RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wZjYu0/RM_2666.ThuNov301832332023 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: 1701397951 Database = /dev/shm/rModeler.wZjYu0/GCA_030014295.1_mLoxAfr1.hap2 - Sequences = 880 - Bases = 3540893228 - N50 = 135789635 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 225734151-241857137 | [ 2 ] 209611165-225734150 | [ 1 ] 193488180-209611165 | [ 1 ] 177365194-193488179 | [ 1 ] 161242209-177365194 | [ 1 ] 145119223-161242208 | [ ] 128996238-145119223 | [ 3 ] 112873252-128996237 | [ 2 ] 96750267-112873252 | [ 2 ] 80627281-96750266 | [ 8 ] 64504296-80627281 | [ 5 ] 48381310-64504295 | [ 1 ] 32258325-48381310 | [ 1 ] 16135339-32258324 | [ 1 ] 12354-16135339 |************************************************** [ 851 ] Storage Throughput = excellent ( 1224.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40119576 bp ( 40039563 non ambiguous ) - Num Contigs Represented = 101 - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:12 (hh:mm:ss) Elapsed Time Round Time: 00:38:59 (hh:mm:ss) Elapsed Time : 278 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16311 repeats masked totaling 4591930 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002420 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10002420 bp After Masking: 5153761 bp Masked: 48.47 % -- Input Database Coverage: 10002420 bp out of 3540893228 bp ( 0.28 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 23638 HSPs Collected Number of families returned by RECON: 706 Round Time: 00:08:52 (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 : 00:01:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49757 repeats masked totaling 13709940 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30117076 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 30037063 bp After Masking: 15233916 bp Masked: 49.28 % -- Input Database Coverage: 40119496 bp out of 3540893228 bp ( 1.13 % ) Sampling Time: 00:06:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:40:12 (hh:mm:ss) Elapsed Time, 533875 HSPs Collected Number of families returned by RECON: 2032 Round Time: 00:50:22 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157809 repeats masked totaling 43067808 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90077090 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 90027777 bp After Masking: 44253589 bp Masked: 50.84 % -- Input Database Coverage: 130196586 bp out of 3540893228 bp ( 3.68 % ) Sampling Time: 00:18:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:38:38 (hh:mm:ss) Elapsed Time, 3078008 HSPs Collected Number of families returned by RECON: 6821 Round Time: 04:02:46 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 529403 repeats masked totaling 140236440 bp(s). - TE Masking time 00:08:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270378679 bp Num Contigs Represented = 303 Non ambiguous bp: Initial: 270037650 bp After Masking: 121448038 bp Masked: 55.03 % -- Input Database Coverage: 400575265 bp out of 3540893228 bp ( 11.31 % ) Sampling Time: 00:58:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 25:03:51 (hh:mm:ss) Elapsed Time, 19995860 HSPs Collected Number of families returned by RECON: 22855 Round Time: 26:59:08 (hh:mm:ss) Elapsed Time : 388 families discovered. RepeatScout/RECON discovery complete: 911 families found Classification Time: 00:44:21 (hh:mm:ss) Elapsed Time Program Time: 33:24:28 (hh:mm:ss) Elapsed Time