RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.nxWNhT/RM_865764.SatApr120154352025 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: 1744448074 Database = /data/tmp/rModeler.nxWNhT/GCA_964341445.1_mMesMir1.hap1.1 - Sequences = 2757 - Bases = 3442419404 - N50 = 130920471 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217261885-232780520 | [ 2 ] 201743250-217261884 | [ ] 186224616-201743250 | [ 3 ] 170705981-186224615 | [ ] 155187346-170705980 | [ ] 139668712-155187346 | [ 3 ] 124150077-139668711 | [ 1 ] 108631442-124150076 | [ 3 ] 93112808-108631442 | [ 2 ] 77594173-93112807 | [ 4 ] 62075538-77594172 | [ 2 ] 46556904-62075538 | [ ] 31038269-46556903 | [ 1 ] 15519634-31038268 | [ ] 1000-15519634 |************************************************** [ 2736 ] Storage Throughput = excellent ( 1554.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028144 bp ( 40024144 non ambiguous ) - Num Contigs Represented = 203 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:31 (hh:mm:ss) Elapsed Time Round Time: 00:27:00 (hh:mm:ss) Elapsed Time : 227 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10667 repeats masked totaling 3147752 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004490 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 10003690 bp After Masking: 5785777 bp Masked: 42.16 % -- Input Database Coverage: 10004490 bp out of 3442419404 bp ( 0.29 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:45 (hh:mm:ss) Elapsed Time, 90999 HSPs Collected Number of families returned by RECON: 502 Round Time: 00:06:54 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33530 repeats masked totaling 10545623 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023650 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 30020450 bp After Masking: 16234755 bp Masked: 45.92 % -- Input Database Coverage: 40028140 bp out of 3442419404 bp ( 1.16 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:16:01 (hh:mm:ss) Elapsed Time, 30467 HSPs Collected Number of families returned by RECON: 1765 Round Time: 00:20:34 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106123 repeats masked totaling 33768792 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019308 bp Num Contigs Represented = 352 Non ambiguous bp: Initial: 90013508 bp After Masking: 46928314 bp Masked: 47.87 % -- Input Database Coverage: 130047448 bp out of 3442419404 bp ( 3.78 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 01:29:20 (hh:mm:ss) Elapsed Time, 309223 HSPs Collected Number of families returned by RECON: 5924 Round Time: 01:42:15 (hh:mm:ss) Elapsed Time : 150 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 357663 repeats masked totaling 110337495 bp(s). - TE Masking time 00:03:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270050429 bp Num Contigs Represented = 783 Non ambiguous bp: Initial: 270030829 bp After Masking: 133868538 bp Masked: 50.42 % -- Input Database Coverage: 400097877 bp out of 3442419404 bp ( 11.62 % ) Sampling Time: 00:31:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23601885 Comparison Time: 08:30:02 (hh:mm:ss) Elapsed Time, 2319609 HSPs Collected Number of families returned by RECON: 21823 Round Time: 09:12:33 (hh:mm:ss) Elapsed Time : 343 families discovered. RepeatScout/RECON discovery complete: 777 families found Classification Time: 00:28:26 (hh:mm:ss) Elapsed Time Program Time: 12:17:42 (hh:mm:ss) Elapsed Time