RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AssA5N/RM_9220.MonNov271023262023 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: 1701109405 Database = /dev/shm/rModeler.AssA5N/GCA_027410445.1_aDisPic1.pri - Sequences = 1318 - Bases = 3872602052 - N50 = 454653243 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 529718113-567555107 | [ 1 ] 491881119-529718112 | [ ] 454044126-491881119 | [ 2 ] 416207132-454044125 | [ 1 ] 378370138-416207131 | [ 1 ] 340533145-378370138 | [ ] 302696151-340533144 | [ ] 264859157-302696150 | [ 1 ] 227022164-264859157 | [ 1 ] 189185170-227022163 | [ 1 ] 151348176-189185169 | [ ] 113511183-151348176 | [ 2 ] 75674189-113511182 | [ 3 ] 37837195-75674188 | [ 1 ] 202-37837195 |************************************************** [ 1304 ] Storage Throughput = excellent ( 1223.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40708454 bp ( 40013880 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:07:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:09 (hh:mm:ss) Elapsed Time Round Time: 00:41:26 (hh:mm:ss) Elapsed Time : 825 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18755 repeats masked totaling 4660749 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10130587 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001154 bp After Masking: 4229702 bp Masked: 57.71 % -- Input Database Coverage: 10130587 bp out of 3872602052 bp ( 0.26 % ) Sampling Time: 00:04:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:54 (hh:mm:ss) Elapsed Time, 15110 HSPs Collected Number of families returned by RECON: 1213 Round Time: 00:12:32 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59286 repeats masked totaling 14977507 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30577862 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30012721 bp After Masking: 11877754 bp Masked: 60.42 % -- Input Database Coverage: 40708449 bp out of 3872602052 bp ( 1.05 % ) Sampling Time: 00:14:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:25:11 (hh:mm:ss) Elapsed Time, 53627 HSPs Collected Number of families returned by RECON: 3881 Round Time: 00:43:08 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:17:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189694 repeats masked totaling 46585873 bp(s). - TE Masking time 00:03:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91393201 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 90024774 bp After Masking: 33069982 bp Masked: 63.27 % -- Input Database Coverage: 132101650 bp out of 3872602052 bp ( 3.41 % ) Sampling Time: 00:48:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2634660 Comparison Time: 02:17:08 (hh:mm:ss) Elapsed Time, 178297 HSPs Collected Number of families returned by RECON: 9709 Round Time: 03:14:20 (hh:mm:ss) Elapsed Time : 373 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:51:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:07:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 616447 repeats masked totaling 150488310 bp(s). - TE Masking time 00:16:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273927825 bp Num Contigs Represented = 245 Non ambiguous bp: Initial: 270027587 bp After Masking: 90080370 bp Masked: 66.64 % -- Input Database Coverage: 406029475 bp out of 3872602052 bp ( 10.48 % ) Sampling Time: 02:16:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23760171 Comparison Time: 15:46:15 (hh:mm:ss) Elapsed Time, 628833 HSPs Collected Number of families returned by RECON: 25592 Round Time: 18:44:25 (hh:mm:ss) Elapsed Time : 1084 families discovered. RepeatScout/RECON discovery complete: 2430 families found Classification Time: 01:44:06 (hh:mm:ss) Elapsed Time Program Time: 25:19:57 (hh:mm:ss) Elapsed Time