RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HsVNZE/RM_26109.WedJul30437332024 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: 1720006652 Database = /dev/shm/rModeler.HsVNZE/GCA_903798025.1_fDanTra1.1 - Sequences = 11344 - Bases = 657340729 - N50 = 6561145 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 16482202-17659431 | [ 2 ] 15304973-16482201 | [ 2 ] 14127744-15304972 | [ 4 ] 12950516-14127744 | [ 2 ] 11773287-12950515 | [ 3 ] 10596058-11773286 | [ 2 ] 9418829-10596057 | [ 4 ] 8241601-9418829 | [ 3 ] 7064372-8241600 | [ 4 ] 5887143-7064371 | [ 3 ] 4709914-5887142 | [ 8 ] 3532686-4709914 | [ 13 ] 2355457-3532685 | [ 19 ] 1178228-2355456 | [ 42 ] 1000-1178228 |************************************************** [ 11233 ] Storage Throughput = excellent ( 1031.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42246166 bp ( 40007980 non ambiguous ) - Num Contigs Represented = 903 - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:05 (hh:mm:ss) Elapsed Time Round Time: 00:24:50 (hh:mm:ss) Elapsed Time : 722 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15483 repeats masked totaling 2133713 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10461723 bp Num Contigs Represented = 295 Non ambiguous bp: Initial: 10001669 bp After Masking: 7783360 bp Masked: 22.18 % -- Input Database Coverage: 10461723 bp out of 657340729 bp ( 1.59 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 94395 Comparison Time: 00:06:56 (hh:mm:ss) Elapsed Time, 15145 HSPs Collected Number of families returned by RECON: 1801 Round Time: 00:08:09 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50877 repeats masked totaling 7196631 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31784400 bp Num Contigs Represented = 699 Non ambiguous bp: Initial: 30006268 bp After Masking: 22575547 bp Masked: 24.76 % -- Input Database Coverage: 42246123 bp out of 657340729 bp ( 6.43 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 823686 Comparison Time: 00:36:32 (hh:mm:ss) Elapsed Time, 67561 HSPs Collected Number of families returned by RECON: 6133 Round Time: 00:40:51 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 169617 repeats masked totaling 24500632 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95791812 bp Num Contigs Represented = 1835 Non ambiguous bp: Initial: 90035697 bp After Masking: 64866862 bp Masked: 27.95 % -- Input Database Coverage: 138037935 bp out of 657340729 bp ( 21.00 % ) Sampling Time: 00:05:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7525260 Comparison Time: 04:11:39 (hh:mm:ss) Elapsed Time, 271961 HSPs Collected Number of families returned by RECON: 18329 Round Time: 04:32:10 (hh:mm:ss) Elapsed Time : 515 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 586623 repeats masked totaling 86695913 bp(s). - TE Masking time 00:12:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 287065925 bp Num Contigs Represented = 5070 Non ambiguous bp: Initial: 270016222 bp After Masking: 181285454 bp Masked: 32.86 % -- Input Database Coverage: 425103860 bp out of 657340729 bp ( 64.67 % ) Sampling Time: 00:22:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 67262601 Comparison Time: 31:45:28 (hh:mm:ss) Elapsed Time, 659159 HSPs Collected Number of families returned by RECON: 57502 Round Time: 33:46:28 (hh:mm:ss) Elapsed Time : 1085 families discovered. RepeatScout/RECON discovery complete: 2516 families found Classification Time: 01:23:02 (hh:mm:ss) Elapsed Time Program Time: 40:55:30 (hh:mm:ss) Elapsed Time