RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.lNZrhu/RM_900522.MonNov180021102024 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: 1731918070 Database = /scratch/tmp/rModeler.lNZrhu/GCF_020745825.1_Agelaius_phoeniceus_1.1 - Sequences = 410 - Bases = 1188547179 - N50 = 73465035 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 144833273-155177309 | [ 1 ] 134489237-144833272 | [ ] 124145202-134489237 | [ ] 113801166-124145201 | [ 2 ] 103457131-113801166 | [ ] 93113095-103457130 | [ ] 82769059-93113094 | [ ] 72425024-82769059 | [ 2 ] 62080988-72425023 | [ 2 ] 51736953-62080988 | [ ] 41392917-51736952 | [ ] 31048881-41392916 | [ 3 ] 20704846-31048881 | [ 5 ] 10360810-20704845 | [ 7 ] 16775-10360810 |************************************************** [ 388 ] Storage Throughput = excellent ( 1545.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008166 bp ( 40005231 non ambiguous ) - Num Contigs Represented = 102 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:49 (hh:mm:ss) Elapsed Time Round Time: 00:13:40 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3948 repeats masked totaling 1243122 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027179 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10025744 bp After Masking: 8116537 bp Masked: 19.04 % -- Input Database Coverage: 10027179 bp out of 1188547179 bp ( 0.84 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:57 (hh:mm:ss) Elapsed Time, 80944 HSPs Collected Number of families returned by RECON: 343 Round Time: 00:03:38 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13330 repeats masked totaling 3575285 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020987 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 30019487 bp After Masking: 25251744 bp Masked: 15.88 % -- Input Database Coverage: 40048166 bp out of 1188547179 bp ( 3.37 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:14:00 (hh:mm:ss) Elapsed Time, 10408 HSPs Collected Number of families returned by RECON: 1925 Round Time: 00:15:42 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41153 repeats masked totaling 10558761 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018024 bp Num Contigs Represented = 152 Non ambiguous bp: Initial: 90012824 bp After Masking: 75605135 bp Masked: 16.01 % -- Input Database Coverage: 130066190 bp out of 1188547179 bp ( 10.94 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:28:32 (hh:mm:ss) Elapsed Time, 270193 HSPs Collected Number of families returned by RECON: 10698 Round Time: 01:38:10 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143147 repeats masked totaling 35522369 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016161 bp Num Contigs Represented = 258 Non ambiguous bp: Initial: 270004861 bp After Masking: 222427049 bp Masked: 17.62 % -- Input Database Coverage: 400082351 bp out of 1188547179 bp ( 33.66 % ) Sampling Time: 00:16:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 11:02:31 (hh:mm:ss) Elapsed Time, 965927 HSPs Collected Number of families returned by RECON: 71620 Round Time: 11:53:15 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatScout/RECON discovery complete: 605 families found Classification Time: 00:28:13 (hh:mm:ss) Elapsed Time Program Time: 14:32:38 (hh:mm:ss) Elapsed Time