RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.RGkJjS/RM_1011660.SatDec72202452024 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: 1733637765 Database = /scratch/tmp/rModeler.RGkJjS/GCA_964148845.1_mMesBid2.hap2.1 - Sequences = 1152 - Bases = 2732770104 - N50 = 116026172 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 214781517-230122983 | [ 1 ] 199440051-214781516 | [ ] 184098586-199440051 | [ 1 ] 168757120-184098585 | [ 2 ] 153415655-168757120 | [ ] 138074189-153415654 | [ 1 ] 122732724-138074189 | [ ] 107391258-122732723 | [ 4 ] 92049793-107391258 | [ 2 ] 76708327-92049792 | [ 6 ] 61366862-76708327 | [ 1 ] 46025396-61366861 | [ 1 ] 30683931-46025396 | [ 1 ] 15342465-30683930 | [ ] 1000-15342465 |************************************************** [ 1132 ] Storage Throughput = excellent ( 1453.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006561 bp ( 40004361 non ambiguous ) - Num Contigs Represented = 157 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:50 (hh:mm:ss) Elapsed Time Round Time: 00:16:19 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9859 repeats masked totaling 2817299 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021050 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10020650 bp After Masking: 6636680 bp Masked: 33.77 % -- Input Database Coverage: 10021050 bp out of 2732770104 bp ( 0.37 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 70230 HSPs Collected Number of families returned by RECON: 729 Round Time: 00:04:05 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34245 repeats masked totaling 10197677 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025431 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 30023631 bp After Masking: 18523271 bp Masked: 38.30 % -- Input Database Coverage: 40046481 bp out of 2732770104 bp ( 1.47 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:12:27 (hh:mm:ss) Elapsed Time, 44261 HSPs Collected Number of families returned by RECON: 2280 Round Time: 00:19:07 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113185 repeats masked totaling 33955303 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017096 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 90012496 bp After Masking: 52213890 bp Masked: 41.99 % -- Input Database Coverage: 130063577 bp out of 2732770104 bp ( 4.76 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:07:31 (hh:mm:ss) Elapsed Time, 171000 HSPs Collected Number of families returned by RECON: 7604 Round Time: 01:17:30 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 375730 repeats masked totaling 111047669 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036403 bp Num Contigs Represented = 552 Non ambiguous bp: Initial: 270018603 bp After Masking: 146646827 bp Masked: 45.69 % -- Input Database Coverage: 400099980 bp out of 2732770104 bp ( 14.64 % ) Sampling Time: 00:18:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 07:12:23 (hh:mm:ss) Elapsed Time, 773981 HSPs Collected Number of families returned by RECON: 28092 Round Time: 07:44:30 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatScout/RECON discovery complete: 786 families found Classification Time: 00:29:23 (hh:mm:ss) Elapsed Time Program Time: 10:10:54 (hh:mm:ss) Elapsed Time