RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Gw0AlH/RM_3289927.FriNov151321482024 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: 1731705708 Database = /scratch/tmp/rModeler.Gw0AlH/GCA_038363095.2_mArtLit.hap1 - Sequences = 487 - Bases = 2311617438 - N50 = 175940624 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 229207642-245578882 | [ 1 ] 212836402-229207642 | [ 1 ] 196465162-212836402 | [ ] 180093922-196465162 | [ 2 ] 163722682-180093922 | [ 1 ] 147351442-163722682 | [ 3 ] 130980202-147351442 | [ ] 114608962-130980202 | [ 2 ] 98237722-114608962 | [ 3 ] 81866482-98237722 | [ ] 65495242-81866482 | [ ] 49124002-65495242 | [ 3 ] 32752762-49124002 | [ 1 ] 16381522-32752762 | [ ] 10282-16381522 |************************************************** [ 470 ] Storage Throughput = excellent ( 1545.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008990 bp ( 40008690 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:36 (hh:mm:ss) Elapsed Time Round Time: 00:14:32 (hh:mm:ss) Elapsed Time : 198 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7906 repeats masked totaling 2244395 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037240 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10037140 bp After Masking: 7609576 bp Masked: 24.19 % -- Input Database Coverage: 10037240 bp out of 2311617438 bp ( 0.43 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:35 (hh:mm:ss) Elapsed Time, 168328 HSPs Collected Number of families returned by RECON: 735 Round Time: 00:06:57 (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 : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28448 repeats masked totaling 7886882 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011746 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30011546 bp After Masking: 21595440 bp Masked: 28.04 % -- Input Database Coverage: 40048986 bp out of 2311617438 bp ( 1.73 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:15:24 (hh:mm:ss) Elapsed Time, 433124 HSPs Collected Number of families returned by RECON: 2337 Round Time: 00:17:54 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 95161 repeats masked totaling 25195780 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037520 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90037520 bp After Masking: 63210979 bp Masked: 29.79 % -- Input Database Coverage: 130086506 bp out of 2311617438 bp ( 5.63 % ) Sampling Time: 00:05:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:53:32 (hh:mm:ss) Elapsed Time, 6265464 HSPs Collected Number of families returned by RECON: 7873 Round Time: 02:02:59 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 318952 repeats masked totaling 84501703 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027126 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 270026526 bp After Masking: 180975229 bp Masked: 32.98 % -- Input Database Coverage: 400113632 bp out of 2311617438 bp ( 17.31 % ) Sampling Time: 00:18:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 11:02:40 (hh:mm:ss) Elapsed Time, 36960931 HSPs Collected Number of families returned by RECON: 34547 Round Time: 11:39:19 (hh:mm:ss) Elapsed Time : 361 families discovered. RepeatScout/RECON discovery complete: 799 families found Classification Time: 00:19:38 (hh:mm:ss) Elapsed Time Program Time: 14:41:19 (hh:mm:ss) Elapsed Time