RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.AlJISc/RM_984475.FriApr110701532025 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: 1744380111 Database = /data/tmp/rModeler.AlJISc/GCA_965119305.1_aPelLes1.hap1.1 - Sequences = 1328 - Bases = 5811246175 - N50 = 688568912 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 836871209-896647653 | [ 1 ] 777094765-836871208 | [ ] 717318322-777094765 | [ 1 ] 657541878-717318321 | [ 2 ] 597765435-657541878 | [ ] 537988991-597765434 | [ 1 ] 478212548-537988991 | [ ] 418436104-478212547 | [ ] 358659661-418436104 | [ ] 298883217-358659660 | [ 3 ] 239106774-298883217 | [ 2 ] 179330330-239106773 | [ 3 ] 119553887-179330330 | [ ] 59777443-119553886 | [ ] 1000-59777443 |************************************************** [ 1315 ] Storage Throughput = excellent ( 1839.50 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039845 bp ( 40035645 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:04:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:11 (hh:mm:ss) Elapsed Time Round Time: 00:19:46 (hh:mm:ss) Elapsed Time : 988 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17448 repeats masked totaling 4939471 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006636 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10005836 bp After Masking: 4039425 bp Masked: 59.63 % -- Input Database Coverage: 10006636 bp out of 5811246175 bp ( 0.17 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 12249 HSPs Collected Number of families returned by RECON: 1523 Round Time: 00:05:47 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53054 repeats masked totaling 15046512 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033129 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30029729 bp After Masking: 11761012 bp Masked: 60.84 % -- Input Database Coverage: 40039765 bp out of 5811246175 bp ( 0.69 % ) Sampling Time: 00:07:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:13:06 (hh:mm:ss) Elapsed Time, 70800 HSPs Collected Number of families returned by RECON: 4821 Round Time: 00:22:06 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 169323 repeats masked totaling 47261058 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024412 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90015612 bp After Masking: 33781651 bp Masked: 62.47 % -- Input Database Coverage: 130064177 bp out of 5811246175 bp ( 2.24 % ) Sampling Time: 00:23:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:08:26 (hh:mm:ss) Elapsed Time, 357793 HSPs Collected Number of families returned by RECON: 13197 Round Time: 01:39:33 (hh:mm:ss) Elapsed Time : 598 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:41:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 583143 repeats masked totaling 160809038 bp(s). - TE Masking time 00:08:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066078 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 270036903 bp After Masking: 81916291 bp Masked: 69.66 % -- Input Database Coverage: 400130255 bp out of 5811246175 bp ( 6.89 % ) Sampling Time: 01:19:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22926606 Comparison Time: 06:25:09 (hh:mm:ss) Elapsed Time, 1041998 HSPs Collected Number of families returned by RECON: 31190 Round Time: 08:15:35 (hh:mm:ss) Elapsed Time : 1548 families discovered. RepeatScout/RECON discovery complete: 3294 families found Classification Time: 01:18:03 (hh:mm:ss) Elapsed Time Program Time: 12:00:50 (hh:mm:ss) Elapsed Time