RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.o3VC7j/RM_1615999.MonApr221433182024 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: 1713821596 Database = /dev/shm/rModeler.o3VC7j/GCF_036323735.1_GRCr8 - Sequences = 76 - Bases = 2849581192 Storage Throughput = excellent ( 1229.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40080680 bp ( 40026033 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:47 (hh:mm:ss) Elapsed Time Round Time: 00:25:04 (hh:mm:ss) Elapsed Time : 328 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 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13093 repeats masked totaling 3352418 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040854 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10026207 bp After Masking: 6278566 bp Masked: 37.38 % -- Input Database Coverage: 10040854 bp out of 2849581192 bp ( 0.35 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:46 (hh:mm:ss) Elapsed Time, 3438 HSPs Collected Number of families returned by RECON: 588 Round Time: 00:07:47 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37505 repeats masked totaling 10114158 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30079750 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30039750 bp After Masking: 18445441 bp Masked: 38.60 % -- Input Database Coverage: 40120604 bp out of 2849581192 bp ( 1.41 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:57 (hh:mm:ss) Elapsed Time, 20506 HSPs Collected Number of families returned by RECON: 2183 Round Time: 00:32:07 (hh:mm:ss) Elapsed Time : 49 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120399 repeats masked totaling 32263892 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90163755 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90014539 bp After Masking: 54039735 bp Masked: 39.97 % -- Input Database Coverage: 130284359 bp out of 2849581192 bp ( 4.57 % ) Sampling Time: 00:13:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 07:59:53 (hh:mm:ss) Elapsed Time, 108970 HSPs Collected Number of families returned by RECON: 7248 Round Time: 08:20:54 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 409570 repeats masked totaling 104646648 bp(s). - TE Masking time 00:06:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270323693 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270022326 bp After Masking: 153068222 bp Masked: 43.31 % -- Input Database Coverage: 400608052 bp out of 2849581192 bp ( 14.06 % ) Sampling Time: 00:40:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 16:42:43 (hh:mm:ss) Elapsed Time, 275645 HSPs Collected Number of families returned by RECON: 28842 Round Time: 17:37:42 (hh:mm:ss) Elapsed Time : 406 families discovered. RepeatScout/RECON discovery complete: 965 families found Classification Time: 00:44:52 (hh:mm:ss) Elapsed Time Program Time: 27:48:27 (hh:mm:ss) Elapsed Time