RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.G9iiAg/RM_4009173.SatJun291545222024 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: 1719701120 Database = /dev/shm/rModeler.G9iiAg/GCF_905237075.1_dlabrax2021 - Sequences = 303 - Bases = 695910406 - N50 = 29990674 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35357242-37882625 | [ 1 ] 32831859-35357242 | [ 4 ] 30306476-32831859 | [ 4 ] 27781093-30306476 | [ 4 ] 25255710-27781093 | [ 5 ] 22730327-25255710 | [ 2 ] 20204944-22730327 | [ 2 ] 17679561-20204944 | [ ] 15154178-17679561 | [ 2 ] 12628795-15154178 | [ ] 10103412-12628795 | [ ] 7578029-10103412 | [ ] 5052646-7578029 | [ ] 2527263-5052646 | [ ] 1880-2527263 |************************************************** [ 279 ] Storage Throughput = good ( 882.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078638 bp ( 40028186 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:33 (hh:mm:ss) Elapsed Time Round Time: 00:22:09 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6628 repeats masked totaling 840618 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024239 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10023639 bp After Masking: 8792217 bp Masked: 12.29 % -- Input Database Coverage: 10024239 bp out of 695910406 bp ( 1.44 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:49 (hh:mm:ss) Elapsed Time, 8279 HSPs Collected Number of families returned by RECON: 1778 Round Time: 00:07:22 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22537 repeats masked totaling 2861805 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30054319 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30004467 bp After Masking: 26261500 bp Masked: 12.47 % -- Input Database Coverage: 40078558 bp out of 695910406 bp ( 5.76 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:30:46 (hh:mm:ss) Elapsed Time, 66267 HSPs Collected Number of families returned by RECON: 6600 Round Time: 00:36:07 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85377 repeats masked totaling 11528638 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039782 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 90005175 bp After Masking: 75355338 bp Masked: 16.28 % -- Input Database Coverage: 130118340 bp out of 695910406 bp ( 18.70 % ) Sampling Time: 00:11:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 03:27:26 (hh:mm:ss) Elapsed Time, 317906 HSPs Collected Number of families returned by RECON: 21772 Round Time: 03:55:09 (hh:mm:ss) Elapsed Time : 510 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 335876 repeats masked totaling 48333296 bp(s). - TE Masking time 00:09:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270492242 bp Num Contigs Represented = 178 Non ambiguous bp: Initial: 270031776 bp After Masking: 213268017 bp Masked: 21.02 % -- Input Database Coverage: 400610582 bp out of 695910406 bp ( 57.57 % ) Sampling Time: 00:37:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 26:02:57 (hh:mm:ss) Elapsed Time, 935889 HSPs Collected Number of families returned by RECON: 77400 Round Time: 29:16:47 (hh:mm:ss) Elapsed Time : 1331 families discovered. RepeatScout/RECON discovery complete: 2373 families found Classification Time: 01:53:56 (hh:mm:ss) Elapsed Time Program Time: 36:11:30 (hh:mm:ss) Elapsed Time