RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.6qCliT/RM_1164467.TueNov121201412024 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: 1731441700 Database = /scratch/tmp/rModeler.6qCliT/GCF_036971685.1_bPatFas1.hap2 - Sequences = 452 - Bases = 1410041145 - N50 = 80804424 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201223936-215596151 | [ 1 ] 186851721-201223935 | [ ] 172479507-186851721 | [ ] 158107292-172479506 | [ 1 ] 143735077-158107291 | [ ] 129362863-143735077 | [ ] 114990648-129362862 | [ 1 ] 100618433-114990647 | [ ] 86246219-100618433 | [ ] 71874004-86246218 | [ 2 ] 57501789-71874003 | [ 1 ] 43129575-57501789 | [ 2 ] 28757360-43129574 | [ 2 ] 14385145-28757359 |* [ 10 ] 12931-14385145 |************************************************** [ 432 ] Storage Throughput = excellent ( 1547.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40197923 bp ( 40008953 non ambiguous ) - Num Contigs Represented = 120 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:55 (hh:mm:ss) Elapsed Time Round Time: 00:16:32 (hh:mm:ss) Elapsed Time : 114 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 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2544 repeats masked totaling 1113191 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10046256 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10005856 bp After Masking: 7895986 bp Masked: 21.09 % -- Input Database Coverage: 10046256 bp out of 1410041145 bp ( 0.71 % ) Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 7619 HSPs Collected Number of families returned by RECON: 179 Round Time: 00:06:36 (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 : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8626 repeats masked totaling 3824545 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30151587 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 30003017 bp After Masking: 23939628 bp Masked: 20.21 % -- Input Database Coverage: 40197843 bp out of 1410041145 bp ( 2.85 % ) Sampling Time: 00:06:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:13:21 (hh:mm:ss) Elapsed Time, 129980 HSPs Collected Number of families returned by RECON: 1043 Round Time: 00:20:28 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28539 repeats masked totaling 11857548 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90672080 bp Num Contigs Represented = 189 Non ambiguous bp: Initial: 90007310 bp After Masking: 70804671 bp Masked: 21.33 % -- Input Database Coverage: 130869923 bp out of 1410041145 bp ( 9.28 % ) Sampling Time: 00:22:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 01:28:41 (hh:mm:ss) Elapsed Time, 1507336 HSPs Collected Number of families returned by RECON: 5979 Round Time: 01:52:48 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:03:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92702 repeats masked totaling 37524421 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271492911 bp Num Contigs Represented = 305 Non ambiguous bp: Initial: 270037993 bp After Masking: 210564921 bp Masked: 22.02 % -- Input Database Coverage: 402362834 bp out of 1410041145 bp ( 28.54 % ) Sampling Time: 01:11:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 10:45:17 (hh:mm:ss) Elapsed Time, 12305265 HSPs Collected Number of families returned by RECON: 39016 Round Time: 12:07:40 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatScout/RECON discovery complete: 430 families found Classification Time: 00:20:21 (hh:mm:ss) Elapsed Time Program Time: 15:04:25 (hh:mm:ss) Elapsed Time