RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qKOBrj/RM_2852.WedJun260142422024 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: 1719391362 Database = /dev/shm/rModeler.qKOBrj/GCF_028885655.2_NHGRI_mPonAbe1-v2.0_pri - Sequences = 30 - Bases = 3259870029 Storage Throughput = excellent ( 1112.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40277817 bp ( 40027807 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:11 (hh:mm:ss) Elapsed Time Round Time: 00:33:06 (hh:mm:ss) Elapsed Time : 243 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12633 repeats masked totaling 2940761 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080289 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000284 bp After Masking: 6059339 bp Masked: 39.41 % -- Input Database Coverage: 10080289 bp out of 3259870029 bp ( 0.31 % ) Sampling Time: 00:04:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 5792 HSPs Collected Number of families returned by RECON: 862 Round Time: 00:09:29 (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 : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38784 repeats masked totaling 8910513 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30197527 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30027522 bp After Masking: 18370547 bp Masked: 38.82 % -- Input Database Coverage: 40277816 bp out of 3259870029 bp ( 1.24 % ) Sampling Time: 00:11:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:26:11 (hh:mm:ss) Elapsed Time, 30356 HSPs Collected Number of families returned by RECON: 2586 Round Time: 00:38:57 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132183 repeats masked totaling 29967576 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90202923 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90000590 bp After Masking: 51881823 bp Masked: 42.35 % -- Input Database Coverage: 130480739 bp out of 3259870029 bp ( 4.00 % ) Sampling Time: 00:33:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:54:25 (hh:mm:ss) Elapsed Time, 120875 HSPs Collected Number of families returned by RECON: 7928 Round Time: 03:39:26 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:20:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 435368 repeats masked totaling 99619810 bp(s). - TE Masking time 00:07:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270970616 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270010708 bp After Masking: 145001787 bp Masked: 46.30 % -- Input Database Coverage: 401451355 bp out of 3259870029 bp ( 12.31 % ) Sampling Time: 01:42:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 21:33:41 (hh:mm:ss) Elapsed Time, 331304 HSPs Collected Number of families returned by RECON: 30305 Round Time: 23:41:47 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 885 families found Classification Time: 00:44:04 (hh:mm:ss) Elapsed Time Program Time: 29:26:49 (hh:mm:ss) Elapsed Time