RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bXFlsE/RM_2790728.MonMar101449552025 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: 1741643394 Database = /dev/shm/rModeler.bXFlsE/GCF_029215685.1_rPitCat1.0.hap2 - Sequences = 649 - Bases = 1682881129 - N50 = 297399204 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 331706200-355398792 | [ 1 ] 308013609-331706200 | [ ] 284321018-308013609 | [ 1 ] 260628427-284321018 | [ ] 236935836-260628427 | [ ] 213243245-236935836 | [ 1 ] 189550654-213243245 | [ ] 165858062-189550653 | [ ] 142165471-165858062 | [ ] 118472880-142165471 | [ 1 ] 94780289-118472880 | [ 2 ] 71087698-94780289 | [ 2 ] 47395107-71087698 | [ ] 23702516-47395107 | [ 6 ] 9925-23702516 |************************************************** [ 635 ] Storage Throughput = excellent ( 1832.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002530 bp ( 40001430 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:55 (hh:mm:ss) Elapsed Time Round Time: 00:19:40 (hh:mm:ss) Elapsed Time : 624 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16249 repeats masked totaling 3993330 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006626 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10006426 bp After Masking: 5435308 bp Masked: 45.68 % -- Input Database Coverage: 10006626 bp out of 1682881129 bp ( 0.59 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:45 (hh:mm:ss) Elapsed Time, 5535 HSPs Collected Number of families returned by RECON: 873 Round Time: 00:04:44 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50572 repeats masked totaling 11999151 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035747 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30034847 bp After Masking: 16126540 bp Masked: 46.31 % -- Input Database Coverage: 40042373 bp out of 1682881129 bp ( 2.38 % ) Sampling Time: 00:06:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:11:46 (hh:mm:ss) Elapsed Time, 26977 HSPs Collected Number of families returned by RECON: 3032 Round Time: 00:18:34 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 159009 repeats masked totaling 37695340 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036365 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 90033056 bp After Masking: 46671034 bp Masked: 48.16 % -- Input Database Coverage: 130078738 bp out of 1682881129 bp ( 7.73 % ) Sampling Time: 00:16:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:00:52 (hh:mm:ss) Elapsed Time, 152287 HSPs Collected Number of families returned by RECON: 9265 Round Time: 01:19:59 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 529976 repeats masked totaling 121346788 bp(s). - TE Masking time 00:03:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022528 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 270012428 bp After Masking: 131646343 bp Masked: 51.24 % -- Input Database Coverage: 400101266 bp out of 1682881129 bp ( 23.77 % ) Sampling Time: 00:53:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 06:49:00 (hh:mm:ss) Elapsed Time, 453893 HSPs Collected Number of families returned by RECON: 28984 Round Time: 07:54:34 (hh:mm:ss) Elapsed Time : 807 families discovered. RepeatScout/RECON discovery complete: 1870 families found Classification Time: 00:36:07 (hh:mm:ss) Elapsed Time Program Time: 10:33:38 (hh:mm:ss) Elapsed Time