RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ScgwzK/RM_2141325.WedMar202056162024 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: 1710993376 Database = /dev/shm/rModeler.ScgwzK/GCA_036373705.1_fAmiCal2.hap1 - Sequences = 390 - Bases = 989120851 - N50 = 44214953 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 60087555-64379224 | [ 2 ] 55795886-60087554 | [ 1 ] 51504217-55795885 | [ 2 ] 47212548-51504216 | [ 2 ] 42920879-47212547 | [ 3 ] 38629210-42920878 | [ 1 ] 34337541-38629209 | [ 3 ] 30045872-34337540 | [ 2 ] 25754203-30045871 | [ 3 ] 21462534-25754202 | [ 4 ] 17170865-21462533 | [ ] 12879196-17170864 | [ ] 8587527-12879195 | [ ] 4295858-8587526 | [ ] 4190-4295858 |************************************************** [ 367 ] Storage Throughput = excellent ( 1515.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025264 bp ( 40024864 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:32 (hh:mm:ss) Elapsed Time Round Time: 00:25:49 (hh:mm:ss) Elapsed Time : 455 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7377 repeats masked totaling 2376747 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003456 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10003456 bp After Masking: 7075247 bp Masked: 29.27 % -- Input Database Coverage: 10003456 bp out of 989120851 bp ( 1.01 % ) Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 7356 HSPs Collected Number of families returned by RECON: 975 Round Time: 00:08:03 (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 : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19499 repeats masked totaling 6838801 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021803 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30021403 bp After Masking: 21392523 bp Masked: 28.74 % -- Input Database Coverage: 40025259 bp out of 989120851 bp ( 4.05 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:57:31 (hh:mm:ss) Elapsed Time, 49480 HSPs Collected Number of families returned by RECON: 3545 Round Time: 01:04:20 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66495 repeats masked totaling 22468343 bp(s). - TE Masking time 00:02:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013778 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 90011178 bp After Masking: 62767986 bp Masked: 30.27 % -- Input Database Coverage: 130039037 bp out of 989120851 bp ( 13.15 % ) Sampling Time: 00:12:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 03:09:03 (hh:mm:ss) Elapsed Time, 285076 HSPs Collected Number of families returned by RECON: 11908 Round Time: 03:28:12 (hh:mm:ss) Elapsed Time : 369 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 237902 repeats masked totaling 76030013 bp(s). - TE Masking time 00:10:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027659 bp Num Contigs Represented = 240 Non ambiguous bp: Initial: 270022859 bp After Masking: 178071063 bp Masked: 34.05 % -- Input Database Coverage: 400066696 bp out of 989120851 bp ( 40.45 % ) Sampling Time: 00:43:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 19:53:34 (hh:mm:ss) Elapsed Time, 1216543 HSPs Collected Number of families returned by RECON: 40358 Round Time: 21:17:37 (hh:mm:ss) Elapsed Time : 947 families discovered. RepeatScout/RECON discovery complete: 1842 families found Classification Time: 01:41:30 (hh:mm:ss) Elapsed Time Program Time: 28:05:31 (hh:mm:ss) Elapsed Time