RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QXNeYz/RM_10198.MonJan150636422024 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: 1705329397 Database = /dev/shm/rModeler.QXNeYz/GCA_963455305.1_mPleAur1.1 - Sequences = 65 - Bases = 2163221563 Storage Throughput = excellent ( 1066.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011210 bp ( 40006361 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:03:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:29 (hh:mm:ss) Elapsed Time Round Time: 00:42:50 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16592 repeats masked totaling 2941780 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040093 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10038893 bp After Masking: 6885383 bp Masked: 31.41 % -- Input Database Coverage: 10040093 bp out of 2163221563 bp ( 0.46 % ) Sampling Time: 00:01:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:10:34 (hh:mm:ss) Elapsed Time, 5774 HSPs Collected Number of families returned by RECON: 870 Round Time: 00:12:38 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52161 repeats masked totaling 10001868 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010959 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30007310 bp After Masking: 19333046 bp Masked: 35.57 % -- Input Database Coverage: 40051052 bp out of 2163221563 bp ( 1.85 % ) Sampling Time: 00:05:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:32:55 (hh:mm:ss) Elapsed Time, 48363 HSPs Collected Number of families returned by RECON: 2430 Round Time: 01:11:34 (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 : 00:08:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164147 repeats masked totaling 31002207 bp(s). - TE Masking time 00:02:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029790 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90019552 bp After Masking: 56719814 bp Masked: 36.99 % -- Input Database Coverage: 130080842 bp out of 2163221563 bp ( 6.01 % ) Sampling Time: 00:15:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:23:42 (hh:mm:ss) Elapsed Time, 318962 HSPs Collected Number of families returned by RECON: 7923 Round Time: 03:44:05 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 525061 repeats masked totaling 99694784 bp(s). - TE Masking time 00:08:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062558 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270030982 bp After Masking: 163876218 bp Masked: 39.31 % -- Input Database Coverage: 400143400 bp out of 2163221563 bp ( 18.50 % ) Sampling Time: 00:49:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 26:36:29 (hh:mm:ss) Elapsed Time, 1606717 HSPs Collected Number of families returned by RECON: 34445 Round Time: 28:05:31 (hh:mm:ss) Elapsed Time : 488 families discovered. RepeatScout/RECON discovery complete: 1136 families found Classification Time: 00:50:39 (hh:mm:ss) Elapsed Time Program Time: 34:47:17 (hh:mm:ss) Elapsed Time