RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.MrJiw5/RM_779590.SatNov162227352024 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: 1731824855 Database = /scratch/tmp/rModeler.MrJiw5/GCA_005190385.3_NGI_Narwhal_2 - Sequences = 101 - Bases = 2341954608 - N50 = 114124568 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 170061550-182208776 |* [ 2 ] 157914325-170061550 | [ 1 ] 145767100-157914325 | [ ] 133619874-145767099 |* [ 2 ] 121472649-133619874 | [ 1 ] 109325424-121472649 |* [ 2 ] 97178199-109325424 |** [ 4 ] 85030973-97178198 |** [ 4 ] 72883748-85030973 |* [ 3 ] 60736523-72883748 | [ ] 48589298-60736523 |* [ 2 ] 36442072-48589297 | [ ] 24294847-36442072 | [ 1 ] 12147622-24294847 | [ ] 397-12147622 |************************************************** [ 79 ] Storage Throughput = excellent ( 1443.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026079 bp ( 40024879 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:37 (hh:mm:ss) Elapsed Time Round Time: 00:13:30 (hh:mm:ss) Elapsed Time : 208 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10099 repeats masked totaling 2592426 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035420 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10035320 bp After Masking: 7333001 bp Masked: 26.93 % -- Input Database Coverage: 10035420 bp out of 2341954608 bp ( 0.43 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 8144 HSPs Collected Number of families returned by RECON: 1016 Round Time: 00:04:02 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37035 repeats masked totaling 9633774 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030584 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30029484 bp After Masking: 20272582 bp Masked: 32.49 % -- Input Database Coverage: 40066004 bp out of 2341954608 bp ( 1.71 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:40 (hh:mm:ss) Elapsed Time, 25076 HSPs Collected Number of families returned by RECON: 2278 Round Time: 00:14:43 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121751 repeats masked totaling 30963911 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004093 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90003593 bp After Masking: 58601239 bp Masked: 34.89 % -- Input Database Coverage: 130070097 bp out of 2341954608 bp ( 5.55 % ) Sampling Time: 00:04:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:13:53 (hh:mm:ss) Elapsed Time, 77730 HSPs Collected Number of families returned by RECON: 8574 Round Time: 01:20:26 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 404023 repeats masked totaling 99701268 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032313 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 270029113 bp After Masking: 168443733 bp Masked: 37.62 % -- Input Database Coverage: 400102410 bp out of 2341954608 bp ( 17.08 % ) Sampling Time: 00:15:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 07:53:24 (hh:mm:ss) Elapsed Time, 248015 HSPs Collected Number of families returned by RECON: 34598 Round Time: 08:18:51 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatScout/RECON discovery complete: 832 families found Classification Time: 00:14:48 (hh:mm:ss) Elapsed Time Program Time: 10:26:20 (hh:mm:ss) Elapsed Time