RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.3b8GZZ/RM_1206493.SatMar291723032025 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: 1743294181 Database = /data/tmp/rModeler.3b8GZZ/GCA_048569485.1_aAnoBae1.hap1 - Sequences = 3642 - Bases = 6265077250 - N50 = 707846305 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 911955041-977094522 | [ 1 ] 846815561-911955041 | [ ] 781676081-846815561 | [ 1 ] 716536601-781676081 | [ ] 651397121-716536601 | [ 2 ] 586257641-651397121 | [ 1 ] 521118161-586257641 | [ 1 ] 455978681-521118161 | [ ] 390839201-455978681 | [ ] 325699721-390839201 | [ ] 260560241-325699721 | [ 2 ] 195420761-260560241 | [ 3 ] 130281281-195420761 | [ 1 ] 65141801-130281281 | [ ] 2321-65141801 |************************************************** [ 3630 ] Storage Throughput = fair ( 697.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017119 bp ( 40011119 non ambiguous ) - Num Contigs Represented = 103 - Sequence extraction : 00:06:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:51 (hh:mm:ss) Elapsed Time Round Time: 00:28:10 (hh:mm:ss) Elapsed Time : 987 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16741 repeats masked totaling 5518173 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033466 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10032166 bp After Masking: 2717479 bp Masked: 72.91 % -- Input Database Coverage: 10033466 bp out of 6265077250 bp ( 0.16 % ) Sampling Time: 00:04:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:05 (hh:mm:ss) Elapsed Time, 11220 HSPs Collected Number of families returned by RECON: 1051 Round Time: 00:08:44 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49496 repeats masked totaling 16949978 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023573 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 30018873 bp After Masking: 7966788 bp Masked: 73.46 % -- Input Database Coverage: 40057039 bp out of 6265077250 bp ( 0.64 % ) Sampling Time: 00:10:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:13:45 (hh:mm:ss) Elapsed Time, 44804 HSPs Collected Number of families returned by RECON: 3141 Round Time: 00:24:29 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 162754 repeats masked totaling 52576668 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037511 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 90026611 bp After Masking: 23032862 bp Masked: 74.42 % -- Input Database Coverage: 130094550 bp out of 6265077250 bp ( 2.08 % ) Sampling Time: 00:31:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:00:18 (hh:mm:ss) Elapsed Time, 241398 HSPs Collected Number of families returned by RECON: 8060 Round Time: 01:35:45 (hh:mm:ss) Elapsed Time : 438 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:40:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:47:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 530835 repeats masked totaling 169319672 bp(s). - TE Masking time 00:06:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035746 bp Num Contigs Represented = 506 Non ambiguous bp: Initial: 270004945 bp After Masking: 55783565 bp Masked: 79.34 % -- Input Database Coverage: 400130296 bp out of 6265077250 bp ( 6.39 % ) Sampling Time: 01:34:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23348361 Comparison Time: 05:47:11 (hh:mm:ss) Elapsed Time, 784175 HSPs Collected Number of families returned by RECON: 18362 Round Time: 07:36:41 (hh:mm:ss) Elapsed Time : 1079 families discovered. RepeatScout/RECON discovery complete: 2617 families found Classification Time: 01:02:16 (hh:mm:ss) Elapsed Time Program Time: 11:16:05 (hh:mm:ss) Elapsed Time