RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.t3aNe0/RM_23833.WedNov291011102023 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: 1701281469 Database = /dev/shm/rModeler.t3aNe0/GCA_028858555.1_bAraAra1.hap2 - Sequences = 274 - Bases = 1302242811 - N50 = 127372135 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 158461083-169778623 | [ 2 ] 147143544-158461083 | [ ] 135826005-147143544 | [ ] 124508466-135826005 | [ 2 ] 113190927-124508466 | [ ] 101873388-113190927 | [ 1 ] 90555849-101873388 | [ 1 ] 79238309-90555848 | [ 1 ] 67920770-79238309 | [ ] 56603231-67920770 | [ 1 ] 45285692-56603231 | [ ] 33968153-45285692 | [ 1 ] 22650614-33968153 | [ 3 ] 11333075-22650614 | [ 5 ] 15536-11333075 |************************************************** [ 257 ] Storage Throughput = excellent ( 1146.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40089175 bp ( 40007389 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:06 (hh:mm:ss) Elapsed Time Round Time: 00:42:33 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3567 repeats masked totaling 1216826 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031995 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10031595 bp After Masking: 7835857 bp Masked: 21.89 % -- Input Database Coverage: 10031995 bp out of 1302242811 bp ( 0.77 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 1295 HSPs Collected Number of families returned by RECON: 176 Round Time: 00:07:49 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10607 repeats masked totaling 3540782 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30097035 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30015649 bp After Masking: 24181363 bp Masked: 19.44 % -- Input Database Coverage: 40129030 bp out of 1302242811 bp ( 3.08 % ) Sampling Time: 00:03:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:32:47 (hh:mm:ss) Elapsed Time, 11568 HSPs Collected Number of families returned by RECON: 990 Round Time: 00:41:31 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33517 repeats masked totaling 10576852 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045940 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 90009566 bp After Masking: 70597597 bp Masked: 21.57 % -- Input Database Coverage: 130174970 bp out of 1302242811 bp ( 10.00 % ) Sampling Time: 00:14:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 04:03:15 (hh:mm:ss) Elapsed Time, 33205 HSPs Collected Number of families returned by RECON: 7043 Round Time: 04:27:32 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108046 repeats masked totaling 34217919 bp(s). - TE Masking time 00:03:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270328127 bp Num Contigs Represented = 167 Non ambiguous bp: Initial: 270002078 bp After Masking: 212833142 bp Masked: 21.17 % -- Input Database Coverage: 400503097 bp out of 1302242811 bp ( 30.75 % ) Sampling Time: 00:43:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 32:02:45 (hh:mm:ss) Elapsed Time, 340168 HSPs Collected Number of families returned by RECON: 47366 Round Time: 33:28:08 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatScout/RECON discovery complete: 341 families found Classification Time: 00:39:37 (hh:mm:ss) Elapsed Time Program Time: 40:07:10 (hh:mm:ss) Elapsed Time