RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.W1Qqqy/RM_1233409.SunDec31441562023 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: 1701643315 Database = /dev/shm/rModeler.W1Qqqy/GCF_020826845.1_mDicBic1.mat.cur - Sequences = 1076 - Bases = 3005535620 - 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 |************************************************** [ 1032 ] Storage Throughput = excellent ( 1332.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024203 bp ( 40023990 non ambiguous ) - Num Contigs Represented = 146 - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:06 (hh:mm:ss) Elapsed Time Round Time: 00:33:32 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10131 repeats masked totaling 3288493 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029624 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 10029611 bp After Masking: 6146029 bp Masked: 38.72 % -- Input Database Coverage: 10029624 bp out of 3005535620 bp ( 0.33 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 17287 HSPs Collected Number of families returned by RECON: 652 Round Time: 00:07:22 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33746 repeats masked totaling 10474591 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034705 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 30034505 bp After Masking: 17882946 bp Masked: 40.46 % -- Input Database Coverage: 40064329 bp out of 3005535620 bp ( 1.33 % ) Sampling Time: 00:03:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:23:52 (hh:mm:ss) Elapsed Time, 36710 HSPs Collected Number of families returned by RECON: 2181 Round Time: 00:28:36 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110220 repeats masked totaling 33022253 bp(s). - TE Masking time 00:02:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90046508 bp Num Contigs Represented = 238 Non ambiguous bp: Initial: 90018625 bp After Masking: 51600062 bp Masked: 42.68 % -- Input Database Coverage: 130110837 bp out of 3005535620 bp ( 4.33 % ) Sampling Time: 00:11:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:30:58 (hh:mm:ss) Elapsed Time, 251907 HSPs Collected Number of families returned by RECON: 7644 Round Time: 02:47:50 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 370123 repeats masked totaling 106457754 bp(s). - TE Masking time 00:09:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270092972 bp Num Contigs Represented = 433 Non ambiguous bp: Initial: 270012855 bp After Masking: 148426768 bp Masked: 45.03 % -- Input Database Coverage: 400203809 bp out of 3005535620 bp ( 13.32 % ) Sampling Time: 00:32:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 18:21:52 (hh:mm:ss) Elapsed Time, 1443937 HSPs Collected Number of families returned by RECON: 29846 Round Time: 19:15:17 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatScout/RECON discovery complete: 867 families found Classification Time: 01:05:15 (hh:mm:ss) Elapsed Time Program Time: 24:17:52 (hh:mm:ss) Elapsed Time