RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BOlHOH/RM_15855.FriJul191931332024 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: 1721442689 Database = /dev/shm/rModeler.BOlHOH/GCF_015846415.1_ASM1584641v1 - Sequences = 51 - Bases = 607940176 Storage Throughput = excellent ( 1049.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009821 bp ( 40009121 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:23 (hh:mm:ss) Elapsed Time Round Time: 00:36:10 (hh:mm:ss) Elapsed Time : 729 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11741 repeats masked totaling 2219514 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001441 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001341 bp After Masking: 7586254 bp Masked: 24.15 % -- Input Database Coverage: 10001441 bp out of 607940176 bp ( 1.65 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:24:11 (hh:mm:ss) Elapsed Time, 11091 HSPs Collected Number of families returned by RECON: 1331 Round Time: 00:26:19 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36557 repeats masked totaling 6842355 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008300 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30007700 bp After Masking: 22471895 bp Masked: 25.11 % -- Input Database Coverage: 40009741 bp out of 607940176 bp ( 6.58 % ) Sampling Time: 00:03:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 01:20:41 (hh:mm:ss) Elapsed Time, 60571 HSPs Collected Number of families returned by RECON: 4904 Round Time: 01:27:05 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116924 repeats masked totaling 21454822 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023980 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90021980 bp After Masking: 66369315 bp Masked: 26.27 % -- Input Database Coverage: 130033721 bp out of 607940176 bp ( 21.39 % ) Sampling Time: 00:09:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 05:55:43 (hh:mm:ss) Elapsed Time, 313758 HSPs Collected Number of families returned by RECON: 15030 Round Time: 06:24:39 (hh:mm:ss) Elapsed Time : 558 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 432466 repeats masked totaling 82789949 bp(s). - TE Masking time 00:15:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020124 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270014819 bp After Masking: 181004387 bp Masked: 32.97 % -- Input Database Coverage: 400053845 bp out of 607940176 bp ( 65.80 % ) Sampling Time: 00:36:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 29:47:53 (hh:mm:ss) Elapsed Time, 842264 HSPs Collected Number of families returned by RECON: 47968 Round Time: 31:57:50 (hh:mm:ss) Elapsed Time : 1236 families discovered. RepeatScout/RECON discovery complete: 2647 families found Classification Time: 02:21:19 (hh:mm:ss) Elapsed Time Program Time: 43:13:22 (hh:mm:ss) Elapsed Time