RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0oSNAP/RM_3753556.SunJul211143452024 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: 1721587423 Database = /dev/shm/rModeler.0oSNAP/GCF_022985175.1_IGBB_LRoh.1.0 - Sequences = 2870 - Bases = 1126558565 - N50 = 38858801 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 62274233-66722287 | [ 1 ] 57826179-62274232 | [ 1 ] 53378125-57826178 | [ 1 ] 48930071-53378124 | [ 1 ] 44482017-48930070 | [ 2 ] 40033963-44482016 | [ 1 ] 35585909-40033962 | [ 8 ] 31137856-35585909 | [ 6 ] 26689802-31137855 | [ 4 ] 22241748-26689801 | [ ] 17793694-22241747 | [ ] 13345640-17793693 | [ ] 8897586-13345639 | [ ] 4449532-8897585 | [ 1 ] 1479-4449532 |************************************************** [ 2844 ] Storage Throughput = good ( 790.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 47141762 bp ( 40038605 non ambiguous ) - Num Contigs Represented = 214 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:41 (hh:mm:ss) Elapsed Time Round Time: 00:24:46 (hh:mm:ss) Elapsed Time : 1016 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20074 repeats masked totaling 3376857 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11742094 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 10013804 bp After Masking: 6350220 bp Masked: 36.59 % -- Input Database Coverage: 11742094 bp out of 1126558565 bp ( 1.04 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48205 Comparison Time: 00:17:47 (hh:mm:ss) Elapsed Time, 16456 HSPs Collected Number of families returned by RECON: 1619 Round Time: 00:20:18 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62147 repeats masked totaling 10176794 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 35399588 bp Num Contigs Represented = 161 Non ambiguous bp: Initial: 30024721 bp After Masking: 19003116 bp Masked: 36.71 % -- Input Database Coverage: 47141682 bp out of 1126558565 bp ( 4.18 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 429201 Comparison Time: 01:10:30 (hh:mm:ss) Elapsed Time, 49157 HSPs Collected Number of families returned by RECON: 5115 Round Time: 01:17:18 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 196274 repeats masked totaling 31912937 bp(s). - TE Masking time 00:03:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 108560874 bp Num Contigs Represented = 413 Non ambiguous bp: Initial: 90014701 bp After Masking: 55476406 bp Masked: 38.37 % -- Input Database Coverage: 155702556 bp out of 1126558565 bp ( 13.82 % ) Sampling Time: 00:14:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4099816 Comparison Time: 06:17:33 (hh:mm:ss) Elapsed Time, 290101 HSPs Collected Number of families returned by RECON: 15662 Round Time: 06:50:07 (hh:mm:ss) Elapsed Time : 600 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 663202 repeats masked totaling 111249286 bp(s). - TE Masking time 00:20:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 319521393 bp Num Contigs Represented = 1041 Non ambiguous bp: Initial: 270018646 bp After Masking: 151247981 bp Masked: 43.99 % -- Input Database Coverage: 475223949 bp out of 1126558565 bp ( 42.18 % ) Sampling Time: 00:53:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36010341 Comparison Time: 57:35:40 (hh:mm:ss) Elapsed Time, 739940 HSPs Collected Number of families returned by RECON: 47222 Round Time: 60:17:24 (hh:mm:ss) Elapsed Time : 1282 families discovered. RepeatScout/RECON discovery complete: 3052 families found Classification Time: 01:47:59 (hh:mm:ss) Elapsed Time Program Time: 70:57:52 (hh:mm:ss) Elapsed Time