RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.o2C3NK/RM_585813.SunJan141941462024 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: 1705290105 Database = /dev/shm/rModeler.o2C3NK/GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri - Sequences = 2611 - Bases = 3365490689 - N50 = 143554639 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217419963-232949852 | [ 1 ] 201890074-217419962 | [ 1 ] 186360185-201890073 | [ 2 ] 170830296-186360184 | [ 1 ] 155300407-170830295 | [ 2 ] 139770518-155300406 | [ 2 ] 124240629-139770517 | [ 4 ] 108710741-124240629 | [ 1 ] 93180852-108710740 | [ 2 ] 77650963-93180851 | [ 3 ] 62121074-77650962 | [ 4 ] 46591185-62121073 | [ 1 ] 31061296-46591184 | [ 1 ] 15531407-31061295 | [ 1 ] 1519-15531407 |************************************************** [ 2585 ] Storage Throughput = good ( 767.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40280936 bp ( 40034053 non ambiguous ) - Num Contigs Represented = 98 - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:52 (hh:mm:ss) Elapsed Time Round Time: 00:28:53 (hh:mm:ss) Elapsed Time : 258 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11836 repeats masked totaling 2985871 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10090736 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10010736 bp After Masking: 5836081 bp Masked: 41.70 % -- Input Database Coverage: 10090736 bp out of 3365490689 bp ( 0.30 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:12:32 (hh:mm:ss) Elapsed Time, 4206 HSPs Collected Number of families returned by RECON: 695 Round Time: 00:15:48 (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 : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38944 repeats masked totaling 9703757 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30190120 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 30023237 bp After Masking: 17666384 bp Masked: 41.16 % -- Input Database Coverage: 40280856 bp out of 3365490689 bp ( 1.20 % ) Sampling Time: 00:08:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:53:37 (hh:mm:ss) Elapsed Time, 27900 HSPs Collected Number of families returned by RECON: 2292 Round Time: 01:03:27 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120905 repeats masked totaling 29816378 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90234440 bp Num Contigs Represented = 170 Non ambiguous bp: Initial: 90014499 bp After Masking: 50667467 bp Masked: 43.71 % -- Input Database Coverage: 130515296 bp out of 3365490689 bp ( 3.88 % ) Sampling Time: 00:35:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 04:19:04 (hh:mm:ss) Elapsed Time, 118057 HSPs Collected Number of families returned by RECON: 7500 Round Time: 05:02:28 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:58:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 413661 repeats masked totaling 102244855 bp(s). - TE Masking time 00:05:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270569602 bp Num Contigs Represented = 406 Non ambiguous bp: Initial: 270005046 bp After Masking: 141917905 bp Masked: 47.44 % -- Input Database Coverage: 401084898 bp out of 3365490689 bp ( 11.92 % ) Sampling Time: 01:22:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23526370 Comparison Time: 17:46:06 (hh:mm:ss) Elapsed Time, 274218 HSPs Collected Number of families returned by RECON: 29542 Round Time: 19:35:18 (hh:mm:ss) Elapsed Time : 403 families discovered. RepeatScout/RECON discovery complete: 931 families found Classification Time: 00:37:00 (hh:mm:ss) Elapsed Time Program Time: 27:02:55 (hh:mm:ss) Elapsed Time