RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.9huwsj/RM_2029704.MonNov182145012024 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: 1731995101 Database = /scratch/tmp/rModeler.9huwsj/GCA_035047345.1_BraVen1.1 - Sequences = 113 - Bases = 2373187502 - N50 = 385923506 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 473066816-506857186 | [ 1 ] 439276447-473066816 | [ ] 405486078-439276447 | [ ] 371695708-405486077 | [ 2 ] 337905339-371695708 | [ ] 304114970-337905339 | [ 1 ] 270324600-304114969 | [ ] 236534231-270324600 | [ 1 ] 202743862-236534231 | [ ] 168953492-202743861 | [ ] 135163123-168953492 | [ 1 ] 101372754-135163123 | [ ] 67582384-101372753 | [ ] 33792015-67582384 |** [ 5 ] 1646-33792015 |************************************************** [ 102 ] Storage Throughput = excellent ( 1463.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011597 bp ( 40011597 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:40 (hh:mm:ss) Elapsed Time Round Time: 00:14:51 (hh:mm:ss) Elapsed Time : 671 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16868 repeats masked totaling 5083586 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015608 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10015608 bp After Masking: 4482714 bp Masked: 55.24 % -- Input Database Coverage: 10015608 bp out of 2373187502 bp ( 0.42 % ) Sampling Time: 00:02:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:44 (hh:mm:ss) Elapsed Time, 4207 HSPs Collected Number of families returned by RECON: 961 Round Time: 00:05:34 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52432 repeats masked totaling 15704743 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035909 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30035909 bp After Masking: 13375928 bp Masked: 55.47 % -- Input Database Coverage: 40051517 bp out of 2373187502 bp ( 1.69 % ) Sampling Time: 00:07:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:10:45 (hh:mm:ss) Elapsed Time, 32811 HSPs Collected Number of families returned by RECON: 3172 Round Time: 00:18:59 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 166061 repeats masked totaling 48139522 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035406 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90035206 bp After Masking: 38094949 bp Masked: 57.69 % -- Input Database Coverage: 130086923 bp out of 2373187502 bp ( 5.48 % ) Sampling Time: 00:26:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 00:54:40 (hh:mm:ss) Elapsed Time, 168769 HSPs Collected Number of families returned by RECON: 8958 Round Time: 01:24:23 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:59:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 538592 repeats masked totaling 154094622 bp(s). - TE Masking time 00:03:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270004470 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 270004370 bp After Masking: 103598457 bp Masked: 61.63 % -- Input Database Coverage: 400091393 bp out of 2373187502 bp ( 16.86 % ) Sampling Time: 01:23:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 05:34:22 (hh:mm:ss) Elapsed Time, 475693 HSPs Collected Number of families returned by RECON: 26779 Round Time: 07:12:01 (hh:mm:ss) Elapsed Time : 864 families discovered. RepeatScout/RECON discovery complete: 1982 families found Classification Time: 00:36:06 (hh:mm:ss) Elapsed Time Program Time: 09:51:54 (hh:mm:ss) Elapsed Time