RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kEdWl6/RM_303343.ThuApr241315022025 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: 1745525702 Database = /dev/shm/rModeler.kEdWl6/GCA_048593225.1_ASM4859322v1 - Sequences = 7 - Bases = 3244907618 Storage Throughput = excellent ( 1912.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40119998 bp ( 40015220 non ambiguous ) - Num Contigs Represented = 7 - Sequence extraction : 00:05:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:13 (hh:mm:ss) Elapsed Time Round Time: 00:19:29 (hh:mm:ss) Elapsed Time : 307 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14511 repeats masked totaling 3036447 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039946 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 10006885 bp After Masking: 6627664 bp Masked: 33.77 % -- Input Database Coverage: 10039946 bp out of 3244907618 bp ( 0.31 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 19501 HSPs Collected Number of families returned by RECON: 1456 Round Time: 00:05:16 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52275 repeats masked totaling 11465044 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30079972 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 30008255 bp After Masking: 17755720 bp Masked: 40.83 % -- Input Database Coverage: 40119918 bp out of 3244907618 bp ( 1.24 % ) Sampling Time: 00:05:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:28 (hh:mm:ss) Elapsed Time, 27145 HSPs Collected Number of families returned by RECON: 3434 Round Time: 00:18:21 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 171861 repeats masked totaling 37543359 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90440084 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 90020982 bp After Masking: 49961196 bp Masked: 44.50 % -- Input Database Coverage: 130560002 bp out of 3244907618 bp ( 4.02 % ) Sampling Time: 00:16:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:15:25 (hh:mm:ss) Elapsed Time, 88818 HSPs Collected Number of families returned by RECON: 10946 Round Time: 01:33:38 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:39:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 575435 repeats masked totaling 122600730 bp(s). - TE Masking time 00:02:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271600561 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 270032086 bp After Masking: 139451043 bp Masked: 48.36 % -- Input Database Coverage: 402160563 bp out of 3244907618 bp ( 12.39 % ) Sampling Time: 00:51:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 08:29:25 (hh:mm:ss) Elapsed Time, 276260 HSPs Collected Number of families returned by RECON: 36629 Round Time: 09:32:41 (hh:mm:ss) Elapsed Time : 440 families discovered. RepeatScout/RECON discovery complete: 1063 families found Classification Time: 00:18:18 (hh:mm:ss) Elapsed Time Program Time: 12:07:43 (hh:mm:ss) Elapsed Time