RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.H1kX4h/RM_108359.FriJan61220572023 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: 1673036456 Database = /dev/shm/rModeler.H1kX4h/GCA_009769525.1_bPteGut1.pri - Sequences = 89 - Bases = 1127422757 Storage Throughput = excellent ( 1224.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40168980 bp ( 40027218 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:08 (hh:mm:ss) Elapsed Time Round Time: 00:26:00 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1500 repeats masked totaling 586795 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043420 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10002795 bp After Masking: 9378528 bp Masked: 6.24 % -- Input Database Coverage: 10043420 bp out of 1127422757 bp ( 0.89 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:52 (hh:mm:ss) Elapsed Time, 733 HSPs Collected Number of families returned by RECON: 211 Round Time: 00:08:52 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4973 repeats masked totaling 1889135 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30125480 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30024343 bp After Masking: 27946331 bp Masked: 6.92 % -- Input Database Coverage: 40168900 bp out of 1127422757 bp ( 3.56 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:39:45 (hh:mm:ss) Elapsed Time, 5807 HSPs Collected Number of families returned by RECON: 1537 Round Time: 00:43:25 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15818 repeats masked totaling 6049229 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90339021 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90038103 bp After Masking: 83525331 bp Masked: 7.23 % -- Input Database Coverage: 130507921 bp out of 1127422757 bp ( 11.58 % ) Sampling Time: 00:06:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 04:54:16 (hh:mm:ss) Elapsed Time, 32023 HSPs Collected Number of families returned by RECON: 9417 Round Time: 05:04:05 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53289 repeats masked totaling 19569483 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270990574 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270039489 bp After Masking: 248634268 bp Masked: 7.93 % -- Input Database Coverage: 401498495 bp out of 1127422757 bp ( 35.61 % ) Sampling Time: 00:23:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 34:14:53 (hh:mm:ss) Elapsed Time, 221815 HSPs Collected Number of families returned by RECON: 63492 Round Time: 35:34:10 (hh:mm:ss) Elapsed Time : 198 families discovered. RepeatScout/RECON discovery complete: 295 families found Classification Time: 00:20:26 (hh:mm:ss) Elapsed Time Program Time: 42:16:58 (hh:mm:ss) Elapsed Time