RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gdLzTG/RM_9765.MonJan160602222023 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: 1673877741 Database = /dev/shm/rModeler.gdLzTG/GCF_014176215.1_mRouAeg1.p - Sequences = 29 - Bases = 1893602072 Storage Throughput = excellent ( 1127.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40920804 bp ( 40013347 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:02:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:53 (hh:mm:ss) Elapsed Time Round Time: 00:27:11 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6009 repeats masked totaling 1289864 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10320128 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10005983 bp After Masking: 8656238 bp Masked: 13.49 % -- Input Database Coverage: 10320128 bp out of 1893602072 bp ( 0.54 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:07:07 (hh:mm:ss) Elapsed Time, 7391 HSPs Collected Number of families returned by RECON: 1032 Round Time: 00:08:48 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23212 repeats masked totaling 5397977 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30600596 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30007284 bp After Masking: 24423421 bp Masked: 18.61 % -- Input Database Coverage: 40920724 bp out of 1893602072 bp ( 2.16 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:36:45 (hh:mm:ss) Elapsed Time, 29745 HSPs Collected Number of families returned by RECON: 2829 Round Time: 00:41:13 (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 : 00:06:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79338 repeats masked totaling 18220729 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91146912 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90014657 bp After Masking: 71255031 bp Masked: 20.84 % -- Input Database Coverage: 132067636 bp out of 1893602072 bp ( 6.97 % ) Sampling Time: 00:09:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 04:14:19 (hh:mm:ss) Elapsed Time, 81126 HSPs Collected Number of families returned by RECON: 9925 Round Time: 04:28:44 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 274224 repeats masked totaling 61956851 bp(s). - TE Masking time 00:04:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273757840 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270006652 bp After Masking: 206471415 bp Masked: 23.53 % -- Input Database Coverage: 405825476 bp out of 1893602072 bp ( 21.43 % ) Sampling Time: 00:31:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23430435 Comparison Time: 33:08:18 (hh:mm:ss) Elapsed Time, 284354 HSPs Collected Number of families returned by RECON: 41433 Round Time: 34:21:32 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 800 families found Classification Time: 00:31:36 (hh:mm:ss) Elapsed Time Program Time: 40:39:05 (hh:mm:ss) Elapsed Time