RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.w7PYtc/RM_310574.TueDec31022192024 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: 1733250139 Database = /scratch/tmp/rModeler.w7PYtc/GCA_964289735.1_bPhaAeh10.maternal.1 - Sequences = 657 - Bases = 1321027743 - N50 = 90167876 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 209221366-224165678 | [ 1 ] 194277054-209221365 | [ ] 179332742-194277053 | [ ] 164388430-179332741 | [ 1 ] 149444118-164388429 | [ ] 134499806-149444117 | [ ] 119555494-134499805 | [ 1 ] 104611183-119555494 | [ ] 89666871-104611182 | [ 1 ] 74722559-89666870 | [ 1 ] 59778247-74722558 | [ 1 ] 44833935-59778246 | [ ] 29889623-44833934 | [ 4 ] 14945311-29889622 | [ 9 ] 1000-14945311 |************************************************** [ 638 ] Storage Throughput = excellent ( 1516.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012700 bp ( 40004900 non ambiguous ) - Num Contigs Represented = 104 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:43 (hh:mm:ss) Elapsed Time Round Time: 00:15:35 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1981 repeats masked totaling 1299315 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001784 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 9999984 bp After Masking: 8460586 bp Masked: 15.39 % -- Input Database Coverage: 10001784 bp out of 1321027743 bp ( 0.76 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 323 HSPs Collected Number of families returned by RECON: 173 Round Time: 00:03:36 (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 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5610 repeats masked totaling 3487838 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010836 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 30004836 bp After Masking: 25436141 bp Masked: 15.23 % -- Input Database Coverage: 40012620 bp out of 1321027743 bp ( 3.03 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:14:34 (hh:mm:ss) Elapsed Time, 16283 HSPs Collected Number of families returned by RECON: 1289 Round Time: 00:16:18 (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 : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18556 repeats masked totaling 10343657 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029719 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 90012720 bp After Masking: 77731484 bp Masked: 13.64 % -- Input Database Coverage: 130042339 bp out of 1321027743 bp ( 9.84 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 01:28:13 (hh:mm:ss) Elapsed Time, 541473 HSPs Collected Number of families returned by RECON: 7227 Round Time: 01:35:27 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65445 repeats masked totaling 33053834 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270078634 bp Num Contigs Represented = 310 Non ambiguous bp: Initial: 270023434 bp After Masking: 229773761 bp Masked: 14.91 % -- Input Database Coverage: 400120973 bp out of 1321027743 bp ( 30.29 % ) Sampling Time: 00:13:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23334696 Comparison Time: 10:42:24 (hh:mm:ss) Elapsed Time, 4888793 HSPs Collected Number of families returned by RECON: 45690 Round Time: 11:08:33 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatScout/RECON discovery complete: 354 families found Classification Time: 00:18:53 (hh:mm:ss) Elapsed Time Program Time: 13:38:22 (hh:mm:ss) Elapsed Time