RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fWsjMx/RM_25722.SunJul212016382024 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: 1721618194 Database = /dev/shm/rModeler.fWsjMx/GCF_018340385.1_ASM1834038v1 - Sequences = 6701 - Bases = 1680134903 - N50 = 30158143 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 45211143-48440497 | [ 3 ] 41981790-45211143 | [ ] 38752437-41981790 | [ 4 ] 35523084-38752437 | [ 4 ] 32293731-35523084 | [ 4 ] 29064378-32293731 | [ 11 ] 25835025-29064378 | [ 12 ] 22605671-25835024 | [ 8 ] 19376318-22605671 | [ 4 ] 16146965-19376318 | [ ] 12917612-16146965 | [ ] 9688259-12917612 | [ ] 6458906-9688259 | [ ] 3229553-6458906 | [ 2 ] 200-3229553 |************************************************** [ 6649 ] Storage Throughput = excellent ( 1175.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40208278 bp ( 40016528 non ambiguous ) - Num Contigs Represented = 251 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:40 (hh:mm:ss) Elapsed Time Round Time: 00:31:34 (hh:mm:ss) Elapsed Time : 836 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11594 repeats masked totaling 2258677 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10060989 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 10011957 bp After Masking: 7530211 bp Masked: 24.79 % -- Input Database Coverage: 10060989 bp out of 1680134903 bp ( 0.60 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:17:27 (hh:mm:ss) Elapsed Time, 13115 HSPs Collected Number of families returned by RECON: 1861 Round Time: 00:19:29 (hh:mm:ss) Elapsed Time : 12 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 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36331 repeats masked totaling 7225697 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30147265 bp Num Contigs Represented = 208 Non ambiguous bp: Initial: 30004547 bp After Masking: 21967502 bp Masked: 26.79 % -- Input Database Coverage: 40208254 bp out of 1680134903 bp ( 2.39 % ) Sampling Time: 00:04:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 364231 Comparison Time: 01:23:13 (hh:mm:ss) Elapsed Time, 105178 HSPs Collected Number of families returned by RECON: 6460 Round Time: 01:31:59 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118393 repeats masked totaling 22941571 bp(s). - TE Masking time 00:03:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90449258 bp Num Contigs Represented = 502 Non ambiguous bp: Initial: 90011624 bp After Masking: 64619939 bp Masked: 28.21 % -- Input Database Coverage: 130657512 bp out of 1680134903 bp ( 7.78 % ) Sampling Time: 00:13:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3334653 Comparison Time: 08:28:45 (hh:mm:ss) Elapsed Time, 413044 HSPs Collected Number of families returned by RECON: 20089 Round Time: 09:20:52 (hh:mm:ss) Elapsed Time : 695 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 453565 repeats masked totaling 89310796 bp(s). - TE Masking time 00:22:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271341092 bp Num Contigs Represented = 1259 Non ambiguous bp: Initial: 270020153 bp After Masking: 173680640 bp Masked: 35.68 % -- Input Database Coverage: 401998604 bp out of 1680134903 bp ( 23.93 % ) Sampling Time: 00:52:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 29826226 Comparison Time: 65:25:37 (hh:mm:ss) Elapsed Time, 1149255 HSPs Collected Number of families returned by RECON: 61855 Round Time: 69:39:32 (hh:mm:ss) Elapsed Time : 1387 families discovered. RepeatScout/RECON discovery complete: 3053 families found Classification Time: 02:33:21 (hh:mm:ss) Elapsed Time Program Time: 83:56:47 (hh:mm:ss) Elapsed Time