RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.5Bmdw6/RM_1985131.FriNov151109262024 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: 1731697766 Database = /scratch/tmp/rModeler.5Bmdw6/GCF_963921805.1_bPhaCar2.1 - Sequences = 350 - Bases = 1283623959 - N50 = 129753630 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204318147-218912229 | [ 1 ] 189724065-204318146 | [ ] 175129983-189724064 | [ ] 160535901-175129982 | [ 1 ] 145941819-160535900 | [ ] 131347737-145941818 | [ ] 116753655-131347736 | [ 1 ] 102159573-116753654 | [ ] 87565491-102159572 | [ ] 72971409-87565490 | [ 2 ] 58377327-72971408 | [ 2 ] 43783245-58377326 | [ 2 ] 29189163-43783244 | [ 1 ] 14595081-29189162 |* [ 7 ] 1000-14595081 |************************************************** [ 333 ] Storage Throughput = excellent ( 1597.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028787 bp ( 40024787 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:10 (hh:mm:ss) Elapsed Time Round Time: 00:14:22 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1509 repeats masked totaling 684732 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026758 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10024958 bp After Masking: 9072263 bp Masked: 9.50 % -- Input Database Coverage: 10026758 bp out of 1283623959 bp ( 0.78 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:26 (hh:mm:ss) Elapsed Time, 19105 HSPs Collected Number of families returned by RECON: 251 Round Time: 00:04:09 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4820 repeats masked totaling 2457139 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041877 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30039677 bp After Masking: 26819292 bp Masked: 10.72 % -- Input Database Coverage: 40068635 bp out of 1283623959 bp ( 3.12 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:14:56 (hh:mm:ss) Elapsed Time, 12886 HSPs Collected Number of families returned by RECON: 1306 Round Time: 00:17:00 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16115 repeats masked totaling 7206078 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019194 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 90011594 bp After Masking: 80530647 bp Masked: 10.53 % -- Input Database Coverage: 130087829 bp out of 1283623959 bp ( 10.13 % ) Sampling Time: 00:06:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:33:08 (hh:mm:ss) Elapsed Time, 100955 HSPs Collected Number of families returned by RECON: 8070 Round Time: 01:46:48 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56887 repeats masked totaling 25200492 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040874 bp Num Contigs Represented = 186 Non ambiguous bp: Initial: 270018757 bp After Masking: 236954401 bp Masked: 12.25 % -- Input Database Coverage: 400128703 bp out of 1283623959 bp ( 31.17 % ) Sampling Time: 00:20:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 11:10:07 (hh:mm:ss) Elapsed Time, 2995568 HSPs Collected Number of families returned by RECON: 53494 Round Time: 11:45:04 (hh:mm:ss) Elapsed Time : 224 families discovered. RepeatScout/RECON discovery complete: 360 families found Classification Time: 00:13:20 (hh:mm:ss) Elapsed Time Program Time: 14:20:43 (hh:mm:ss) Elapsed Time