RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AbFXzb/RM_3862765.FriJan121747202024 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: 1705110435 Database = /dev/shm/rModeler.AbFXzb/GCF_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 ( 1019.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40050242 bp ( 40011840 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:30 (hh:mm:ss) Elapsed Time Round Time: 00:38:36 (hh:mm:ss) Elapsed Time : 194 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9251 repeats masked totaling 2698676 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10052990 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10016327 bp After Masking: 6537439 bp Masked: 34.73 % -- Input Database Coverage: 10052990 bp out of 2678442663 bp ( 0.38 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:23:35 (hh:mm:ss) Elapsed Time, 26142 HSPs Collected Number of families returned by RECON: 677 Round Time: 00:26:46 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30911 repeats masked totaling 9775294 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037251 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30035512 bp After Masking: 18757716 bp Masked: 37.55 % -- Input Database Coverage: 40090241 bp out of 2678442663 bp ( 1.50 % ) Sampling Time: 00:06:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:57:55 (hh:mm:ss) Elapsed Time, 31006 HSPs Collected Number of families returned by RECON: 2363 Round Time: 01:05:41 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104022 repeats masked totaling 31891344 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90238798 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 90036540 bp After Masking: 54321671 bp Masked: 39.67 % -- Input Database Coverage: 130329039 bp out of 2678442663 bp ( 4.87 % ) Sampling Time: 00:16:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 04:00:52 (hh:mm:ss) Elapsed Time, 216119 HSPs Collected Number of families returned by RECON: 8674 Round Time: 04:25:29 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:43 (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... 364416 repeats masked totaling 102795936 bp(s). - TE Masking time 00:05:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270362080 bp Num Contigs Represented = 294 Non ambiguous bp: Initial: 270003654 bp After Masking: 155378446 bp Masked: 42.45 % -- Input Database Coverage: 400691119 bp out of 2678442663 bp ( 14.96 % ) Sampling Time: 00:53:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 21:43:03 (hh:mm:ss) Elapsed Time, 1540477 HSPs Collected Number of families returned by RECON: 31650 Round Time: 23:01:08 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 817 families found Classification Time: 00:36:10 (hh:mm:ss) Elapsed Time Program Time: 30:13:50 (hh:mm:ss) Elapsed Time