RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.5qrlui/RM_2309722.SunApr200253022025 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: 1745142782 Database = /data/tmp/rModeler.5qrlui/GCF_040894005.1_aEngPut4.maternal - Sequences = 936 - Bases = 2158203323 - N50 = 228224547 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 285887154-306306954 | [ 1 ] 265467354-285887153 | [ 1 ] 245047555-265467354 | [ ] 224627755-245047554 | [ 2 ] 204207956-224627755 | [ 1 ] 183788156-204207955 | [ 2 ] 163368357-183788156 | [ ] 142948557-163368356 | [ ] 122528758-142948557 | [ 1 ] 102108958-122528757 | [ 2 ] 81689159-102108958 | [ 1 ] 61269359-81689158 | [ ] 40849560-61269359 | [ ] 20429760-40849559 | [ ] 9961-20429760 |************************************************** [ 925 ] Storage Throughput = good ( 997.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026612 bp ( 40024612 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:05:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:47 (hh:mm:ss) Elapsed Time Round Time: 00:28:41 (hh:mm:ss) Elapsed Time : 689 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15667 repeats masked totaling 3321332 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033470 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10033070 bp After Masking: 4859079 bp Masked: 51.57 % -- Input Database Coverage: 10033470 bp out of 2158203323 bp ( 0.46 % ) Sampling Time: 00:04:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:25 (hh:mm:ss) Elapsed Time, 21705 HSPs Collected Number of families returned by RECON: 1376 Round Time: 00:11:13 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47855 repeats masked totaling 10756264 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033062 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30031462 bp After Masking: 13827341 bp Masked: 53.96 % -- Input Database Coverage: 40066532 bp out of 2158203323 bp ( 1.86 % ) Sampling Time: 00:12:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:23:09 (hh:mm:ss) Elapsed Time, 59162 HSPs Collected Number of families returned by RECON: 4120 Round Time: 00:40:36 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155661 repeats masked totaling 34504246 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042646 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 90038846 bp After Masking: 38842254 bp Masked: 56.86 % -- Input Database Coverage: 130109178 bp out of 2158203323 bp ( 6.03 % ) Sampling Time: 00:40:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 02:04:23 (hh:mm:ss) Elapsed Time, 307301 HSPs Collected Number of families returned by RECON: 11436 Round Time: 03:50:28 (hh:mm:ss) Elapsed Time : 443 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:17:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 532082 repeats masked totaling 117566709 bp(s). - TE Masking time 00:07:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034664 bp Num Contigs Represented = 269 Non ambiguous bp: Initial: 270023909 bp After Masking: 104077952 bp Masked: 61.46 % -- Input Database Coverage: 400143842 bp out of 2158203323 bp ( 18.54 % ) Sampling Time: 01:51:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 14:07:18 (hh:mm:ss) Elapsed Time, 916819 HSPs Collected Number of families returned by RECON: 31400 Round Time: 18:00:08 (hh:mm:ss) Elapsed Time : 1127 families discovered. RepeatScout/RECON discovery complete: 2400 families found Classification Time: 01:31:27 (hh:mm:ss) Elapsed Time Program Time: 24:42:33 (hh:mm:ss) Elapsed Time