RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.t6Qwol/RM_2806398.WedApr231932152025 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: 1745461934 Database = /dev/shm/rModeler.t6Qwol/GCA_048771875.1_mCteGun2.hap1 - Sequences = 535 - Bases = 2184404205 - N50 = 113086689 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195152147-209091037 | [ 1 ] 181213257-195152146 | [ ] 167274367-181213256 | [ ] 153335477-167274366 | [ ] 139396587-153335476 | [ 2 ] 125457697-139396586 | [ 1 ] 111518807-125457696 | [ 3 ] 97579918-111518807 | [ 3 ] 83641028-97579917 | [ 4 ] 69702138-83641027 | [ 4 ] 55763248-69702137 | [ 1 ] 41824358-55763247 | [ 1 ] 27885468-41824357 | [ ] 13946578-27885467 | [ ] 7689-13946578 |************************************************** [ 515 ] Storage Throughput = excellent ( 1897.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000495 bp ( 40000395 non ambiguous ) - Num Contigs Represented = 57 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:18 (hh:mm:ss) Elapsed Time Round Time: 00:10:26 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12893 repeats masked totaling 2339076 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024427 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10024427 bp After Masking: 7602887 bp Masked: 24.16 % -- Input Database Coverage: 10024427 bp out of 2184404205 bp ( 0.46 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 6908 HSPs Collected Number of families returned by RECON: 507 Round Time: 00:03:43 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:52 (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... 41051 repeats masked totaling 7439716 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015988 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30015888 bp After Masking: 22214992 bp Masked: 25.99 % -- Input Database Coverage: 40040415 bp out of 2184404205 bp ( 1.83 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:13:26 (hh:mm:ss) Elapsed Time, 33457 HSPs Collected Number of families returned by RECON: 2004 Round Time: 00:15:20 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132692 repeats masked totaling 24511641 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022329 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 90021629 bp After Masking: 64575180 bp Masked: 28.27 % -- Input Database Coverage: 130062744 bp out of 2184404205 bp ( 5.95 % ) Sampling Time: 00:04:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:19:20 (hh:mm:ss) Elapsed Time, 331629 HSPs Collected Number of families returned by RECON: 7084 Round Time: 01:25:27 (hh:mm:ss) Elapsed Time : 126 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 433211 repeats masked totaling 78632445 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270029042 bp Num Contigs Represented = 201 Non ambiguous bp: Initial: 270026742 bp After Masking: 188738366 bp Masked: 30.10 % -- Input Database Coverage: 400091786 bp out of 2184404205 bp ( 18.32 % ) Sampling Time: 00:14:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 09:13:53 (hh:mm:ss) Elapsed Time, 2063560 HSPs Collected Number of families returned by RECON: 32176 Round Time: 09:37:04 (hh:mm:ss) Elapsed Time : 324 families discovered. RepeatScout/RECON discovery complete: 679 families found Classification Time: 00:18:38 (hh:mm:ss) Elapsed Time Program Time: 11:50:38 (hh:mm:ss) Elapsed Time