RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Vzd5J5/RM_24901.WedJul240153442024 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: 1721811199 Database = /dev/shm/rModeler.Vzd5J5/GCF_018831695.1_ASM1883169v1 - Sequences = 1122 - Bases = 730818536 - N50 = 25613461 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38920944-41700998 | [ 1 ] 36140891-38920944 | [ ] 33360838-36140891 | [ ] 30580785-33360838 | [ 2 ] 27800732-30580785 | [ 3 ] 25020678-27800731 | [ 7 ] 22240625-25020678 | [ 4 ] 19460572-22240625 | [ 3 ] 16680519-19460572 | [ 4 ] 13900466-16680519 | [ 1 ] 11120412-13900465 | [ ] 8340359-11120412 | [ ] 5560306-8340359 | [ ] 2780253-5560306 | [ 4 ] 200-2780253 |************************************************** [ 1093 ] Storage Throughput = excellent ( 1035.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40053849 bp ( 40033101 non ambiguous ) - Num Contigs Represented = 155 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:20 (hh:mm:ss) Elapsed Time Round Time: 00:42:12 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7223 repeats masked totaling 1076431 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041884 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10035617 bp After Masking: 8291708 bp Masked: 17.38 % -- Input Database Coverage: 10041884 bp out of 730818536 bp ( 1.37 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 01:08:55 (hh:mm:ss) Elapsed Time, 12722 HSPs Collected Number of families returned by RECON: 1397 Round Time: 01:13:44 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24186 repeats masked totaling 3555023 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30051936 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 30037455 bp After Masking: 24521878 bp Masked: 18.36 % -- Input Database Coverage: 40093820 bp out of 730818536 bp ( 5.49 % ) Sampling Time: 00:06:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 311655 Comparison Time: 02:56:26 (hh:mm:ss) Elapsed Time, 44532 HSPs Collected Number of families returned by RECON: 5236 Round Time: 03:11:38 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85731 repeats masked totaling 12591472 bp(s). - TE Masking time 00:02:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90063242 bp Num Contigs Represented = 290 Non ambiguous bp: Initial: 90018982 bp After Masking: 71640752 bp Masked: 20.42 % -- Input Database Coverage: 130157062 bp out of 730818536 bp ( 17.81 % ) Sampling Time: 00:19:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2807265 Comparison Time: 11:35:33 (hh:mm:ss) Elapsed Time, 283972 HSPs Collected Number of families returned by RECON: 17596 Round Time: 12:28:27 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 309830 repeats masked totaling 50310002 bp(s). - TE Masking time 00:14:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270190937 bp Num Contigs Represented = 569 Non ambiguous bp: Initial: 270038722 bp After Masking: 203054272 bp Masked: 24.81 % -- Input Database Coverage: 400347999 bp out of 730818536 bp ( 54.78 % ) Sampling Time: 01:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24939453 Comparison Time: 59:09:52 (hh:mm:ss) Elapsed Time, 1263556 HSPs Collected Number of families returned by RECON: 58055 Round Time: 62:03:46 (hh:mm:ss) Elapsed Time : 889 families discovered. RepeatScout/RECON discovery complete: 1799 families found Classification Time: 02:57:11 (hh:mm:ss) Elapsed Time Program Time: 82:36:58 (hh:mm:ss) Elapsed Time