RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Knt3Kn/RM_14081.TueNov282318212023 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: 1701242299 Database = /dev/shm/rModeler.Knt3Kn/GCA_028023285.1_mBalRic1.hap2 - Sequences = 774 - Bases = 2678442663 - N50 = 122106598 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 181290038-194239256 | [ 3 ] 168340821-181290038 | [ ] 155391604-168340821 | [ 1 ] 142442387-155391604 | [ 1 ] 129493170-142442387 | [ 1 ] 116543953-129493170 | [ 3 ] 103594736-116543953 | [ 4 ] 90645519-103594736 | [ 3 ] 77696302-90645519 | [ 3 ] 64747085-77696302 | [ 1 ] 51797868-64747085 | [ 1 ] 38848651-51797868 | [ 1 ] 25899434-38848651 | [ ] 12950217-25899434 | [ ] 1000-12950217 |************************************************** [ 752 ] Storage Throughput = excellent ( 1170.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40048735 bp ( 40024466 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:12 (hh:mm:ss) Elapsed Time Round Time: 00:49:49 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10659 repeats masked totaling 3056788 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009360 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10009360 bp After Masking: 6677438 bp Masked: 33.29 % -- Input Database Coverage: 10009360 bp out of 2678442663 bp ( 0.37 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 21739 HSPs Collected Number of families returned by RECON: 812 Round Time: 00:07:36 (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 : 00:01:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35562 repeats masked totaling 9941882 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039295 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30015026 bp After Masking: 18510915 bp Masked: 38.33 % -- Input Database Coverage: 40048655 bp out of 2678442663 bp ( 1.50 % ) Sampling Time: 00:05:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:26:10 (hh:mm:ss) Elapsed Time, 26014 HSPs Collected Number of families returned by RECON: 2301 Round Time: 00:32:25 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116608 repeats masked totaling 32212321 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90170444 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 90004989 bp After Masking: 54302593 bp Masked: 39.67 % -- Input Database Coverage: 130219099 bp out of 2678442663 bp ( 4.86 % ) Sampling Time: 00:14:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 03:00:22 (hh:mm:ss) Elapsed Time, 107056 HSPs Collected Number of families returned by RECON: 7549 Round Time: 03:17:53 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383296 repeats masked totaling 104480053 bp(s). - TE Masking time 00:07:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270320472 bp Num Contigs Represented = 268 Non ambiguous bp: Initial: 270012952 bp After Masking: 154017386 bp Masked: 42.96 % -- Input Database Coverage: 400539571 bp out of 2678442663 bp ( 14.95 % ) Sampling Time: 00:53:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 22:54:07 (hh:mm:ss) Elapsed Time, 1186183 HSPs Collected Number of families returned by RECON: 32054 Round Time: 24:13:17 (hh:mm:ss) Elapsed Time : 328 families discovered. RepeatScout/RECON discovery complete: 755 families found Classification Time: 00:34:03 (hh:mm:ss) Elapsed Time Program Time: 29:35:03 (hh:mm:ss) Elapsed Time