RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.J8XdXE/RM_2735532.FriApr180255052025 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: 1744970102 Database = /data/tmp/rModeler.J8XdXE/GCA_963693515.1_mPipNat.pri - Sequences = 153 - Bases = 1804478338 - N50 = 102345800 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195250964-209197390 | [ 2 ] 181304538-195250964 | [ 1 ] 167358112-181304538 | [ ] 153411686-167358112 | [ ] 139465260-153411686 | [ ] 125518834-139465260 | [ ] 111572408-125518834 | [ ] 97625982-111572408 | [ 2 ] 83679556-97625982 |* [ 4 ] 69733130-83679556 |* [ 3 ] 55786704-69733130 | [ 1 ] 41840278-55786704 |* [ 5 ] 27893852-41840278 | [ 1 ] 13947426-27893852 | [ 2 ] 1000-13947426 |************************************************** [ 132 ] Storage Throughput = excellent ( 1627.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040277 bp ( 40039277 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:41 (hh:mm:ss) Elapsed Time Round Time: 00:15:21 (hh:mm:ss) Elapsed Time : 293 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13158 repeats masked totaling 2318889 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009754 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10009554 bp After Masking: 7428314 bp Masked: 25.79 % -- Input Database Coverage: 10009754 bp out of 1804478338 bp ( 0.55 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:59 (hh:mm:ss) Elapsed Time, 7286 HSPs Collected Number of families returned by RECON: 871 Round Time: 00:05:27 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42652 repeats masked totaling 7384597 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030443 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30029643 bp After Masking: 21662118 bp Masked: 27.86 % -- Input Database Coverage: 40040197 bp out of 1804478338 bp ( 2.22 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:19:31 (hh:mm:ss) Elapsed Time, 23282 HSPs Collected Number of families returned by RECON: 2396 Round Time: 00:22:46 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140331 repeats masked totaling 24149137 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025796 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90022660 bp After Masking: 63261657 bp Masked: 29.73 % -- Input Database Coverage: 130065993 bp out of 1804478338 bp ( 7.21 % ) Sampling Time: 00:08:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:41:05 (hh:mm:ss) Elapsed Time, 164042 HSPs Collected Number of families returned by RECON: 8558 Round Time: 01:51:09 (hh:mm:ss) Elapsed Time : 220 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 457681 repeats masked totaling 81243000 bp(s). - TE Masking time 00:03:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045518 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 270036894 bp After Masking: 181536906 bp Masked: 32.77 % -- Input Database Coverage: 400111511 bp out of 1804478338 bp ( 22.17 % ) Sampling Time: 00:24:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 12:47:42 (hh:mm:ss) Elapsed Time, 388738 HSPs Collected Number of families returned by RECON: 36100 Round Time: 13:29:03 (hh:mm:ss) Elapsed Time : 431 families discovered. RepeatScout/RECON discovery complete: 1028 families found Classification Time: 00:24:10 (hh:mm:ss) Elapsed Time Program Time: 16:27:56 (hh:mm:ss) Elapsed Time