RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VrP0R6/RM_33852.FriJan60030022023 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: 1672993801 Database = /dev/shm/rModeler.VrP0R6/GCA_020826845.1_mDicBic1.mat.cur - Sequences = 1075 - Bases = 3005519209 - N50 = 67717171 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130599750-139927959 | [ 1 ] 121271542-130599750 | [ ] 111943334-121271542 | [ ] 102615126-111943334 | [ 2 ] 93286918-102615126 | [ 4 ] 83958710-93286918 | [ 4 ] 74630502-83958710 | [ 2 ] 65302294-74630502 | [ 3 ] 55974086-65302294 | [ 8 ] 46645878-55974086 | [ 3 ] 37317670-46645878 | [ 7 ] 27989462-37317670 | [ 5 ] 18661254-27989462 | [ 2 ] 9333046-18661254 | [ 3 ] 4838-9333046 |************************************************** [ 1031 ] Storage Throughput = excellent ( 1370.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078892 bp ( 40038881 non ambiguous ) - Num Contigs Represented = 150 - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:18 (hh:mm:ss) Elapsed Time Round Time: 00:48:43 (hh:mm:ss) Elapsed Time : 256 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (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... 11274 repeats masked totaling 3405574 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10069261 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 10029250 bp After Masking: 6121761 bp Masked: 38.96 % -- Input Database Coverage: 10069261 bp out of 3005519209 bp ( 0.34 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:06 (hh:mm:ss) Elapsed Time, 3472 HSPs Collected Number of families returned by RECON: 596 Round Time: 00:08:05 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34789 repeats masked totaling 10380784 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009609 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 30009609 bp After Masking: 18039090 bp Masked: 39.89 % -- Input Database Coverage: 40078870 bp out of 3005519209 bp ( 1.33 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:27:49 (hh:mm:ss) Elapsed Time, 26275 HSPs Collected Number of families returned by RECON: 2209 Round Time: 00:32:53 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113639 repeats masked totaling 33491799 bp(s). - TE Masking time 00:02:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90051716 bp Num Contigs Represented = 227 Non ambiguous bp: Initial: 90015867 bp After Masking: 52161114 bp Masked: 42.05 % -- Input Database Coverage: 130130586 bp out of 3005519209 bp ( 4.33 % ) Sampling Time: 00:12:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:37:21 (hh:mm:ss) Elapsed Time, 112413 HSPs Collected Number of families returned by RECON: 7552 Round Time: 02:54:44 (hh:mm:ss) Elapsed Time : 177 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 369724 repeats masked totaling 110075805 bp(s). - TE Masking time 00:09:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270187351 bp Num Contigs Represented = 416 Non ambiguous bp: Initial: 270023560 bp After Masking: 145319102 bp Masked: 46.18 % -- Input Database Coverage: 400317937 bp out of 3005519209 bp ( 13.32 % ) Sampling Time: 00:34:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 18:14:47 (hh:mm:ss) Elapsed Time, 320724 HSPs Collected Number of families returned by RECON: 29106 Round Time: 19:23:41 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 861 families found Classification Time: 01:09:04 (hh:mm:ss) Elapsed Time Program Time: 24:57:10 (hh:mm:ss) Elapsed Time