RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qRryK4/RM_667250.WedMar50158092025 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: 1741168689 Database = /dev/shm/rModeler.qRryK4/GCA_048164855.1_mCanLup2.hap1 - Sequences = 250 - Bases = 2495606587 - N50 = 65588690 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116887328-125236116 | [ 2 ] 108538540-116887327 | [ ] 100189752-108538539 | [ ] 91840964-100189751 | [ 1 ] 83492177-91840964 | [ 3 ] 75143389-83492176 |* [ 5 ] 66794601-75143388 | [ 2 ] 58445813-66794600 |* [ 8 ] 50097025-58445812 |* [ 5 ] 41748238-50097025 |* [ 8 ] 33399450-41748237 | [ 2 ] 25050662-33399449 | [ 3 ] 16701874-25050661 | [ ] 8353086-16701873 | [ 1 ] 4299-8353086 |************************************************** [ 210 ] Storage Throughput = excellent ( 1668.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020779 bp ( 40020579 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:25 (hh:mm:ss) Elapsed Time Round Time: 00:11:27 (hh:mm:ss) Elapsed Time : 197 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 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13546 repeats masked totaling 2734553 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021984 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10021984 bp After Masking: 7164329 bp Masked: 28.51 % -- Input Database Coverage: 10021984 bp out of 2495606587 bp ( 0.40 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:41 (hh:mm:ss) Elapsed Time, 5440 HSPs Collected Number of families returned by RECON: 847 Round Time: 00:03:20 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43186 repeats masked totaling 8113438 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038872 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30038672 bp After Masking: 21516739 bp Masked: 28.37 % -- Input Database Coverage: 40060856 bp out of 2495606587 bp ( 1.61 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:09 (hh:mm:ss) Elapsed Time, 25667 HSPs Collected Number of families returned by RECON: 2809 Round Time: 00:14:08 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142318 repeats masked totaling 27975869 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009943 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90008643 bp After Masking: 60668244 bp Masked: 32.60 % -- Input Database Coverage: 130070799 bp out of 2495606587 bp ( 5.21 % ) Sampling Time: 00:04:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:11:14 (hh:mm:ss) Elapsed Time, 58826 HSPs Collected Number of families returned by RECON: 8586 Round Time: 01:16:47 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 455999 repeats masked totaling 89757790 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015250 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 270011750 bp After Masking: 175938468 bp Masked: 34.84 % -- Input Database Coverage: 400086049 bp out of 2495606587 bp ( 16.03 % ) Sampling Time: 00:14:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 08:31:24 (hh:mm:ss) Elapsed Time, 204565 HSPs Collected Number of families returned by RECON: 37273 Round Time: 08:56:41 (hh:mm:ss) Elapsed Time : 346 families discovered. RepeatScout/RECON discovery complete: 761 families found Classification Time: 00:13:58 (hh:mm:ss) Elapsed Time Program Time: 10:56:21 (hh:mm:ss) Elapsed Time