RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nji2Hq/RM_105706.ThuApr170701142025 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: 1744898472 Database = /dev/shm/rModeler.nji2Hq/GCA_964662095.1_mMusNiv2.hap2.1 - Sequences = 2239 - Bases = 2835054152 - N50 = 141755683 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202634858-217108705 | [ 1 ] 188161011-202634858 | [ 1 ] 173687164-188161011 | [ ] 159213317-173687164 | [ 3 ] 144739470-159213317 | [ 2 ] 130265623-144739470 | [ 1 ] 115791776-130265623 | [ 1 ] 101317929-115791776 | [ 3 ] 86844082-101317929 | [ 2 ] 72370235-86844082 | [ 1 ] 57896388-72370235 | [ 3 ] 43422541-57896388 | [ 1 ] 28948694-43422541 | [ 1 ] 14474847-28948694 | [ ] 1000-14474847 |************************************************** [ 2219 ] Storage Throughput = excellent ( 1673.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012940 bp ( 40006347 non ambiguous ) - Num Contigs Represented = 179 - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:26 (hh:mm:ss) Elapsed Time Round Time: 00:13:51 (hh:mm:ss) Elapsed Time : 167 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 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13037 repeats masked totaling 3595789 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035503 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10034965 bp After Masking: 6399548 bp Masked: 36.23 % -- Input Database Coverage: 10035503 bp out of 2835054152 bp ( 0.35 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:01 (hh:mm:ss) Elapsed Time, 3997 HSPs Collected Number of families returned by RECON: 636 Round Time: 00:03:48 (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 : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41903 repeats masked totaling 11794068 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017308 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 30011253 bp After Masking: 18088550 bp Masked: 39.73 % -- Input Database Coverage: 40052811 bp out of 2835054152 bp ( 1.41 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:12:24 (hh:mm:ss) Elapsed Time, 39106 HSPs Collected Number of families returned by RECON: 2048 Round Time: 00:14:32 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 130721 repeats masked totaling 37313380 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030245 bp Num Contigs Represented = 357 Non ambiguous bp: Initial: 90017845 bp After Masking: 52318889 bp Masked: 41.88 % -- Input Database Coverage: 130083056 bp out of 2835054152 bp ( 4.59 % ) Sampling Time: 00:05:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 01:03:49 (hh:mm:ss) Elapsed Time, 92080 HSPs Collected Number of families returned by RECON: 7063 Round Time: 01:10:37 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 420499 repeats masked totaling 118859872 bp(s). - TE Masking time 00:03:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270088477 bp Num Contigs Represented = 775 Non ambiguous bp: Initial: 270037077 bp After Masking: 150090422 bp Masked: 44.42 % -- Input Database Coverage: 400171533 bp out of 2835054152 bp ( 14.12 % ) Sampling Time: 00:15:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23526370 Comparison Time: 07:06:54 (hh:mm:ss) Elapsed Time, 208584 HSPs Collected Number of families returned by RECON: 28848 Round Time: 07:30:20 (hh:mm:ss) Elapsed Time : 323 families discovered. RepeatScout/RECON discovery complete: 684 families found Classification Time: 00:21:32 (hh:mm:ss) Elapsed Time Program Time: 09:34:40 (hh:mm:ss) Elapsed Time