RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.SdcchF/RM_4119936.SunDec81023012024 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: 1733682181 Database = /scratch/tmp/rModeler.SdcchF/GCA_964106785.1_rPodGai1.hap2.1 - Sequences = 127 - Bases = 1422314362 - N50 = 100508744 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 128048643-137194904 | [ 1 ] 118902383-128048643 | [ 2 ] 109756123-118902383 | [ ] 100609862-109756122 | [ 2 ] 91463602-100609862 | [ 1 ] 82317342-91463602 | [ 2 ] 73171082-82317342 | [ 2 ] 64024821-73171081 | [ 1 ] 54878561-64024821 | [ 2 ] 45732301-54878561 | [ 2 ] 36586041-45732301 | [ 2 ] 27439780-36586040 | [ ] 18293520-27439780 | [ ] 9147260-18293520 | [ 1 ] 1000-9147260 |************************************************* [ 109 ] Storage Throughput = excellent ( 1469.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024756 bp ( 40021156 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:48 (hh:mm:ss) Elapsed Time Round Time: 00:10:45 (hh:mm:ss) Elapsed Time : 547 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17684 repeats masked totaling 3273282 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028077 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10026877 bp After Masking: 6398543 bp Masked: 36.19 % -- Input Database Coverage: 10028077 bp out of 1422314362 bp ( 0.71 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 8837 HSPs Collected Number of families returned by RECON: 1272 Round Time: 00:03:32 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54148 repeats masked totaling 9770774 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036606 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30034206 bp After Masking: 19370341 bp Masked: 35.51 % -- Input Database Coverage: 40064683 bp out of 1422314362 bp ( 2.82 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:55 (hh:mm:ss) Elapsed Time, 52082 HSPs Collected Number of families returned by RECON: 4462 Round Time: 00:15:18 (hh:mm:ss) Elapsed Time : 136 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179510 repeats masked totaling 31996838 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043991 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 90035191 bp After Masking: 55551829 bp Masked: 38.30 % -- Input Database Coverage: 130108674 bp out of 1422314362 bp ( 9.15 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:11:50 (hh:mm:ss) Elapsed Time, 248754 HSPs Collected Number of families returned by RECON: 13493 Round Time: 01:20:31 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 588701 repeats masked totaling 104347989 bp(s). - TE Masking time 00:02:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046493 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 270016482 bp After Masking: 157532215 bp Masked: 41.66 % -- Input Database Coverage: 400155167 bp out of 1422314362 bp ( 28.13 % ) Sampling Time: 00:15:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 07:38:30 (hh:mm:ss) Elapsed Time, 825458 HSPs Collected Number of families returned by RECON: 48644 Round Time: 08:24:23 (hh:mm:ss) Elapsed Time : 1011 families discovered. RepeatScout/RECON discovery complete: 2139 families found Classification Time: 00:29:46 (hh:mm:ss) Elapsed Time Program Time: 10:44:15 (hh:mm:ss) Elapsed Time