RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jP3OTR/RM_3650521.ThuApr171158032025 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: 1744916282 Database = /dev/shm/rModeler.jP3OTR/GCA_964417125.1_bLarArg3.hap2.1 - Sequences = 533 - Bases = 1256866793 - N50 = 130187588 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 205097219-219746949 | [ 1 ] 190447489-205097218 | [ ] 175797759-190447488 | [ ] 161148029-175797758 | [ 1 ] 146498299-161148028 | [ ] 131848569-146498298 | [ ] 117198839-131848568 | [ 1 ] 102549109-117198838 | [ ] 87899379-102549108 | [ 1 ] 73249649-87899378 | [ 2 ] 58599919-73249648 | [ 1 ] 43950189-58599918 | [ 2 ] 29300459-43950188 | [ 1 ] 14650729-29300458 | [ 4 ] 1000-14650729 |************************************************* [ 519 ] Storage Throughput = excellent ( 1654.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039132 bp ( 40035949 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:07 (hh:mm:ss) Elapsed Time Round Time: 00:12:03 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3995 repeats masked totaling 1001580 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026037 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10025054 bp After Masking: 8359669 bp Masked: 16.61 % -- Input Database Coverage: 10026037 bp out of 1256866793 bp ( 0.80 % ) Sampling Time: 00:00:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:03 (hh:mm:ss) Elapsed Time, 503 HSPs Collected Number of families returned by RECON: 193 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12226 repeats masked totaling 3130240 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013015 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30010815 bp After Masking: 25768651 bp Masked: 14.14 % -- Input Database Coverage: 40039052 bp out of 1256866793 bp ( 3.19 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:14:19 (hh:mm:ss) Elapsed Time, 8581 HSPs Collected Number of families returned by RECON: 1224 Round Time: 00:16:09 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40182 repeats masked totaling 10669923 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026968 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 90020615 bp After Masking: 75247021 bp Masked: 16.41 % -- Input Database Coverage: 130066020 bp out of 1256866793 bp ( 10.35 % ) Sampling Time: 00:04:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 01:26:01 (hh:mm:ss) Elapsed Time, 39915 HSPs Collected Number of families returned by RECON: 6887 Round Time: 01:56:11 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121530 repeats masked totaling 34171409 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026579 bp Num Contigs Represented = 259 Non ambiguous bp: Initial: 270008515 bp After Masking: 220870974 bp Masked: 18.20 % -- Input Database Coverage: 400092599 bp out of 1256866793 bp ( 31.83 % ) Sampling Time: 00:14:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 10:21:26 (hh:mm:ss) Elapsed Time, 162898 HSPs Collected Number of families returned by RECON: 43021 Round Time: 10:48:16 (hh:mm:ss) Elapsed Time : 189 families discovered. RepeatScout/RECON discovery complete: 328 families found Classification Time: 00:14:41 (hh:mm:ss) Elapsed Time Program Time: 13:30:59 (hh:mm:ss) Elapsed Time