RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tOCTEf/RM_2256600.TueJul91011002024 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: 1720545060 Database = /dev/shm/rModeler.tOCTEf/GCF_030265065.1_ASM3026506v1 - Sequences = 109 - Bases = 1326793283 - N50 = 59712696 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 79429030-85101349 | [ 1 ] 73756711-79429029 | [ 1 ] 68084393-73756711 | [ ] 62412074-68084392 |** [ 4 ] 56739755-62412073 |**** [ 7 ] 51067437-56739755 |* [ 3 ] 45395118-51067436 |* [ 2 ] 39722799-45395117 |* [ 3 ] 34050481-39722799 | [ 1 ] 28378162-34050480 | [ ] 22705843-28378161 | [ ] 17033525-22705843 | [ ] 11361206-17033524 | [ 1 ] 5688887-11361205 | [ 1 ] 16569-5688887 |************************************************** [ 85 ] Storage Throughput = excellent ( 1122.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003222 bp ( 40003222 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:09 (hh:mm:ss) Elapsed Time Round Time: 00:23:53 (hh:mm:ss) Elapsed Time : 1001 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21009 repeats masked totaling 5546645 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001958 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001958 bp After Masking: 3274086 bp Masked: 67.27 % -- Input Database Coverage: 10001958 bp out of 1326793283 bp ( 0.75 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:24 (hh:mm:ss) Elapsed Time, 7947 HSPs Collected Number of families returned by RECON: 828 Round Time: 00:06:10 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66836 repeats masked totaling 17348038 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001184 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30001184 bp After Masking: 9897638 bp Masked: 67.01 % -- Input Database Coverage: 40003142 bp out of 1326793283 bp ( 3.02 % ) Sampling Time: 00:03:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:19:33 (hh:mm:ss) Elapsed Time, 35236 HSPs Collected Number of families returned by RECON: 2499 Round Time: 00:24:04 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 207480 repeats masked totaling 53133498 bp(s). - TE Masking time 00:03:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029469 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90029449 bp After Masking: 28153888 bp Masked: 68.73 % -- Input Database Coverage: 130032611 bp out of 1326793283 bp ( 9.80 % ) Sampling Time: 00:10:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:41:00 (hh:mm:ss) Elapsed Time, 168824 HSPs Collected Number of families returned by RECON: 6648 Round Time: 01:56:24 (hh:mm:ss) Elapsed Time : 376 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 670767 repeats masked totaling 167370005 bp(s). - TE Masking time 00:13:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035213 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 270035153 bp After Masking: 76085399 bp Masked: 71.82 % -- Input Database Coverage: 400067824 bp out of 1326793283 bp ( 30.15 % ) Sampling Time: 00:38:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 10:36:27 (hh:mm:ss) Elapsed Time, 414240 HSPs Collected Number of families returned by RECON: 18976 Round Time: 11:34:18 (hh:mm:ss) Elapsed Time : 776 families discovered. RepeatScout/RECON discovery complete: 2266 families found Classification Time: 01:16:37 (hh:mm:ss) Elapsed Time Program Time: 15:41:26 (hh:mm:ss) Elapsed Time