RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wzX8M7/RM_1258586.SatFeb80647072025 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: 1739026001 Database = /dev/shm/rModeler.wzX8M7/GCA_046255725.1_fAmbSpe1.hap2 - Sequences = 667 - Bases = 865090090 - N50 = 32944955 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 42539709-45577379 | [ 1 ] 39502039-42539708 | [ ] 36464370-39502039 | [ 3 ] 33426700-36464369 | [ 6 ] 30389031-33426700 | [ 8 ] 27351361-30389030 | [ 5 ] 24313692-27351361 | [ ] 21276022-24313691 | [ ] 18238353-21276022 | [ ] 15200683-18238352 | [ ] 12163014-15200683 | [ ] 9125344-12163013 | [ ] 6087675-9125344 | [ ] 3050005-6087674 | [ 1 ] 12336-3050005 |************************************************** [ 643 ] Storage Throughput = excellent ( 1787.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037574 bp ( 40031174 non ambiguous ) - Num Contigs Represented = 126 - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:50 (hh:mm:ss) Elapsed Time Round Time: 01:23:42 (hh:mm:ss) Elapsed Time : 702 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9662 repeats masked totaling 2615949 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014061 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10012461 bp After Masking: 5574030 bp Masked: 44.33 % -- Input Database Coverage: 10014061 bp out of 865090090 bp ( 1.16 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 01:58:23 (hh:mm:ss) Elapsed Time, 18699 HSPs Collected Number of families returned by RECON: 1236 Round Time: 02:04:19 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30755 repeats masked totaling 8612897 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023433 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 30018633 bp After Masking: 16476551 bp Masked: 45.11 % -- Input Database Coverage: 40037494 bp out of 865090090 bp ( 4.63 % ) Sampling Time: 00:07:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 05:57:04 (hh:mm:ss) Elapsed Time, 43957 HSPs Collected Number of families returned by RECON: 4111 Round Time: 06:25:18 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 96420 repeats masked totaling 25890580 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012436 bp Num Contigs Represented = 221 Non ambiguous bp: Initial: 90001636 bp After Masking: 48442081 bp Masked: 46.18 % -- Input Database Coverage: 130049930 bp out of 865090090 bp ( 15.03 % ) Sampling Time: 00:18:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 17:37:02 (hh:mm:ss) Elapsed Time, 403921 HSPs Collected Number of families returned by RECON: 13060 Round Time: 19:07:20 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 351386 repeats masked totaling 93660818 bp(s). - TE Masking time 00:04:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033547 bp Num Contigs Represented = 378 Non ambiguous bp: Initial: 270006147 bp After Masking: 131204744 bp Masked: 51.41 % -- Input Database Coverage: 400083477 bp out of 865090090 bp ( 46.25 % ) Sampling Time: 00:54:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23389380 Comparison Time: 21:58:55 (hh:mm:ss) Elapsed Time, 1118772 HSPs Collected Number of families returned by RECON: 41472 Round Time: 23:16:07 (hh:mm:ss) Elapsed Time : 1073 families discovered. RepeatScout/RECON discovery complete: 2388 families found Classification Time: 00:58:59 (hh:mm:ss) Elapsed Time Program Time: 53:15:45 (hh:mm:ss) Elapsed Time