RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Qsly1R/RM_2757094.MonFeb242234172025 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: 1740465257 Database = /dev/shm/rModeler.Qsly1R/GCA_965140925.1_bAytMar2.hap2.1 - Sequences = 459 - Bases = 1053096367 - N50 = 120156277 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 192995037-206780326 | [ 1 ] 179209749-192995037 | [ ] 165424460-179209748 | [ ] 151639172-165424460 | [ 1 ] 137853884-151639172 | [ ] 124068595-137853883 | [ ] 110283307-124068595 | [ 1 ] 96498018-110283306 | [ ] 82712730-96498018 | [ ] 68927442-82712730 | [ 1 ] 55142153-68927441 | [ 1 ] 41356865-55142153 | [ ] 27571576-41356864 | [ 3 ] 13786288-27571576 |* [ 9 ] 1000-13786288 |************************************************** [ 442 ] Storage Throughput = excellent ( 1694.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023092 bp ( 40018692 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:58 (hh:mm:ss) Elapsed Time Round Time: 00:11:59 (hh:mm:ss) Elapsed Time : 70 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 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1966 repeats masked totaling 720232 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031651 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10030651 bp After Masking: 9166558 bp Masked: 8.61 % -- Input Database Coverage: 10031651 bp out of 1053096367 bp ( 0.95 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:03:46 (hh:mm:ss) Elapsed Time, 412 HSPs Collected Number of families returned by RECON: 268 Round Time: 00:04:35 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (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... 5357 repeats masked totaling 2044675 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031290 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30027890 bp After Masking: 27417265 bp Masked: 8.69 % -- Input Database Coverage: 40062941 bp out of 1053096367 bp ( 3.80 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:19:23 (hh:mm:ss) Elapsed Time, 4517 HSPs Collected Number of families returned by RECON: 1807 Round Time: 00:22:24 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17290 repeats masked totaling 6370485 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047878 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 90036789 bp After Masking: 81801807 bp Masked: 9.15 % -- Input Database Coverage: 130110819 bp out of 1053096367 bp ( 12.36 % ) Sampling Time: 00:08:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 02:08:19 (hh:mm:ss) Elapsed Time, 45981 HSPs Collected Number of families returned by RECON: 10977 Round Time: 02:18:15 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60703 repeats masked totaling 22283750 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042497 bp Num Contigs Represented = 220 Non ambiguous bp: Initial: 270015326 bp After Masking: 242030407 bp Masked: 10.36 % -- Input Database Coverage: 400153316 bp out of 1053096367 bp ( 38.00 % ) Sampling Time: 00:25:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 16:50:03 (hh:mm:ss) Elapsed Time, 291507 HSPs Collected Number of families returned by RECON: 69376 Round Time: 17:53:46 (hh:mm:ss) Elapsed Time : 198 families discovered. RepeatScout/RECON discovery complete: 334 families found Classification Time: 00:12:28 (hh:mm:ss) Elapsed Time Program Time: 21:03:27 (hh:mm:ss) Elapsed Time