RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.US5MAo/RM_3651546.ThuMay180839432023 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: 1684424383 Database = /dev/shm/rModeler.US5MAo/GCF_023343835.1_bLagMut1_primary - Sequences = 165 - Bases = 1026771810 - N50 = 75337723 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 181913838-194907523 | [ 1 ] 168920154-181913838 | [ ] 155926470-168920154 | [ ] 142932785-155926469 | [ ] 129939101-142932785 | [ ] 116945417-129939101 | [ ] 103951732-116945416 | [ 1 ] 90958048-103951732 | [ 1 ] 77964364-90958048 | [ ] 64970679-77964363 |* [ 3 ] 51976995-64970679 | [ 1 ] 38983311-51976995 | [ 1 ] 25989626-38983310 | [ 1 ] 12995942-25989626 |** [ 8 ] 2258-12995942 |************************************************** [ 148 ] Storage Throughput = excellent ( 1330.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025422 bp ( 40022522 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:28 (hh:mm:ss) Elapsed Time Round Time: 00:19:31 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3193 repeats masked totaling 859934 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014002 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10012502 bp After Masking: 8982021 bp Masked: 10.29 % -- Input Database Coverage: 10014002 bp out of 1026771810 bp ( 0.98 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:08:21 (hh:mm:ss) Elapsed Time, 843 HSPs Collected Number of families returned by RECON: 235 Round Time: 00:09:32 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (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... 9901 repeats masked totaling 2674515 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011340 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30009940 bp After Masking: 26734604 bp Masked: 10.91 % -- Input Database Coverage: 40025342 bp out of 1026771810 bp ( 3.90 % ) Sampling Time: 00:04:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:41:06 (hh:mm:ss) Elapsed Time, 5492 HSPs Collected Number of families returned by RECON: 1403 Round Time: 00:45:39 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31565 repeats masked totaling 8347718 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037615 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90028900 bp After Masking: 80060283 bp Masked: 11.07 % -- Input Database Coverage: 130062957 bp out of 1026771810 bp ( 12.67 % ) Sampling Time: 00:10:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 04:19:12 (hh:mm:ss) Elapsed Time, 190835 HSPs Collected Number of families returned by RECON: 9591 Round Time: 04:32:16 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99073 repeats masked totaling 27262345 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023868 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270007076 bp After Masking: 238157900 bp Masked: 11.80 % -- Input Database Coverage: 400086825 bp out of 1026771810 bp ( 38.97 % ) Sampling Time: 00:34:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 30:27:25 (hh:mm:ss) Elapsed Time, 2937533 HSPs Collected Number of families returned by RECON: 64848 Round Time: 31:38:56 (hh:mm:ss) Elapsed Time : 219 families discovered. RepeatScout/RECON discovery complete: 376 families found Classification Time: 00:26:35 (hh:mm:ss) Elapsed Time Program Time: 37:52:29 (hh:mm:ss) Elapsed Time