RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6Bgke2/RM_24620.FriJul191744262024 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: 1721436255 Database = /dev/shm/rModeler.6Bgke2/GCF_014905685.2_NemWhi1 - Sequences = 18998 - Bases = 1218316901 - N50 = 51351675 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 88803859-95146955 | [ 1 ] 82460763-88803858 | [ ] 76117667-82460762 | [ ] 69774571-76117666 | [ ] 63431475-69774570 | [ ] 57088379-63431474 | [ 3 ] 50745283-57088378 | [ 6 ] 44402187-50745282 | [ 6 ] 38059091-44402186 | [ 4 ] 31715995-38059090 | [ 2 ] 25372899-31715994 | [ ] 19029803-25372898 | [ 1 ] 12686707-19029802 | [ ] 6343611-12686706 | [ ] 516-6343611 |************************************************** [ 18975 ] Storage Throughput = good ( 816.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43303441 bp ( 40017743 non ambiguous ) - Num Contigs Represented = 729 - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:51 (hh:mm:ss) Elapsed Time Round Time: 00:38:30 (hh:mm:ss) Elapsed Time : 772 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17454 repeats masked totaling 5035673 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10785545 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 10000997 bp After Masking: 4753319 bp Masked: 52.47 % -- Input Database Coverage: 10785545 bp out of 1218316901 bp ( 0.89 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 100128 Comparison Time: 00:40:44 (hh:mm:ss) Elapsed Time, 8383 HSPs Collected Number of families returned by RECON: 935 Round Time: 00:43:18 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54739 repeats masked totaling 14761483 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32517816 bp Num Contigs Represented = 534 Non ambiguous bp: Initial: 30016666 bp After Masking: 14599030 bp Masked: 51.36 % -- Input Database Coverage: 43303361 bp out of 1218316901 bp ( 3.55 % ) Sampling Time: 00:03:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 816003 Comparison Time: 01:49:29 (hh:mm:ss) Elapsed Time, 32758 HSPs Collected Number of families returned by RECON: 3042 Round Time: 01:55:10 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 170353 repeats masked totaling 45983031 bp(s). - TE Masking time 00:03:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 97694383 bp Num Contigs Represented = 1613 Non ambiguous bp: Initial: 90021587 bp After Masking: 41988119 bp Masked: 53.36 % -- Input Database Coverage: 140997744 bp out of 1218316901 bp ( 11.57 % ) Sampling Time: 00:10:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7556328 Comparison Time: 06:19:57 (hh:mm:ss) Elapsed Time, 182781 HSPs Collected Number of families returned by RECON: 8974 Round Time: 06:40:34 (hh:mm:ss) Elapsed Time : 354 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 553636 repeats masked totaling 148462121 bp(s). - TE Masking time 00:14:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 293951157 bp Num Contigs Represented = 4564 Non ambiguous bp: Initial: 270013347 bp After Masking: 115491109 bp Masked: 57.23 % -- Input Database Coverage: 434948901 bp out of 1218316901 bp ( 35.70 % ) Sampling Time: 00:35:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 65774715 Comparison Time: 25:13:29 (hh:mm:ss) Elapsed Time, 522444 HSPs Collected Number of families returned by RECON: 28905 Round Time: 26:27:28 (hh:mm:ss) Elapsed Time : 869 families discovered. RepeatScout/RECON discovery complete: 2071 families found Classification Time: 01:43:47 (hh:mm:ss) Elapsed Time Program Time: 38:08:47 (hh:mm:ss) Elapsed Time