RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HUoEnr/RM_64283.FriApr250715402025 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: 1745590540 Database = /dev/shm/rModeler.HUoEnr/GCA_048537225.1_ASM4853722v1 - Sequences = 846 - Bases = 722757191 - N50 = 28970215 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 40117464-42982685 | [ 1 ] 37252244-40117464 | [ ] 34387024-37252244 | [ 2 ] 31521804-34387024 | [ 2 ] 28656584-31521804 | [ 6 ] 25791364-28656584 | [ 7 ] 22926144-25791364 | [ 1 ] 20060923-22926143 | [ 3 ] 17195703-20060923 | [ 1 ] 14330483-17195703 | [ 1 ] 11465263-14330483 | [ ] 8600043-11465263 | [ ] 5734823-8600043 | [ ] 2869603-5734823 | [ ] 4383-2869603 |************************************************* [ 822 ] Storage Throughput = excellent ( 1868.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016372 bp ( 40012172 non ambiguous ) - Num Contigs Represented = 104 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:16 (hh:mm:ss) Elapsed Time Round Time: 00:16:24 (hh:mm:ss) Elapsed Time : 542 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 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6160 repeats masked totaling 861918 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005453 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10004253 bp After Masking: 7740192 bp Masked: 22.63 % -- Input Database Coverage: 10005453 bp out of 722757191 bp ( 1.38 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 5216 HSPs Collected Number of families returned by RECON: 1446 Round Time: 00:04:22 (hh:mm:ss) Elapsed Time : 6 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 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20095 repeats masked totaling 3052805 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010891 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 30007891 bp After Masking: 22813700 bp Masked: 23.97 % -- Input Database Coverage: 40016344 bp out of 722757191 bp ( 5.54 % ) Sampling Time: 00:05:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:13:13 (hh:mm:ss) Elapsed Time, 54083 HSPs Collected Number of families returned by RECON: 5886 Round Time: 00:19:08 (hh:mm:ss) Elapsed Time : 109 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 00:18:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71933 repeats masked totaling 10713740 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026222 bp Num Contigs Represented = 189 Non ambiguous bp: Initial: 90015322 bp After Masking: 66408329 bp Masked: 26.23 % -- Input Database Coverage: 130042566 bp out of 722757191 bp ( 17.99 % ) Sampling Time: 00:20:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2659971 Comparison Time: 01:16:48 (hh:mm:ss) Elapsed Time, 287857 HSPs Collected Number of families returned by RECON: 18254 Round Time: 01:41:57 (hh:mm:ss) Elapsed Time : 533 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 284922 repeats masked totaling 45506493 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270072193 bp Num Contigs Represented = 446 Non ambiguous bp: Initial: 270035214 bp After Masking: 186547768 bp Masked: 30.92 % -- Input Database Coverage: 400114759 bp out of 722757191 bp ( 55.36 % ) Sampling Time: 00:56:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23953581 Comparison Time: 09:07:08 (hh:mm:ss) Elapsed Time, 943750 HSPs Collected Number of families returned by RECON: 64669 Round Time: 10:45:16 (hh:mm:ss) Elapsed Time : 1281 families discovered. RepeatScout/RECON discovery complete: 2471 families found Classification Time: 00:49:18 (hh:mm:ss) Elapsed Time Program Time: 13:56:25 (hh:mm:ss) Elapsed Time