RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.LgurxJ/RM_29649.ThuDec51248092024 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: 1733431687 Database = /scratch/tmp/rModeler.LgurxJ/GCA_036850655.1_bMerOct1.hap2 - Sequences = 720 - Bases = 1213885900 - N50 = 131793809 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207002503-221787178 | [ 1 ] 192217828-207002502 | [ ] 177433153-192217827 | [ 1 ] 162648478-177433152 | [ ] 147863804-162648478 | [ ] 133079129-147863803 | [ ] 118294454-133079128 | [ 1 ] 103509779-118294453 | [ ] 88725104-103509778 | [ ] 73940430-88725104 | [ 1 ] 59155755-73940429 | [ 1 ] 44371080-59155754 | [ ] 29586405-44371079 | [ 3 ] 14801730-29586404 | [ 10 ] 17056-14801730 |************************************************** [ 702 ] Storage Throughput = fair ( 641.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025017 bp ( 40023417 non ambiguous ) - Num Contigs Represented = 127 - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:27:42 (hh:mm:ss) Elapsed Time Round Time: 00:42:28 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1739 repeats masked totaling 905075 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005197 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10004397 bp After Masking: 8114987 bp Masked: 18.89 % -- Input Database Coverage: 10005197 bp out of 1213885900 bp ( 0.82 % ) Sampling Time: 00:07:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:25 (hh:mm:ss) Elapsed Time, 26637 HSPs Collected Number of families returned by RECON: 317 Round Time: 00:15:13 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6565 repeats masked totaling 3392859 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019740 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 30018940 bp After Masking: 23707229 bp Masked: 21.03 % -- Input Database Coverage: 40024937 bp out of 1213885900 bp ( 3.30 % ) Sampling Time: 00:20:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:44:50 (hh:mm:ss) Elapsed Time, 20839 HSPs Collected Number of families returned by RECON: 1555 Round Time: 01:06:52 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19834 repeats masked totaling 10231510 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012493 bp Num Contigs Represented = 205 Non ambiguous bp: Initial: 90008932 bp After Masking: 71675216 bp Masked: 20.37 % -- Input Database Coverage: 130037430 bp out of 1213885900 bp ( 10.71 % ) Sampling Time: 00:44:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 05:41:16 (hh:mm:ss) Elapsed Time, 67590 HSPs Collected Number of families returned by RECON: 9625 Round Time: 06:31:43 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:27:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70504 repeats masked totaling 33474442 bp(s). - TE Masking time 00:04:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012795 bp Num Contigs Represented = 425 Non ambiguous bp: Initial: 270003231 bp After Masking: 212111666 bp Masked: 21.44 % -- Input Database Coverage: 400050225 bp out of 1213885900 bp ( 32.96 % ) Sampling Time: 02:46:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 47:17:29 (hh:mm:ss) Elapsed Time, 489685 HSPs Collected Number of families returned by RECON: 56803 Round Time: 51:08:35 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatScout/RECON discovery complete: 312 families found Classification Time: 00:23:15 (hh:mm:ss) Elapsed Time Program Time: 60:08:06 (hh:mm:ss) Elapsed Time