Masking: 6575449 bp Masked: 34.50 % -- Input Database Coverage: 10041218 bp out of 2917154053 bp ( 0.34 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 7360 HSPs Collected Number of families returned by RECON: 940 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43915 repeats masked totaling 10778033 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042427 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30036043 bp After Masking: 18985784 bp Masked: 36.79 % -- Input Database Coverage: 40083645 bp out of 2917154053 bp ( 1.37 % ) Sampling Time: 00:04:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:30:01 (hh:mm:ss) Elapsed Time, 29151 HSPs Collected Number of families returned by RECON: 2590 Round Time: 00:35:30 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 141496 repeats masked totaling 34151872 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90243076 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90008033 bp After Masking: 55187165 bp Masked: 38.69 % -- Input Database Coverage: 130326721 bp out of 2917154053 bp ( 4.47 % ) Sampling Time: 00:12:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:54:18 (hh:mm:ss) Elapsed Time, 110444 HSPs Collected Number of families returned by RECON: 8589 Round Time: 03:11:31 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 473673 repeats masked totaling 113166275 bp(s). - TE Masking time 00:07:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270567039 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 270015429 bp After Masking: 154899443 bp Masked: 42.63 % -- Input Database Coverage: 400893760 bp out of 2917154053 bp ( 13.74 % ) Sampling Time: 00:35:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 21:01:14 (hh:mm:ss) Elapsed Time, 249477 HSPs Collected Number of families returned by RECON: 32015 Round Time: 21:57:48 (hh:mm:ss) Elapsed Time : 449 families discovered. RepeatScout/RECON discovery complete: 1013 families found Classification Time: 00:47:51 (hh:mm:ss) Elapsed Time Program Time: 27:08:15 (hh:mm:ss) Elapsed Time