RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.xVV85S/RM_2410077.MonDec91030282024 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: 1733769028 Database = /scratch/tmp/rModeler.xVV85S/GCA_042242125.1_fPemKlu1.hap2 - Sequences = 84 - Bases = 632781980 Storage Throughput = excellent ( 1503.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013984 bp ( 40012784 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:43 (hh:mm:ss) Elapsed Time Round Time: 00:10:58 (hh:mm:ss) Elapsed Time : 262 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4732 repeats masked totaling 658074 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007569 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10007169 bp After Masking: 8840741 bp Masked: 11.66 % -- Input Database Coverage: 10007569 bp out of 632781980 bp ( 1.58 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:02 (hh:mm:ss) Elapsed Time, 16712 HSPs Collected Number of families returned by RECON: 1424 Round Time: 00:03:46 (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 : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16156 repeats masked totaling 2487906 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006402 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30005602 bp After Masking: 26394439 bp Masked: 12.03 % -- Input Database Coverage: 40013971 bp out of 632781980 bp ( 6.32 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:14:17 (hh:mm:ss) Elapsed Time, 73644 HSPs Collected Number of families returned by RECON: 5910 Round Time: 00:16:30 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58650 repeats masked totaling 8951055 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024499 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90021699 bp After Masking: 77026291 bp Masked: 14.44 % -- Input Database Coverage: 130038470 bp out of 632781980 bp ( 20.55 % ) Sampling Time: 00:04:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:27:24 (hh:mm:ss) Elapsed Time, 292286 HSPs Collected Number of families returned by RECON: 21373 Round Time: 01:37:58 (hh:mm:ss) Elapsed Time : 380 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 233199 repeats masked totaling 37184571 bp(s). - TE Masking time 00:02:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017330 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 270008630 bp After Masking: 220627100 bp Masked: 18.29 % -- Input Database Coverage: 400055800 bp out of 632781980 bp ( 63.22 % ) Sampling Time: 00:14:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 10:27:22 (hh:mm:ss) Elapsed Time, 1491559 HSPs Collected Number of families returned by RECON: 86376 Round Time: 11:42:44 (hh:mm:ss) Elapsed Time : 1051 families discovered. RepeatScout/RECON discovery complete: 1794 families found Classification Time: 00:36:16 (hh:mm:ss) Elapsed Time Program Time: 14:28:12 (hh:mm:ss) Elapsed Time