RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4PrLu1/RM_2698974.MonApr211259302025 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: 1745265569 Database = /dev/shm/rModeler.4PrLu1/GCA_965194805.1_mBalBor1.hap1.1 - Sequences = 2572 - Bases = 3234573494 - N50 = 120409621 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 181591738-194562506 | [ 3 ] 168620971-181591738 | [ ] 155650204-168620971 | [ ] 142679437-155650204 | [ 2 ] 129708670-142679437 | [ 3 ] 116737903-129708670 | [ 3 ] 103767136-116737903 | [ 3 ] 90796369-103767136 | [ 2 ] 77825602-90796369 | [ 3 ] 64854835-77825602 | [ 1 ] 51884068-64854835 | [ 1 ] 38913301-51884068 | [ ] 25942534-38913301 | [ 1 ] 12971767-25942534 | [ ] 1000-12971767 |************************************************** [ 2550 ] Storage Throughput = excellent ( 1772.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039409 bp ( 40037409 non ambiguous ) - Num Contigs Represented = 207 - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:55 (hh:mm:ss) Elapsed Time Round Time: 00:17:40 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9358 repeats masked totaling 3843090 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035925 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10035525 bp After Masking: 5762892 bp Masked: 42.58 % -- Input Database Coverage: 10035925 bp out of 3234573494 bp ( 0.31 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:48 (hh:mm:ss) Elapsed Time, 7487 HSPs Collected Number of families returned by RECON: 732 Round Time: 00:03:41 (hh:mm:ss) Elapsed Time : 17 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 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29919 repeats masked totaling 12477978 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003404 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 30001804 bp After Masking: 16036998 bp Masked: 46.55 % -- Input Database Coverage: 40039329 bp out of 3234573494 bp ( 1.24 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:11:13 (hh:mm:ss) Elapsed Time, 47024 HSPs Collected Number of families returned by RECON: 2136 Round Time: 00:13:44 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99358 repeats masked totaling 39200440 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021793 bp Num Contigs Represented = 432 Non ambiguous bp: Initial: 90016393 bp After Masking: 47155521 bp Masked: 47.61 % -- Input Database Coverage: 130061122 bp out of 3234573494 bp ( 4.02 % ) Sampling Time: 00:06:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2618616 Comparison Time: 01:00:33 (hh:mm:ss) Elapsed Time, 200536 HSPs Collected Number of families returned by RECON: 6668 Round Time: 01:10:05 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 334153 repeats masked totaling 126372632 bp(s). - TE Masking time 00:02:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270054115 bp Num Contigs Represented = 913 Non ambiguous bp: Initial: 270036752 bp After Masking: 131357859 bp Masked: 51.36 % -- Input Database Coverage: 400115237 bp out of 3234573494 bp ( 12.37 % ) Sampling Time: 00:21:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23588146 Comparison Time: 06:35:31 (hh:mm:ss) Elapsed Time, 3056954 HSPs Collected Number of families returned by RECON: 23689 Round Time: 07:02:13 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatScout/RECON discovery complete: 735 families found Classification Time: 00:17:23 (hh:mm:ss) Elapsed Time Program Time: 09:04:46 (hh:mm:ss) Elapsed Time