RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Nj2wS3/RM_5771.FriJan131436242023 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: 1673649383 Database = /dev/shm/rModeler.Nj2wS3/GCF_008692025.1_mPhoSin1.pri - Sequences = 64 - Bases = 2371524154 Storage Throughput = excellent ( 1224.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40163276 bp ( 40038482 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:02:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:47 (hh:mm:ss) Elapsed Time Round Time: 00:35:49 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9211 repeats masked totaling 2700486 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040204 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001684 bp After Masking: 7253154 bp Masked: 27.48 % -- Input Database Coverage: 10040204 bp out of 2371524154 bp ( 0.42 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:42 (hh:mm:ss) Elapsed Time, 8260 HSPs Collected Number of families returned by RECON: 1010 Round Time: 00:08:32 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32620 repeats masked totaling 9282294 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30122992 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30036718 bp After Masking: 20622569 bp Masked: 31.34 % -- Input Database Coverage: 40163196 bp out of 2371524154 bp ( 1.69 % ) Sampling Time: 00:03:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:31:38 (hh:mm:ss) Elapsed Time, 27159 HSPs Collected Number of families returned by RECON: 2457 Round Time: 00:36:09 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109711 repeats masked totaling 31498030 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90402409 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90010949 bp After Masking: 58104281 bp Masked: 35.45 % -- Input Database Coverage: 130565605 bp out of 2371524154 bp ( 5.51 % ) Sampling Time: 00:10:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:15:55 (hh:mm:ss) Elapsed Time, 73917 HSPs Collected Number of families returned by RECON: 7984 Round Time: 03:30:31 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 358545 repeats masked totaling 99261722 bp(s). - TE Masking time 00:05:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271001182 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 270010749 bp After Masking: 169509191 bp Masked: 37.22 % -- Input Database Coverage: 401566787 bp out of 2371524154 bp ( 16.93 % ) Sampling Time: 00:31:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 24:50:20 (hh:mm:ss) Elapsed Time, 193603 HSPs Collected Number of families returned by RECON: 35623 Round Time: 25:51:30 (hh:mm:ss) Elapsed Time : 357 families discovered. RepeatScout/RECON discovery complete: 814 families found Classification Time: 00:29:30 (hh:mm:ss) Elapsed Time Program Time: 31:12:01 (hh:mm:ss) Elapsed Time