RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wDJORH/RM_2808818.SunJul140036382024 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: 1720942597 Database = /dev/shm/rModeler.wDJORH/GCF_027474105.1_Auburn_PproV2 - Sequences = 415 - Bases = 674152735 - N50 = 8479109 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 24513136-26263342 | [ 2 ] 22762930-24513135 | [ ] 21012724-22762929 | [ ] 19262518-21012723 | [ 3 ] 17512313-19262518 | [ 2 ] 15762107-17512312 | [ 1 ] 14011901-15762106 | [ 4 ] 12261695-14011900 | [ 2 ] 10511489-12261694 | [ 3 ] 8761284-10511489 | [ 4 ] 7011078-8761283 |* [ 7 ] 5260872-7011077 |** [ 14 ] 3510666-5260871 |* [ 13 ] 1760460-3510665 |*** [ 22 ] 10255-1760460 |************************************************** [ 338 ] Storage Throughput = excellent ( 1228.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036715 bp ( 40025715 non ambiguous ) - Num Contigs Represented = 170 - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:52 (hh:mm:ss) Elapsed Time Round Time: 00:18:40 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6353 repeats masked totaling 957970 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029041 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 10018841 bp After Masking: 8645064 bp Masked: 13.71 % -- Input Database Coverage: 10029041 bp out of 674152735 bp ( 1.49 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:37 (hh:mm:ss) Elapsed Time, 8378 HSPs Collected Number of families returned by RECON: 1345 Round Time: 00:09:22 (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 : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21302 repeats masked totaling 3481882 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007594 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 30006794 bp After Masking: 25564312 bp Masked: 14.80 % -- Input Database Coverage: 40036635 bp out of 674152735 bp ( 5.94 % ) Sampling Time: 00:03:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:36:51 (hh:mm:ss) Elapsed Time, 36359 HSPs Collected Number of families returned by RECON: 4741 Round Time: 00:41:31 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75868 repeats masked totaling 12120856 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038702 bp Num Contigs Represented = 240 Non ambiguous bp: Initial: 90037432 bp After Masking: 74402148 bp Masked: 17.37 % -- Input Database Coverage: 130075337 bp out of 674152735 bp ( 19.29 % ) Sampling Time: 00:13:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 03:46:16 (hh:mm:ss) Elapsed Time, 220775 HSPs Collected Number of families returned by RECON: 16206 Round Time: 04:20:01 (hh:mm:ss) Elapsed Time : 334 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 290040 repeats masked totaling 48812544 bp(s). - TE Masking time 00:07:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270029344 bp Num Contigs Represented = 342 Non ambiguous bp: Initial: 270008961 bp After Masking: 210997334 bp Masked: 21.86 % -- Input Database Coverage: 400104681 bp out of 674152735 bp ( 59.35 % ) Sampling Time: 00:39:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23355195 Comparison Time: 27:05:00 (hh:mm:ss) Elapsed Time, 614460 HSPs Collected Number of families returned by RECON: 62493 Round Time: 28:57:07 (hh:mm:ss) Elapsed Time : 822 families discovered. RepeatScout/RECON discovery complete: 1557 families found Classification Time: 01:34:12 (hh:mm:ss) Elapsed Time Program Time: 36:00:53 (hh:mm:ss) Elapsed Time