RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Rcq7o9/RM_3646148.FriJul120624012024 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: 1720790641 Database = /dev/shm/rModeler.Rcq7o9/GCF_027744805.1_RoL_Ddac_1.1 - Sequences = 157 - Bases = 670648883 - N50 = 32761191 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48429084-51887073 | [ 2 ] 44971095-48429084 | [ ] 41513106-44971095 | [ ] 38055117-41513106 | [ 1 ] 34597128-38055117 | [ 1 ] 31139139-34597128 |** [ 7 ] 27681150-31139139 |* [ 4 ] 24223161-27681150 | [ 2 ] 20765172-24223161 | [ 1 ] 17307183-20765172 |* [ 3 ] 13849194-17307183 | [ ] 10391205-13849194 | [ ] 6933216-10391205 | [ ] 3475227-6933216 | [ ] 17238-3475227 |************************************************* [ 136 ] Storage Throughput = excellent ( 1553.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002228 bp ( 40002228 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:28 (hh:mm:ss) Elapsed Time Round Time: 00:20:43 (hh:mm:ss) Elapsed Time : 1096 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25949 repeats masked totaling 3646107 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017086 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10017086 bp After Masking: 5882390 bp Masked: 41.28 % -- Input Database Coverage: 10017086 bp out of 670648883 bp ( 1.49 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 21241 HSPs Collected Number of families returned by RECON: 1574 Round Time: 00:09:39 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78529 repeats masked totaling 11381236 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025142 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30025142 bp After Masking: 17173511 bp Masked: 42.80 % -- Input Database Coverage: 40042228 bp out of 670648883 bp ( 5.97 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:07 (hh:mm:ss) Elapsed Time, 70144 HSPs Collected Number of families returned by RECON: 4842 Round Time: 00:32:53 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 259930 repeats masked totaling 37709422 bp(s). - TE Masking time 00:02:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039287 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90039267 bp After Masking: 48954177 bp Masked: 45.63 % -- Input Database Coverage: 130081515 bp out of 670648883 bp ( 19.40 % ) Sampling Time: 00:10:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 02:30:53 (hh:mm:ss) Elapsed Time, 264212 HSPs Collected Number of families returned by RECON: 14268 Round Time: 02:52:55 (hh:mm:ss) Elapsed Time : 523 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 844826 repeats masked totaling 125510526 bp(s). - TE Masking time 00:09:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270007245 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 270007045 bp After Masking: 132794973 bp Masked: 50.82 % -- Input Database Coverage: 400088760 bp out of 670648883 bp ( 59.66 % ) Sampling Time: 00:34:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 16:03:28 (hh:mm:ss) Elapsed Time, 556752 HSPs Collected Number of families returned by RECON: 44186 Round Time: 17:30:47 (hh:mm:ss) Elapsed Time : 1015 families discovered. RepeatScout/RECON discovery complete: 2844 families found Classification Time: 01:18:00 (hh:mm:ss) Elapsed Time Program Time: 22:44:57 (hh:mm:ss) Elapsed Time